diff --git a/.ci/flake8_blacklist.txt b/.ci/flake8_blacklist.txt
index 33db66f40a0..26ece30af32 100644
--- a/.ci/flake8_blacklist.txt
+++ b/.ci/flake8_blacklist.txt
@@ -2,6 +2,10 @@
 .tox
 .venv
 .venv3
+packages/*/.venv
+packages/*/build
+packages/*/dist
+packages/venv
 node_modules
 database
 doc/build
diff --git a/.ci/jenkins/selenium-compose/Dockerfile b/.ci/jenkins/selenium-compose/Dockerfile
index a453ac6d215..d9f3def9761 100644
--- a/.ci/jenkins/selenium-compose/Dockerfile
+++ b/.ci/jenkins/selenium-compose/Dockerfile
@@ -1,5 +1,5 @@
 FROM toolshed/requirements
-MAINTAINER John Chilton, jmchilton@gmail.com
+LABEL maintainer="John Chilton <jmchilton@gmail.com>"
 
 RUN apt-get -qq update && \
     apt-get install --no-install-recommends -y postgresql-client python-pip libffi-dev python-cffi && \
diff --git a/.ci/validate_test_tools.sh b/.ci/validate_test_tools.sh
index 9b43e7a6c46..258799dc95d 100755
--- a/.ci/validate_test_tools.sh
+++ b/.ci/validate_test_tools.sh
@@ -1,11 +1,11 @@
 #!/bin/sh
 
-cd `dirname $0`/..
+cd "$(dirname "$0")"/..
 
 xsd_path="lib/galaxy/tools/xsd/galaxy.xsd"
 # Lint the XSD
 xmllint --noout "$xsd_path"
 
 test_tools_path='test/functional/tools'
-tool_files_list=$(ls "$test_tools_path"/*xml | grep -v '_conf.xml$')
+tool_files_list=$(ls "$test_tools_path"/*.xml | grep -v '_conf.xml$')
 sh scripts/validate_tools.sh $tool_files_list
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 01b3105991a..32dfbce7036 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -25,7 +25,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -83,7 +83,7 @@ jobs:
             - ~/repo
   py27_lint:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -91,7 +91,7 @@ jobs:
       - run: tox -e py27-lint
   py27_unit:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -99,7 +99,7 @@ jobs:
       - run: tox -e py27-unit
   py27_docstring:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -107,7 +107,7 @@ jobs:
       - run: tox -e py27-lint_docstring_include_list
   py27_first_startup:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -139,14 +139,14 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - *install_tox
       - run: sudo apt-get update
       # For uwsgi
       - run: sudo apt-get install -y libpython3.5-dev
+      - *install_tox
       - run: tox -e py35-first_startup
   validate_test_tools:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -154,9 +154,17 @@ jobs:
       - run: sudo apt-get install -y libxml2-utils
       - *install_tox
       - run: tox -e validate_test_tools
+  test_galaxy_packages:
+    docker:
+      - image: circleci/python:3.5
+    <<: *set_workdir
+    steps:
+      - *restore_repo_cache
+      - *install_tox
+      - run: tox -e test_galaxy_packages
   check_py3_compatibility:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -202,6 +210,8 @@ workflows:
           <<: *requires_get_code
       - py35_first_startup:
           <<: *requires_get_code
+      - test_galaxy_packages:
+          <<: *requires_get_code
       - validate_test_tools:
           <<: *requires_get_code
       - check_py3_compatibility:
diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index 5b5c90440a8..7dc40777623 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -1,13 +1,18 @@
 module.exports = {
     extends: ["eslint:recommended", "plugin:vue/essential"], // airbnb-base, eventually
     env: {
-        browser: true
+        browser: true,
+        commonjs: true,
+        es6: true,
+        node: true,
+        mocha: true
     },
     parserOptions: { parser: "babel-eslint" },
     plugins: ["html"],
     rules: {
         "no-console": "off",
         "no-unused-vars": ["error", { args: "none" }],
+        "prefer-const": "error",
         // I'd love to turn on camelcase, but it's a big shift with tons of current errors.
         // camelcase: [
         //     "error",
@@ -15,5 +20,10 @@ module.exports = {
         //         properties: "always"
         //     }
         // ]
+    },
+    globals: {
+        // chai tests
+        assert: true,
+        expect: true
     }
 };
diff --git a/client/README.md b/client/README.md
index 3094d6b69d7..b312c525c3d 100644
--- a/client/README.md
+++ b/client/README.md
@@ -8,8 +8,8 @@ the client as a part of server startup, when it detects changes, unless that
 functionality is explicitly disabled.
 
 The base dependencies used are Node.js and Yarn.  Galaxy now includes these in
-the virtual environment, and they can be accessed by activating that with
-`. .venv/bin/activate` from the Galaxy root directory.
+the virtual environment, and they can be accessed by activating that with `.
+.venv/bin/activate` from the Galaxy root directory.
 
 If you'd like to install your own dependencies, on OSX the easiest way to get
 set up is using `homebrew` and the command `brew install nodejs yarn`.  More
@@ -18,10 +18,9 @@ https://nodejs.org/ and https://yarnpkg.com/ .
 
 The Galaxy client build has necessarily grown more complex in the past several
 years, but we are still trying to keep things as simple as possible for
-everyone.  If you're having any trouble with building the
-client after following the instructions below, please create an issue on GitHub
-or reach out for help directly on Gitter at
-https://gitter.im/galaxyproject/Lobby .
+everyone.  If you're having any trouble with building the client after
+following the instructions below, please create an issue on GitHub or reach out
+for help directly on Gitter at https://gitter.im/galaxyproject/Lobby .
 
 
 Complete Client Build
@@ -37,7 +36,8 @@ during the build process.
 
     make client
 
-For a production build, suitable for deploying to a live server, use the following:
+For a production build, suitable for deploying to a live server, use the
+following:
 
     make client-production
 
@@ -80,3 +80,219 @@ On build, the compiled css bundle is served at `/static/style/base.css`.
 As mentioned above, `make client` will rebuild styles, as a part of the webpack
 build.  For iterative development, "Watch Mode" rebuilds as described above do
 include style changes.
+
+
+# Client-Side Unit Testing
+
+Galaxy's client is undergoing an extensive refactoring and modernizing process.
+As part of this initiative, we would like to request that all new client-side
+code submissions come with accompanying javascript unit-tests for the
+developer-facing API of your new code.
+
+## Testing Technologies
+
+[Galaxy uses Mocha](https://mochajs.org/) for its client-side unit testing
+framework with [Chai as its assertion library](https://www.chaijs.com/) and
+[karma as a test runner](https://karma-runner.github.io/latest/index.html).
+The karma configs are contained in the client/karma folder. Unit tests are run
+using Chrome headless by default.
+
+For testing Vue components, we use the [Vue testing
+utils](https://vue-test-utils.vuejs.org/) to mount individual components in a
+test bed and check them for rendered features.
+
+We use the [babel plugin
+Rewire](https://github.com/speedskater/babel-plugin-rewire) to mock imported
+ES6 dependencies during unit-testing. [Sinon](https://sinonjs.org/) is also
+available for more robust stubbing, mocking and spying utilities.
+
+A set of older qUnit tests also exist which will likely be phased-out as the
+code they support is replaced with modern component-based implementations. In
+the meantime, karma runs both the mocha and qunit tests in sequence.
+
+
+## Running the tests
+
+### At Build-Time
+To simply run all the javascript unit tests, you can use make from the root
+directory. This is what happens during a complete client build.
+
+     make client-test
+
+
+### During Development
+
+During client-side development, it is more convenient to have granular testing
+options. The various testing scripts are defined inside package.json within the
+client folder, and are called either with npm (or yarn) as follows:
+
+
+#### Run all tests (mocha and qunit):
+
+     npm run test
+
+#### Watch and rerun all client-side unit-tests every time a source file changes:
+
+     npm run test-watch
+
+#### Run only specified test files when a source file changes:
+
+    npm run test-watch watch-only="Tags/*.test.js"
+
+(The above watch-only parameter will be mapped to the following glob expression "**/Tags/*.test.js")
+
+#### Run qunit legacy tests
+
+    npm run test-qunit
+
+
+## Writing a test file
+
+The karma configs are setup to look at any file ending in "*.test.js". Please
+place your test files inside client/galaxy/scripts folders right next to
+whatever files that they are testing.
+
+```javascript
+// yourtestfile.test.js
+
+import { things } from "./yourtestfile.js";
+
+describe("some module you wrote", () => {
+
+    let transientVariables, serviceInstances, testData;
+
+    beforeEach(() => {
+        // setup your code (if necessary)
+    })
+
+    afterEach(() => {
+        // teardown your code (so it doesn't ruin the next test)
+    })
+
+    it("should do something or other", () => {
+        assert(somethingThatShouldTrue, "explain what went wrong");
+        expect(something).to.eq(true);
+    })
+})
+```
+
+
+## Testing ~~Suggestions~~ Obligations
+
+
+### Clearly document the intent of your test
+
+Please remember that these tests are not *for* you. They're for the people who
+come after you. It will be a lot easier to modify, repair and upgrade your code
+if they can figure out what you were originally hoping to accomplish.
+
+Add a couple of comments. Use variable names that mean something. Use the
+assertion failure description parameters when possible. Nobody's code is as
+self-documenting as they believe it to be.
+
+```javascript
+
+// NOT AWESOME
+// this test forces the next victim to have to
+// read every single line of source code you wrote
+it("should work", async () => {
+    let thing = await svc.loadHistories();
+    assert(thing);
+})
+
+// BETTER
+// With this test, you can just read at the errors on the mocha 
+// test output to have a pretty good idea of what went sour.
+it("should have resolved to an array of integer IDs", async () => {
+    let historyIds = await historyService.loadHistories();
+    assert(historyIds, "History service should have had a result");
+    assert(historyIds instanceof Array, "History results should have been an array");
+    assert(historyIds.length == 4, "History call should have returned 4 ids");
+})
+
+```
+
+
+### Only test the public API that you define (carefully!)
+
+Internal implementations come and go with library upgrades and new tech. But
+the point of the unit test is to make sure your units work as designed....
+which means you need to... you know... design your code to work in units.
+
+Separate your concerns and identify the developer-facing methods and functions
+you expect them to use. Test THOSE. Everything else should probably be
+considered an implementation detail.
+
+Assume nobody cares *how* your code works, we just need to know that the public
+API you designed *does* work. If performance problems or new tech necessitate a
+re-write, these tests become a guide for the next implementation.
+
+
+### Wrap native browser resources in a function so they can be easily mocked
+
+If your javascript needs to talk to the window object, or navigator, etc. wrap
+that in a function call so that it can be easily mocked during testing.
+
+```javascript
+
+// myModule.js
+
+// ... other code
+
+export function redirectTo(url) {
+    window.location = url;
+}
+
+
+// myModule.test.js
+
+import { __RewireAPI__ as myModuleRewire} from "./myModule";
+
+function fakeRedirect(url) {
+    console.log(`I would have gone to: ${url}`);
+}
+
+describe("some module", () => {
+
+    beforeEach(() => {
+        myModuleRewire.__Rewire__("redirectTo", fakeRedirect);
+    })
+
+    // ....
+})
+```
+
+### Implement logic in pure functions when possible
+
+The more of your logic that is written in deterministic functions (i.e. no
+side-effects, same inputs always result in same outputs) the easier it is to
+test. Just load up the functions and supply suitable test inputs.
+
+There is almost definitely no such thing as a well-written 1000 line function.
+Most of whatever happened in that thing was probably deterministic and can be
+broken up into easily testable chunks.
+
+
+## Specific test scenarios & examples
+
+[Mocking an imported dependency](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/tagService.test.js)
+
+[Testing async operations](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/tagService.test.js)
+
+[Testing a Vue component for expected rendering output](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/StatelessTags.test.js)
+
+[Firing an event against a shallow mounted vue component](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/StatelessTags.test.js)
+
+
+## The dirty secret about testing
+
+It's good to have tests, but testing code isn't really about testing at all,
+it's actually about software design. 
+
+Maintainable software is testable software. If you can run a unit test on your
+code, then that means you must have necessarily separated your code into
+testable units and you will have almost definitely written better, more
+modular, more easily manipulated code, and nobody will ever contemplate using
+git-blame to figure out what went wrong.
+
+Probably.
diff --git a/client/galaxy/scripts/admin.toolshed.js b/client/galaxy/scripts/admin.toolshed.js
index 8a94d153909..04182abfda5 100644
--- a/client/galaxy/scripts/admin.toolshed.js
+++ b/client/galaxy/scripts/admin.toolshed.js
@@ -9,19 +9,6 @@ import mod_repo_status_view from "mvc/toolshed/repo-status-view";
 import mod_workflows_view from "mvc/toolshed/workflows-view";
 
 var AdminToolshedRouter = Backbone.Router.extend({
-    initialize: function() {
-        this.routesHit = 0;
-        // keep count of number of routes handled by the application
-        Backbone.history.on(
-            "route",
-            function() {
-                this.routesHit++;
-            },
-            this
-        );
-        this.bind("route", this.trackPageview);
-    },
-
     routes: {
         "": "toolsheds",
         sheds: "toolsheds",
@@ -32,20 +19,6 @@ var AdminToolshedRouter = Backbone.Router.extend({
         "categories/s/:tool_shed": "categories",
         "category/s/:tool_shed/c/:category_id/k/:sort_key/p/:page/t/:sort_order": "repositories",
         "repository/s/:tool_shed/r/:repository_id": "repository"
-    },
-
-    /**
-     * If more than one route has been hit the user did not land on current
-     * page directly so we can go back safely. Otherwise go to the home page.
-     * Use replaceState if available so the navigation doesn't create an
-     * extra history entry
-     */
-    back: function() {
-        if (this.routesHit > 1) {
-            window.history.back();
-        } else {
-            this.navigate("#", { trigger: true, replace: true });
-        }
     }
 });
 
@@ -55,7 +28,7 @@ var GalaxyAdminToolshedApp = Backbone.View.extend({
     },
 
     initialize: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         Galaxy.admintoolshedapp = this;
         this.admin_toolshed_router = new AdminToolshedRouter();
diff --git a/client/galaxy/scripts/app/galaxy.js b/client/galaxy/scripts/app/galaxy.js
index 3a43a178877..b9d547f103a 100644
--- a/client/galaxy/scripts/app/galaxy.js
+++ b/client/galaxy/scripts/app/galaxy.js
@@ -26,12 +26,12 @@ export function GalaxyApp(options = {}, bootstrapped = {}) {
 addLogging(GalaxyApp, "GalaxyApp");
 
 // a debug flag can be set via local storage and made available during script/page loading
-var DEBUGGING_KEY = "galaxy:debug";
+const DEBUGGING_KEY = "galaxy:debug";
 
-var NAMESPACE_KEY = `${DEBUGGING_KEY}:namespaces`;
-var FLATTEN_LOG_MESSAGES_KEY = `${DEBUGGING_KEY}:flatten`;
+const NAMESPACE_KEY = `${DEBUGGING_KEY}:namespaces`;
+const FLATTEN_LOG_MESSAGES_KEY = `${DEBUGGING_KEY}:flatten`;
 
-var localDebugging = false;
+let localDebugging = false;
 try {
     localDebugging = localStorage.getItem(DEBUGGING_KEY) == "true";
 } catch (storageErr) {
@@ -40,51 +40,50 @@ try {
 
 /** initalize options and sub-components */
 GalaxyApp.prototype._init = function(options, bootstrapped) {
-    var self = this;
-    _.extend(self, Backbone.Events);
+    _.extend(this, Backbone.Events);
     if (localDebugging) {
-        self.logger = console;
+        this.logger = console;
         console.debug("debugging galaxy:", "options:", options, "bootstrapped:", bootstrapped);
     }
 
-    self._processOptions(options);
-    self._initConfig(options.config || {});
+    this._processOptions(options);
+    this._initConfig(options.config || {});
 
     // Patch if this galaxy instance is replacing an existing one
     // _patchGalaxy depends on options.patchExisting
     // TODO: rethink this behavior
-    let existingGalaxy = getGalaxyInstance();
+    const existingGalaxy = getGalaxyInstance();
     if (existingGalaxy) {
-        self._patchGalaxy(existingGalaxy);
+        this._patchGalaxy(existingGalaxy);
     }
 
     // add root and url parameters
-    self.root = options.root || "/";
-    self.params = options.params || {};
-    self.session_csrf_token = options.session_csrf_token || null;
+    this.root = options.root || "/";
+    this.params = options.params || {};
+    this.session_csrf_token = options.session_csrf_token || null;
 
-    self._initLogger(self.options.loggerOptions || {});
+    this._initLogger(this.options.loggerOptions || {});
     // at this point, either logging or not and namespaces are enabled - chat it up
-    self.debug("GalaxyApp.options: ", self.options);
-    self.debug("GalaxyApp.config: ", self.config);
-    self.debug("GalaxyApp.logger: ", self.logger);
+    this.debug("GalaxyApp.options: ", this.options);
+    this.debug("GalaxyApp.config: ", this.config);
+    this.debug("GalaxyApp.logger: ", this.logger);
 
-    self._initLocale();
-    self.debug("GalaxyApp.localize: ", self.localize);
+    this._initLocale();
+    this.debug("GalaxyApp.localize: ", this.localize);
 
-    self.config = options.config || {};
-    self.debug("GalaxyApp.config: ", self.config);
+    this.config = options.config || {};
+    this.debug("GalaxyApp.config: ", this.config);
 
-    self._initUser(options.user || {});
-    self.debug("GalaxyApp.user: ", self.user);
+    this._initUser(options.user || {});
+    this.debug("GalaxyApp.user: ", this.user);
 
-    self._initUserLocale();
-    self.debug("currentLocale: ", sessionStorage.getItem("currentLocale"));
+    this._initUserLocale();
+    this.debug("currentLocale: ", sessionStorage.getItem("currentLocale"));
 
-    self._setUpListeners();
-    self.trigger("ready", self);
+    this._setUpListeners();
+    this.trigger("ready", this);
 
-    return self;
+    return this;
 };
 
 /** default options */
@@ -98,41 +97,38 @@ GalaxyApp.prototype.defaultOptions = {
 
 /** filter to options present in defaultOptions (and default to them) */
 GalaxyApp.prototype._processOptions = function _processOptions(options) {
-    var self = this;
-    var defaults = self.defaultOptions;
+    const defaults = this.defaultOptions;
 
-    self.options = {};
-    for (var k in defaults) {
+    this.options = {};
+    for (const k in defaults) {
         if (defaults.hasOwnProperty(k)) {
-            self.options[k] = options.hasOwnProperty(k) ? options[k] : defaults[k];
+            this.options[k] = options.hasOwnProperty(k) ? options[k] : defaults[k];
         }
     }
-    return self;
+    return this;
 };
 
 /** parse the config and any extra info derived from it */
 GalaxyApp.prototype._initConfig = function _initConfig(config) {
-    var self = this;
-    self.config = config;
+    this.config = config;
 
     // give precendence to localdebugging for this setting
-    self.config.debug = localDebugging || self.config.debug;
+    this.config.debug = localDebugging || this.config.debug;
 
-    return self;
+    return this;
 };
 
 // TODO: Remove this behavior when we can, it is kind of non-intuitive
 GalaxyApp.prototype._patchGalaxy = function _patchGalaxy(patchWith) {
-    var self = this;
     // in case req or plain script tag order has created a prev. version of the Galaxy obj...
-    if (self.options.patchExisting && patchWith) {
-        // self.debug( 'found existing Galaxy object:', patchWith );
+    if (this.options.patchExisting && patchWith) {
+        // this.debug( 'found existing Galaxy object:', patchWith );
         // ...(for now) monkey patch any added attributes that the previous Galaxy may have had
         //TODO: move those attributes to more formal assignment in GalaxyApp
-        for (var k in patchWith) {
+        for (const k in patchWith) {
             if (patchWith.hasOwnProperty(k)) {
-                // self.debug( '\t patching in ' + k + ' to Galaxy:', self[ k ] );
-                self[k] = patchWith[k];
+                // this.debug( '\t patching in ' + k + ' to Galaxy:', this[ k ] );
+                this[k] = patchWith[k];
             }
         }
     }
@@ -140,10 +136,8 @@ GalaxyApp.prototype._patchGalaxy = function _patchGalaxy(patchWith) {
 
 /** set up the metrics logger (utils/metrics-logger) and pass loggerOptions */
 GalaxyApp.prototype._initLogger = function _initLogger(loggerOptions) {
-    var self = this;
-
     // default to console logging at the debug level if the debug flag is set
-    if (self.config.debug) {
+    if (this.config.debug) {
         loggerOptions.consoleLogger = loggerOptions.consoleLogger || console;
         loggerOptions.consoleLevel = loggerOptions.consoleLevel || metricsLogger.MetricsLogger.ALL;
         // load any logging namespaces from localStorage if we can
@@ -160,45 +154,42 @@ GalaxyApp.prototype._initLogger = function _initLogger(loggerOptions) {
         console.log(loggerOptions.consoleFlattenMessages);
     }
 
-    self.logger = new metricsLogger.MetricsLogger(loggerOptions);
-    self.emit = {};
+    this.logger = new metricsLogger.MetricsLogger(loggerOptions);
+    this.emit = {};
     ["log", "debug", "info", "warn", "error", "metric"].map(i => {
-        self.emit[i] = function(data) {
-            self.logger.emit(i, arguments[0], Array.prototype.slice.call(arguments, 1));
+        this.emit[i] = data => {
+            this.logger.emit(i, arguments[0], Array.prototype.slice.call(arguments, 1));
         };
     });
 
-    if (self.config.debug) {
+    if (this.config.debug) {
         // add this logger to mvc's loggable mixin so that all models can use the logger
-        BASE_MVC.LoggableMixin.logger = self.logger;
+        BASE_MVC.LoggableMixin.logger = this.logger;
     }
-    return self;
+    return this;
 };
 
 /** add the localize fn to this object and the window namespace (as '_l') */
 GalaxyApp.prototype._initLocale = function _initLocale(options) {
-    var self = this;
-    self.debug("_initLocale:", options);
-    self.localize = localize;
+    this.debug("_initLocale:", options);
+    this.localize = localize;
     // add to window as global shortened alias
     // TODO: temporary - remove when can require for plugins
-    window._l = self.localize;
-    return self;
+    window._l = this.localize;
+    return this;
 };
 
 /** add the localize fn to this object and the window namespace (as '_l') */
 GalaxyApp.prototype._initUserLocale = function _initUserLocale(options) {
-    var self = this;
-
     // Choose best locale
-    var global_locale = self.config.default_locale ? self.config.default_locale.toLowerCase() : false;
+    const global_locale = this.config.default_locale ? this.config.default_locale.toLowerCase() : false;
 
-    var extra_user_preferences = {};
-    if (self.user && self.user.attributes.preferences && "extra_user_preferences" in self.user.attributes.preferences) {
-        extra_user_preferences = JSON.parse(self.user.attributes.preferences.extra_user_preferences);
+    let extra_user_preferences = {};
+    if (this.user && this.user.attributes.preferences && "extra_user_preferences" in this.user.attributes.preferences) {
+        extra_user_preferences = JSON.parse(this.user.attributes.preferences.extra_user_preferences);
     }
 
-    var user_locale =
+    let user_locale =
         "localization|locale" in extra_user_preferences
             ? extra_user_preferences["localization|locale"].toLowerCase()
             : false;
@@ -207,52 +198,48 @@ GalaxyApp.prototype._initUserLocale = function _initUserLocale(options) {
         user_locale = false;
     }
 
-    var nav_locale =
+    const nav_locale =
         typeof navigator === "undefined"
             ? "__root"
             : (navigator.language || navigator.userLanguage || "__root").toLowerCase();
 
-    let locale = user_locale || global_locale || nav_locale;
+    const locale = user_locale || global_locale || nav_locale;
 
     sessionStorage.setItem("currentLocale", locale);
 };
 
 /** set up the current user as a Backbone model (mvc/user/user-model) */
 GalaxyApp.prototype._initUser = function _initUser(userJSON) {
-    var self = this;
-    self.debug("_initUser:", userJSON);
-    self.user = new userModel.User(userJSON);
-    self.user.logger = self.logger;
-    return self;
+    this.debug("_initUser:", userJSON);
+    this.user = new userModel.User(userJSON);
+    this.user.logger = this.logger;
+    return this;
 };
 
 /** Set up DOM/jQuery/Backbone event listeners enabled for all pages */
 GalaxyApp.prototype._setUpListeners = function _setUpListeners() {
-    var self = this;
-
     // hook to jq beforeSend to record the most recent ajax call and cache some data about it
     /** cached info about the last ajax call made through jQuery */
-    self.lastAjax = {};
+    this.lastAjax = {};
     $(document).bind("ajaxSend", (ev, xhr, options) => {
-        var data = options.data;
+        let data = options.data;
         try {
             data = JSON.parse(data);
         } catch (err) {
             // data isn't JSON, skip.
         }
 
-        self.lastAjax = {
+        this.lastAjax = {
             url: location.href.slice(0, -1) + options.url,
             data: data
         };
         //TODO:?? we might somehow manage to *retry* ajax using either this hook or Backbone.sync
     });
-    return self;
+    return this;
 };
 
 /** Turn debugging/console-output on/off by passing boolean. Pass nothing to get current setting. */
 GalaxyApp.prototype.debugging = function _debugging(setting) {
-    var self = this;
     try {
         if (setting === undefined) {
             return localStorage.getItem(DEBUGGING_KEY) === "true";
@@ -264,7 +251,7 @@ GalaxyApp.prototype.debugging = function _debugging(setting) {
 
         localStorage.removeItem(DEBUGGING_KEY);
         // also remove all namespaces
-        self.debuggingNamespaces(null);
+        this.debuggingNamespaces(null);
     } catch (storageErr) {
         console.log(localize("localStorage not available for debug flag retrieval"));
     }
@@ -278,19 +265,18 @@ GalaxyApp.prototype.debugging = function _debugging(setting) {
  *  Returns the new/current namespaces as an array;
  */
 GalaxyApp.prototype.debuggingNamespaces = function _debuggingNamespaces(namespaces) {
-    var self = this;
     try {
         if (namespaces === undefined) {
-            var csv = localStorage.getItem(NAMESPACE_KEY);
+            const csv = localStorage.getItem(NAMESPACE_KEY);
             return typeof csv === "string" ? csv.split(",") : [];
         } else if (namespaces === null) {
             localStorage.removeItem(NAMESPACE_KEY);
         } else {
             localStorage.setItem(NAMESPACE_KEY, namespaces);
         }
-        var newSettings = self.debuggingNamespaces();
-        if (self.logger) {
-            self.logger.options.consoleNamespaceWhitelist = newSettings;
+        const newSettings = this.debuggingNamespaces();
+        if (this.logger) {
+            this.logger.options.consoleNamespaceWhitelist = newSettings;
         }
         return newSettings;
     } catch (storageErr) {
@@ -300,7 +286,7 @@ GalaxyApp.prototype.debuggingNamespaces = function _debuggingNamespaces(namespac
 
 /** string rep */
 GalaxyApp.prototype.toString = function toString() {
-    var userEmail = this.user ? this.user.get("email") || "(anonymous)" : "uninitialized";
+    const userEmail = this.user ? this.user.get("email") || "(anonymous)" : "uninitialized";
     return `GalaxyApp(${userEmail})`;
 };
 
diff --git a/client/galaxy/scripts/app/singleton.js b/client/galaxy/scripts/app/singleton.js
index 482ffbb6391..fa96b99f734 100644
--- a/client/galaxy/scripts/app/singleton.js
+++ b/client/galaxy/scripts/app/singleton.js
@@ -9,7 +9,7 @@ import { serverPath } from "utils/serverPath";
 export function setGalaxyInstance(factory) {
     console.warn("setGalaxyInstance", serverPath());
 
-    let storage = getStorage();
+    const storage = getStorage();
     let newInstance = factory(GalaxyApp);
     if (!(newInstance instanceof GalaxyApp)) {
         newInstance = new GalaxyApp(newInstance);
@@ -24,12 +24,12 @@ export function setGalaxyInstance(factory) {
 }
 
 export function getGalaxyInstance() {
-    let storage = getStorage();
+    const storage = getStorage();
     return storage._galaxyInstance;
 }
 
 export function galaxyIsInitialized() {
-    let instance = getGalaxyInstance();
+    const instance = getGalaxyInstance();
     return instance !== null;
 }
 
diff --git a/client/galaxy/scripts/bundleEntries.js b/client/galaxy/scripts/bundleEntries.js
index be5c973607f..0390749fb83 100644
--- a/client/galaxy/scripts/bundleEntries.js
+++ b/client/galaxy/scripts/bundleEntries.js
@@ -32,6 +32,9 @@ export { default as HDAModel } from "mvc/history/hda-model";
 export { default as LegacyGridView } from "legacy/grid/grid-view";
 export { create_chart, create_histogram } from "reports/run_stats";
 export { default as ToolshedGroups } from "toolshed/toolshed.groups";
+export { default as IES } from "galaxy.interactive_environments";
+
+export { Toast } from "ui/toast"; // TODO: remove when external consumers are updated/gone (IES right now)
 
 export function adminToolshed(options) {
     new AdminToolshed.GalaxyApp(options);
@@ -54,14 +57,14 @@ export function library(options) {
 }
 
 export function multiHistory(options) {
-    let histories = new HistoryCollection([], {
+    const histories = new HistoryCollection([], {
         includeDeleted: options.includingDeleted,
         order: options.order,
         limitOnFirstFetch: options.limit,
         limitPerFetch: options.limit,
         currentHistoryId: options.current_history_id
     });
-    let multipanel = new MultiPanel.MultiPanelColumns({
+    const multipanel = new MultiPanel.MultiPanelColumns({
         el: $("#center").get(0),
         histories: histories
     });
@@ -76,6 +79,7 @@ export function multiHistory(options) {
 export { default as panels } from "layout/panel";
 export { show_in_overlay, hide_modal, show_message, show_modal, Modal } from "layout/modal";
 export { make_popupmenu, make_popup_menus } from "ui/popupmenu";
+export { render_embedded_items } from "mvc/embedded-objects";
 export { default as async_save_text } from "utils/async-save-text";
 
 // Previously "chart"
@@ -88,7 +92,7 @@ export function chart(options) {
     return new Client(options);
 }
 
-export let chartUtilities = {
+export const chartUtilities = {
     Datasets: Datasets,
     Jobs: Jobs,
     Series: Series
@@ -97,6 +101,8 @@ export let chartUtilities = {
 export { initMasthead } from "components/Masthead/initMasthead";
 export { panelManagement } from "onload/globalInits/panelManagement";
 export { mountMakoTags } from "components/Tags";
+export { mountJobMetrics } from "components/JobMetrics";
+export { mountJobParameters } from "components/JobParameters";
 
 // Used in common.mako
 export { default as store } from "storemodern";
diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index 86d9af002f8..46c960f3b9f 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -29,12 +29,16 @@
 </template>
 <script>
 import _ from "underscore";
-import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
+import Vue from "vue";
+import BootstrapVue from "bootstrap-vue";
+import { getAppRoot } from "onload/loadConfig";
 import * as bibtexParse from "libs/bibtexParse";
 import { convertLaTeX } from "latex-to-unicode-converter";
 import { stringifyLaTeX } from "latex-parser";
 
+Vue.use(BootstrapVue);
+
 export default {
     props: {
         source: {
@@ -71,17 +75,17 @@ export default {
             .get(`${getAppRoot()}api/${this.source}/${this.id}/citations`)
             .then(response => {
                 this.content = "";
-                for (var rawCitation of response.data) {
+                for (const rawCitation of response.data) {
                     try {
-                        var citation = {
+                        const citation = {
                             fields: {},
                             entryType: undefined
                         };
-                        var parsed = bibtexParse.toJSON(rawCitation.content);
+                        let parsed = bibtexParse.toJSON(rawCitation.content);
                         if (parsed) {
                             parsed = _.first(parsed);
                             citation.entryType = parsed.entryType || undefined;
-                            for (var key in parsed.entryTags) {
+                            for (const key in parsed.entryTags) {
                                 citation.fields[key.toLowerCase()] = parsed.entryTags[key];
                             }
                         }
@@ -98,18 +102,18 @@ export default {
     },
     methods: {
         formattedReference: function(citation) {
-            var entryType = citation.entryType;
-            var fields = citation.fields;
+            const entryType = citation.entryType;
+            const fields = citation.fields;
 
-            var ref = "";
-            var authorsAndYear = `${this._asSentence(
+            let ref = "";
+            const authorsAndYear = `${this._asSentence(
                 (fields.author ? fields.author : "") + (fields.year ? ` (${fields.year})` : "")
             )} `;
-            var title = fields.title || "";
-            var pages = fields.pages ? `pp. ${fields.pages}` : "";
-            var address = fields.address;
+            const title = fields.title || "";
+            const pages = fields.pages ? `pp. ${fields.pages}` : "";
+            const address = fields.address;
             if (entryType == "article") {
-                var volume =
+                const volume =
                     (fields.volume ? fields.volume : "") +
                     (fields.number ? ` (${fields.number})` : "") +
                     (pages ? `, ${pages}` : "");
@@ -144,19 +148,19 @@ export default {
                     fields.howpublished
                 )}${this._asSentence(fields.note)}`;
             }
-            var doiUrl = "";
+            let doiUrl = "";
             if (fields.doi) {
                 doiUrl = `https://doi.org/${fields.doi}`;
                 ref += `[<a href="${doiUrl}" target="_blank">doi:${fields.doi}</a>]`;
             }
-            var url = fields.url || doiUrl;
+            const url = fields.url || doiUrl;
             if (url) {
                 ref += `[<a href="${url}" target="_blank">Link</a>]`;
             }
             return convertLaTeX({ onError: (error, latex) => `{${stringifyLaTeX(latex)}}` }, ref);
         },
         _formatBookInfo: function(fields) {
-            var info = "";
+            let info = "";
             if (fields.chapter) {
                 info += `${fields.chapter} in `;
             }
diff --git a/client/galaxy/scripts/components/DataDialog/DataDialog.test.js b/client/galaxy/scripts/components/DataDialog/DataDialog.test.js
index 682ff54a4a4..b8264857e1d 100644
--- a/client/galaxy/scripts/components/DataDialog/DataDialog.test.js
+++ b/client/galaxy/scripts/components/DataDialog/DataDialog.test.js
@@ -98,7 +98,7 @@ describe("services.js/Services", () => {
         let items = services.getItems(rawData);
         expect(items.length).to.equals(1);
         let first = items[0];
-        expect(first.name).to.equals("1: name_1");
+        expect(first.label).to.equals("1: name_1");
         expect(first.download).to.equals("host/api/histories/0/contents/1/display");
     });
 });
@@ -153,11 +153,9 @@ describe("DataDialog.vue", () => {
         emitted = wrapper.emitted();
         expect(wrapper.classes()).contain("data-dialog-modal");
         expect(wrapper.find(".fa-spinner").text()).to.equals("");
-        expect(wrapper.find(".btn-secondary").text()).to.equals("Clear");
-        expect(wrapper.find(".btn-primary").text()).to.equals("Ok");
         expect(wrapper.contains(".fa-spinner")).to.equals(true);
         return Vue.nextTick().then(() => {
-            expect(wrapper.findAll(".fa-copy").length).to.equals(2);
+            expect(wrapper.findAll(".fa-folder").length).to.equals(2);
             expect(wrapper.findAll(".fa-file-o").length).to.equals(2);
         });
     });
@@ -169,11 +167,9 @@ describe("DataDialog.vue", () => {
         emitted = wrapper.emitted();
         expect(wrapper.classes()).contain("data-dialog-modal");
         expect(wrapper.find(".fa-spinner").text()).to.equals("");
-        expect(wrapper.find(".btn-secondary").text()).to.equals("Clear");
-        expect(wrapper.find(".btn-primary").text()).to.equals("Ok");
         expect(wrapper.contains(".fa-spinner")).to.equals(true);
         return Vue.nextTick().then(() => {
-            expect(wrapper.findAll(".fa-copy").length).to.equals(2);
+            expect(wrapper.findAll(".fa-folder").length).to.equals(2);
             expect(wrapper.findAll(".fa-file-o").length).to.equals(2);
         });
     });
diff --git a/client/galaxy/scripts/components/DataDialog/DataDialog.vue b/client/galaxy/scripts/components/DataDialog/DataDialog.vue
index 04abd4d86a2..5b75fc5a1ad 100644
--- a/client/galaxy/scripts/components/DataDialog/DataDialog.vue
+++ b/client/galaxy/scripts/components/DataDialog/DataDialog.vue
@@ -20,7 +20,14 @@
                 <div class="fa fa-caret-left mr-1" />
                 Back
             </b-btn>
-            <b-btn size="sm" class="float-right ml-1" variant="primary" @click="finalize" :disabled="!hasValue">
+            <b-btn
+                v-if="multiple"
+                size="sm"
+                class="float-right ml-1"
+                variant="primary"
+                @click="finalize"
+                :disabled="!hasValue"
+            >
                 Ok
             </b-btn>
             <b-btn size="sm" class="float-right" @click="modalShow = false"> Cancel </b-btn>
@@ -99,7 +106,7 @@ export default {
         },
         /** Add highlighting for record variations, i.e. datasets vs. libraries/collections **/
         formatRows() {
-            for (let item of this.items) {
+            for (const item of this.items) {
                 let _rowVariant = "active";
                 if (item.isDataset) {
                     _rowVariant = this.model.exists(item.id) ? "success" : "default";
@@ -117,11 +124,13 @@ export default {
                 } else {
                     this.finalize();
                 }
+            } else {
+                this.load(record.url);
             }
         },
         /** Called when selection is complete, values are formatted and parsed to external callback **/
         finalize: function() {
-            let results = this.model.finalize();
+            const results = this.model.finalize();
             this.modalShow = false;
             this.callback(results);
         },
@@ -136,7 +145,7 @@ export default {
                 .then(items => {
                     if (this.library && this.urlTracker.atRoot()) {
                         items.unshift({
-                            name: "Data Libraries",
+                            label: "Data Libraries",
                             url: `${this.root}api/libraries`
                         });
                     }
diff --git a/client/galaxy/scripts/components/DataDialog/DataDialogSearch.vue b/client/galaxy/scripts/components/DataDialog/DataDialogSearch.vue
index fc6a6f4ec07..ed57a831ead 100644
--- a/client/galaxy/scripts/components/DataDialog/DataDialogSearch.vue
+++ b/client/galaxy/scripts/components/DataDialog/DataDialogSearch.vue
@@ -2,7 +2,7 @@
     <b-input-group>
         <b-input v-model="filter" placeholder="Type to Search" />
         <b-input-group-append>
-            <b-btn :disabled="!filter" @click="filter = ''">Clear</b-btn>
+            <b-btn :disabled="!filter" @click="filter = ''"><i class="fa fa-times"/></b-btn>
         </b-input-group-append>
     </b-input-group>
 </template>
@@ -21,7 +21,7 @@ export default {
                 return this.value;
             },
             set(val) {
-                this.$emit('input', val);
+                this.$emit("input", val);
             }
         }
     }
diff --git a/client/galaxy/scripts/components/DataDialog/DataDialogTable.vue b/client/galaxy/scripts/components/DataDialog/DataDialogTable.vue
index c3ad745bdab..3542664d104 100644
--- a/client/galaxy/scripts/components/DataDialog/DataDialogTable.vue
+++ b/client/galaxy/scripts/components/DataDialog/DataDialogTable.vue
@@ -11,8 +11,8 @@
             @row-clicked="clicked"
             @filtered="filtered"
         >
-            <template slot="name" slot-scope="data">
-                <i v-if="data.item.isDataset" class="fa fa-file-o" /> <i v-else class="fa fa-copy" />
+            <template slot="label" slot-scope="data">
+                <i v-if="data.item.isDataset" class="fa fa-file-o" /> <i v-else class="fa fa-folder" />
                 {{ data.value ? data.value : "-" }}
             </template>
             <template slot="details" slot-scope="data">
@@ -21,17 +21,6 @@
             <template slot="time" slot-scope="data">
                 {{ data.value ? data.value : "-" }}
             </template>
-            <template slot="arrow" slot-scope="data">
-                <b-button
-                    variant="link"
-                    size="sm"
-                    class="py-0"
-                    v-if="!data.item.isDataset"
-                    @click.stop="load(data.item.url)"
-                >
-                    View
-                </b-button>
-            </template>
         </b-table>
         <div v-if="nItems === 0">
             <div v-if="filter">
@@ -69,7 +58,7 @@ export default {
         return {
             currentPage: 1,
             fields: {
-                name: {
+                label: {
                     sortable: true
                 },
                 details: {
@@ -77,11 +66,6 @@ export default {
                 },
                 time: {
                     sortable: true
-                },
-                arrow: {
-                    label: "",
-                    sortable: false,
-                    class: "text-right"
                 }
             },
             nItems: 0,
@@ -105,10 +89,6 @@ export default {
         /** Collects selected datasets in value array **/
         clicked: function(record) {
             this.$emit("clicked", record);
-        },
-        /** Performs server request to retrieve data records **/
-        load: function(url) {
-            this.$emit("load", url);
         }
     }
 };
diff --git a/client/galaxy/scripts/components/DataDialog/model.js b/client/galaxy/scripts/components/DataDialog/model.js
index 072445a0f5f..5163a01f469 100644
--- a/client/galaxy/scripts/components/DataDialog/model.js
+++ b/client/galaxy/scripts/components/DataDialog/model.js
@@ -10,7 +10,7 @@ export class Model {
         if (!this.multiple) {
             this.values = {};
         }
-        let key = record && record.id;
+        const key = record && record.id;
         if (key) {
             if (!this.values[key]) {
                 this.values[key] = record;
diff --git a/client/galaxy/scripts/components/DataDialog/services.js b/client/galaxy/scripts/components/DataDialog/services.js
index debf80724c7..3b35d4915b0 100644
--- a/client/galaxy/scripts/components/DataDialog/services.js
+++ b/client/galaxy/scripts/components/DataDialog/services.js
@@ -12,7 +12,7 @@ export class Services {
             axios
                 .get(url)
                 .then(response => {
-                    let items = this.getItems(response.data);
+                    const items = this.getItems(response.data);
                     resolve(items);
                 })
                 .catch(e => {
@@ -27,10 +27,10 @@ export class Services {
 
     /** Returns the formatted results **/
     getItems(data) {
-        let items = [];
-        let stack = [data];
+        const items = [];
+        const stack = [data];
         while (stack.length > 0) {
-            let root = stack.pop();
+            const root = stack.pop();
             if (Array.isArray(root)) {
                 root.forEach(element => {
                     stack.push(element);
@@ -40,7 +40,7 @@ export class Services {
             } else if (root.object) {
                 stack.push(root.object);
             } else {
-                let record = this.getRecord(root);
+                const record = this.getRecord(root);
                 if (record) {
                     items.push(record);
                 }
@@ -58,16 +58,16 @@ export class Services {
             record.time = record.time.substring(0, 16).replace("T", " ");
         }
         if (record.model_class == "Library") {
+            record.label = record.name;
             record.url = `${this.root}api/libraries/${record.id}/contents`;
             return record;
         } else if (record.hid) {
-            record.name = `${record.hid}: ${record.name}`;
+            record.label = `${record.hid}: ${record.name}`;
             record.download = `${this.host}/api/histories/${record.history_id}/contents/${record.id}/display`;
             return record;
         } else if (record.type == "file") {
-            if (record.name && record.name[0] === "/") {
-                record.name = record.name.substring(1);
-            }
+            record.src = "ldda";
+            record.label = record.name;
             record.download = `${this.host}${this.root}api/libraries/datasets/download/uncompressed?ld_ids=${
                 record.id
             }`;
diff --git a/client/galaxy/scripts/components/DataDialog/utilities.js b/client/galaxy/scripts/components/DataDialog/utilities.js
index 8ebcd1c3132..becc62ffdf8 100644
--- a/client/galaxy/scripts/components/DataDialog/utilities.js
+++ b/client/galaxy/scripts/components/DataDialog/utilities.js
@@ -11,7 +11,7 @@ export class UrlTracker {
             this.navigation.push(url);
         } else {
             this.navigation.pop();
-            let navigationLength = this.navigation.length;
+            const navigationLength = this.navigation.length;
             if (navigationLength > 0) {
                 url = this.navigation[navigationLength - 1];
             } else {
diff --git a/client/galaxy/scripts/components/DisplayStructured.vue b/client/galaxy/scripts/components/DisplayStructured.vue
index 9a6adbeb813..9fdc6cda8d8 100644
--- a/client/galaxy/scripts/components/DisplayStructured.vue
+++ b/client/galaxy/scripts/components/DisplayStructured.vue
@@ -32,8 +32,8 @@ export default {
         };
     },
     created: function() {
-        let historyId = this.id,
-            url = "";
+        const historyId = this.id;
+        let url = "";
         if (historyId !== undefined && historyId !== "" && historyId !== null) {
             url = getAppRoot() + "history/display_structured?id=" + historyId;
         } else {
@@ -56,13 +56,13 @@ export default {
                 });
         },
         _updateHistoryData: function(response) {
-            let historyItems = response.data;
+            const historyItems = response.data;
             this.historyTemplate = historyItems.template;
             this.historyJSON = historyItems.history_json;
         },
         makeHistoryView: function(historyDict) {
             window.hdas = historyDict.map(hda => {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 return new HDAListItemEdit.HDAListItemEdit({
                     model: new HDAModel.HistoryDatasetAssociation(hda),
                     el: $("#hda-" + hda.id),
@@ -74,7 +74,7 @@ export default {
             // toggle the body section of each item in the structure
             $(function() {
                 $(".workflow, .tool").each((index, element) => {
-                    let body = $(element).children(".body");
+                    const body = $(element).children(".body");
                     $(element)
                         .children(".header")
                         .click(e => {
diff --git a/client/galaxy/scripts/components/HistoryImport.vue b/client/galaxy/scripts/components/HistoryImport.vue
index 4889a8a0940..042b5b7b91e 100644
--- a/client/galaxy/scripts/components/HistoryImport.vue
+++ b/client/galaxy/scripts/components/HistoryImport.vue
@@ -36,7 +36,7 @@ export default {
             if (!this.sourceFile && !this.sourceURL) {
                 this.errorMessage = "You must provide a history archive URL or file.";
             } else {
-                let formData = new FormData();
+                const formData = new FormData();
                 formData.append("archive_file", this.sourceFile);
                 formData.append("archive_source", this.sourceURL);
                 axios
@@ -47,7 +47,7 @@ export default {
                         }&status=success`;
                     })
                     .catch(error => {
-                        let message = error.response.data && error.response.data.err_msg;
+                        const message = error.response.data && error.response.data.err_msg;
                         this.errorMessage = message || "Import failed for an unknown reason.";
                     });
             }
diff --git a/client/galaxy/scripts/components/HistoryView.vue b/client/galaxy/scripts/components/HistoryView.vue
index 99f40bc46fa..2692bfa76d5 100644
--- a/client/galaxy/scripts/components/HistoryView.vue
+++ b/client/galaxy/scripts/components/HistoryView.vue
@@ -59,7 +59,7 @@ export default {
         };
     },
     created: function() {
-        let url = getAppRoot() + "history/view/" + this.id;
+        const url = getAppRoot() + "history/view/" + this.id;
         this.ajaxCall(url, this.updateHistoryView);
     },
     methods: {
@@ -86,7 +86,7 @@ export default {
         },
         makeHistoryView: function(history) {
             $(function() {
-                let options = {
+                const options = {
                     hasMasthead: history.use_panels ? "true" : "false",
                     userIsOwner: history.user_is_owner ? "true" : "false",
                     isCurrent: history.history_is_current ? "true" : "false",
@@ -104,14 +104,14 @@ export default {
             });
         },
         showStructure: function() {
-            let Galaxy = getGalaxyInstance();
-            let displayStructureInstance = Vue.extend(DisplayStructure),
+            const Galaxy = getGalaxyInstance();
+            const displayStructureInstance = Vue.extend(DisplayStructure),
                 mountView = document.createElement("div");
             Galaxy.page.center.display(mountView);
             new displayStructureInstance({ propsData: { id: QueryStringParsing.get("id") } }).$mount(mountView);
         },
         switchHistory: function() {
-            let url = getAppRoot() + "history/switch_to_history?hist_id=" + this.historyHistory["id"];
+            const url = getAppRoot() + "history/switch_to_history?hist_id=" + this.historyHistory["id"];
             this.ajaxCall(url, this.reloadPage);
         },
         reloadPage: function() {
diff --git a/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue b/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
new file mode 100644
index 00000000000..039e3c9a9f9
--- /dev/null
+++ b/client/galaxy/scripts/components/JobMetrics/JobMetrics.vue
@@ -0,0 +1,78 @@
+<template>
+    <div v-if="metricsByPlugins">
+        <h3 v-if="includeTitle">Job Metrics</h3>
+        <div v-for="plugin in orderedPlugins" v-bind:key="plugin">
+            <h4>{{ plugin }}</h4>
+            <table class="tabletip info_data_table">
+                <tbody>
+                    <tr v-for="(metricValue, metricTitle) in metricsByPlugins[plugin]" v-bind:key="metricTitle">
+                        <td>{{ metricTitle }}</td>
+                        <td>{{ metricValue }}</td>
+                    </tr>
+                </tbody>
+            </table>
+        </div>
+    </div>
+</template>
+
+<script>
+import { mapCacheActions } from "vuex-cache";
+import { mapGetters } from "vuex";
+
+export default {
+    props: {
+        jobId: {
+            type: String
+        },
+        datasetId: {
+            type: String
+        },
+        datasetType: {
+            type: String,
+            default: "hda"
+        },
+        includeTitle: {
+            type: Boolean,
+            default: true
+        }
+    },
+    data() {
+        return {};
+    },
+    created: function() {
+        if (this.jobId) {
+            this.fetchJobMetricsForJobId(this.jobId);
+        } else {
+            this.fetchJobMetricsForDatasetId({ datasetId: this.datasetId, datasetType: this.datasetType });
+        }
+    },
+    computed: {
+        ...mapGetters(["getJobMetricsByDatasetId", "getJobMetricsByJobId"]),
+        jobMetrics: function() {
+            if (this.jobId) {
+                return this.getJobMetricsByJobId(this.jobId);
+            } else {
+                return this.getJobMetricsByDatasetId(this.datasetId, this.datasetType);
+            }
+        },
+        metricsByPlugins: function() {
+            const metricsByPlugins = {};
+            const metrics = this.jobMetrics;
+            metrics.forEach(metric => {
+                if (!(metric.plugin in metricsByPlugins)) {
+                    metricsByPlugins[metric.plugin] = {};
+                }
+                const metricsForPlugin = metricsByPlugins[metric.plugin];
+                metricsForPlugin[metric.title] = metric.value;
+            });
+            return metricsByPlugins;
+        },
+        orderedPlugins: function() {
+            return Object.keys(this.metricsByPlugins).sort();
+        }
+    },
+    methods: {
+        ...mapCacheActions(["fetchJobMetricsForDatasetId", "fetchJobMetricsForJobId"])
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/JobMetrics/index.js b/client/galaxy/scripts/components/JobMetrics/index.js
new file mode 100644
index 00000000000..416a80e8339
--- /dev/null
+++ b/client/galaxy/scripts/components/JobMetrics/index.js
@@ -0,0 +1,4 @@
+export { default as JobMetrics } from "./JobMetrics";
+
+// functions for mounting job metrics in non-Vue environments
+export { mountJobMetrics } from "./mount";
diff --git a/client/galaxy/scripts/components/JobMetrics/mount.js b/client/galaxy/scripts/components/JobMetrics/mount.js
new file mode 100644
index 00000000000..04b1bfe0c57
--- /dev/null
+++ b/client/galaxy/scripts/components/JobMetrics/mount.js
@@ -0,0 +1,18 @@
+/**
+ * Endpoint for mounting job metrics from non-Vue environment.
+ */
+import $ from "jquery";
+import JobMetrics from "./JobMetrics.vue";
+import { mountVueComponent } from "utils/mountVueComponent";
+
+export const mountJobMetrics = (propsData = {}) => {
+    $(".job-metrics").each((index, el) => {
+        const jobId = $(el).attr("job_id");
+        const datasetId = $(el).attr("dataset_id");
+        const datasetType = $(el).attr("dataset_type") || "hda";
+        propsData.jobId = jobId;
+        propsData.datasetId = datasetId;
+        propsData.datasetType = datasetType;
+        mountVueComponent(JobMetrics)(propsData, el);
+    });
+};
diff --git a/client/galaxy/scripts/components/JobParameters/JobParameters.vue b/client/galaxy/scripts/components/JobParameters/JobParameters.vue
new file mode 100644
index 00000000000..0d63d32773c
--- /dev/null
+++ b/client/galaxy/scripts/components/JobParameters/JobParameters.vue
@@ -0,0 +1,121 @@
+<template>
+    <div class="tool-parameters">
+        <h3 v-if="includeTitle">Tool Parameters</h3>
+        <table class="tabletip" id="tool-parameters">
+            <thead>
+                <tr>
+                    <th>Input Parameter</th>
+                    <th>Value</th>
+                    <th v-if="anyNotes">Note for rerun</th>
+                </tr>
+            </thead>
+            <tbody>
+                <tr v-for="(parameter, index) in parameters" v-bind:key="index">
+                    <td v-bind:style="{ 'padding-left': `${(parameter.depth - 1) * 10}px` }">
+                        {{ parameter.text }}
+                    </td>
+                    <td v-if="Array.isArray(parameter.value)">
+                        <ul style="padding-inline-start: 25px;">
+                            <li v-for="(elVal, index) in parameter.value" v-bind:key="index">
+                                <span v-if="elVal.src == 'hda'">
+                                    <a :href="appRoot() + 'datasets/' + elVal.id + '/show_params'">
+                                        {{ elVal.hid }}: {{ elVal.name }}
+                                    </a>
+                                </span>
+                                <span v-else> {{ elVal.hid }}: {{ elVal.name }} </span>
+                            </li>
+                        </ul>
+                    </td>
+                    <td v-else>
+                        {{ parameter.value }}
+                    </td>
+                    <td v-if="anyNotes">
+                        <em v-if="parameter.notes">{{ parameter.notes }}</em>
+                    </td>
+                </tr>
+            </tbody>
+        </table>
+        <b-alert :show="hasParameterErrors" variant="danger">
+            One or more of your original parameters may no longer be valid or displayed properly.
+        </b-alert>
+    </div>
+</template>
+
+<script>
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+import Vue from "vue";
+import BootstrapVue from "bootstrap-vue";
+
+Vue.use(BootstrapVue);
+
+export default {
+    props: {
+        jobId: {
+            type: String
+        },
+        datasetId: {
+            type: String
+        },
+        datasetType: {
+            type: String,
+            default: "hda"
+        },
+        includeTitle: {
+            type: Boolean,
+            default: true
+        }
+    },
+    data() {
+        return {
+            parameters: [],
+            hasParameterErrors: false
+        };
+    },
+    created: function() {
+        let url;
+        if (this.jobId) {
+            url = `${getAppRoot()}api/jobs/${this.jobId}/parameters_display`;
+        } else {
+            url = `${getAppRoot()}api/datasets/${this.datasetId}/parameters_display?hda_ldda=${this.datasetType}`;
+        }
+        this.ajaxCall(url);
+    },
+    computed: {
+        anyNotes: function() {
+            let hasNotes = false;
+            this.parameters.forEach(parameter => {
+                hasNotes = hasNotes || parameter.notes;
+            });
+            return hasNotes;
+        }
+    },
+    methods: {
+        appRoot: function() {
+            return getAppRoot();
+        },
+        ajaxCall: function(url) {
+            axios
+                .get(url)
+                .then(response => response.data)
+                .then(data => {
+                    this.hasParameterErrors = data.has_parameter_errors;
+                    this.parameters = data.parameters;
+                })
+                .catch(e => {
+                    console.error(e);
+                });
+        }
+    }
+};
+</script>
+<style scoped>
+table.info_data_table {
+    table-layout: fixed;
+    word-break: break-word;
+}
+table.info_data_table td:nth-child(1) {
+    width: 25%;
+}
+</style>
diff --git a/client/galaxy/scripts/components/JobParameters/index.js b/client/galaxy/scripts/components/JobParameters/index.js
new file mode 100644
index 00000000000..8d76729387f
--- /dev/null
+++ b/client/galaxy/scripts/components/JobParameters/index.js
@@ -0,0 +1,4 @@
+export { default as JobParameters } from "./JobParameters";
+
+// functions for mounting job parameters display in non-Vue environments
+export { mountJobParameters } from "./mount";
diff --git a/client/galaxy/scripts/components/JobParameters/mount.js b/client/galaxy/scripts/components/JobParameters/mount.js
new file mode 100644
index 00000000000..4e7e9f67fb6
--- /dev/null
+++ b/client/galaxy/scripts/components/JobParameters/mount.js
@@ -0,0 +1,19 @@
+/**
+ * Endpoint for mounting job parameters from non-Vue environment.
+ */
+import $ from "jquery";
+import Vue from "vue";
+import JobParameters from "./JobParameters.vue";
+
+export const mountJobParameters = (propsData = {}) => {
+    $(".job-parameters").each((index, el) => {
+        const jobId = $(el).attr("job_id");
+        const datasetId = $(el).attr("dataset_id");
+        const datasetType = $(el).attr("dataset_type") || "hda";
+        const component = Vue.extend(JobParameters);
+        propsData.jobId = jobId;
+        propsData.datasetId = datasetId;
+        propsData.datasetType = datasetType;
+        return new component({ propsData: propsData }).$mount(el);
+    });
+};
diff --git a/client/galaxy/scripts/components/MaskedInput.js b/client/galaxy/scripts/components/MaskedInput.js
new file mode 100644
index 00000000000..7cac27045eb
--- /dev/null
+++ b/client/galaxy/scripts/components/MaskedInput.js
@@ -0,0 +1,29 @@
+import BInput from "bootstrap-vue/es/components/form-input/form-input";
+import { createMask } from "imask";
+
+export default {
+    extends: BInput,
+    props: {
+        mask: {
+            type: String,
+            required: false,
+            default: ""
+        }
+    },
+    computed: {
+        masker() {
+            return createMask({
+                mask: this.mask
+            });
+        }
+    },
+    methods: {
+        getFormatted(value) {
+            const result = this.stringifyValue(value);
+            if (this.mask.length) {
+                return this.masker.resolve(result);
+            }
+            return result;
+        }
+    }
+};
diff --git a/client/galaxy/scripts/components/Masthead/index.vue b/client/galaxy/scripts/components/Masthead/index.vue
index ba0b6f6ba08..f232e2302b0 100644
--- a/client/galaxy/scripts/components/Masthead/index.vue
+++ b/client/galaxy/scripts/components/Masthead/index.vue
@@ -22,7 +22,7 @@ export default {
                 return;
             }
 
-            let galaxy = getGalaxyInstance();
+            const galaxy = getGalaxyInstance();
 
             // old backbone view
             if (!galaxy.masthead) {
@@ -30,7 +30,7 @@ export default {
             }
 
             // bolt the rendered DOM onto the vue component's element
-            let backboneDom = galaxy.masthead.render();
+            const backboneDom = galaxy.masthead.render();
             this.$el.appendChild(backboneDom.$el[0]);
         }
     }
diff --git a/client/galaxy/scripts/components/Masthead/initMasthead.js b/client/galaxy/scripts/components/Masthead/initMasthead.js
index c8b69693cae..9df6e15e230 100644
--- a/client/galaxy/scripts/components/Masthead/initMasthead.js
+++ b/client/galaxy/scripts/components/Masthead/initMasthead.js
@@ -7,7 +7,7 @@ import Masthead from "components/Masthead";
 
 export function initMasthead(config, container) {
     console.log("initMasthead");
-    let Component = Vue.extend(Masthead);
+    const Component = Vue.extend(Masthead);
     return new Component({
         props: Object.keys(config),
         propsData: config,
diff --git a/client/galaxy/scripts/components/Nametags/Nametag.vue b/client/galaxy/scripts/components/Nametags/Nametag.vue
index 183db221f7b..89cfc4a6251 100644
--- a/client/galaxy/scripts/components/Nametags/Nametag.vue
+++ b/client/galaxy/scripts/components/Nametags/Nametag.vue
@@ -14,7 +14,7 @@ export default {
             return this.tag.startsWith("name:") ? this.tag.replace("name:", "") : this.tag;
         },
         tagStyles() {
-            let { primary, contrasting, darker } = keyedColorScheme(this.tag);
+            const { primary, contrasting, darker } = keyedColorScheme(this.tag);
             return {
                 "background-color": primary,
                 color: contrasting,
diff --git a/client/galaxy/scripts/components/PageEditor/PageEditor.vue b/client/galaxy/scripts/components/PageEditor/PageEditor.vue
new file mode 100644
index 00000000000..f589b15e23a
--- /dev/null
+++ b/client/galaxy/scripts/components/PageEditor/PageEditor.vue
@@ -0,0 +1,38 @@
+<template>
+    <span>
+        <div class="unified-panel-header" unselectable="on">
+            <div class="unified-panel-header-inner">
+                Page Editor: {{ title }}
+                <a id="save-button" class="btn btn-secondary fa fa-save float-right" @click="saveContent"></a>
+            </div>
+        </div>
+        <page-editor-html :page-id="pageId" :content="content" ref="contentEditor" />
+    </span>
+</template>
+
+<script>
+import PageEditorHtml from "./PageEditorHtml";
+
+export default {
+    props: {
+        pageId: {
+            required: true,
+            type: String
+        },
+        content: {
+            type: String
+        },
+        title: {
+            type: String
+        }
+    },
+    methods: {
+        saveContent: function() {
+            this.$refs.contentEditor.saveContent();
+        }
+    },
+    components: {
+        PageEditorHtml
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/PageEditor/PageEditorHtml.vue b/client/galaxy/scripts/components/PageEditor/PageEditorHtml.vue
new file mode 100644
index 00000000000..bce1497ac72
--- /dev/null
+++ b/client/galaxy/scripts/components/PageEditor/PageEditorHtml.vue
@@ -0,0 +1,682 @@
+<template>
+    <div class="unified-panel-body">
+        <textarea name="page_content" :val="content"></textarea>
+    </div>
+</template>
+
+<script>
+import $ from "jquery";
+import _l from "utils/localization";
+
+import GridView from "mvc/grid/grid-view";
+import { show_modal, hide_modal } from "layout/modal";
+import { make_popupmenu } from "ui/popupmenu";
+import { getGalaxyInstance } from "app";
+import { buildConfig } from "utils/genericConfig";
+import { getAppRoot } from "onload/loadConfig";
+import { save } from "./util";
+
+// Built a generic config container for the properties that
+// are passed in from python then used (formerly) globally
+const configs = buildConfig();
+
+// Turn these window variables into config props list_objects_url,
+// set_accessible_url, get_name_and_link_url, editor_base_path,
+// iframe_base_path, save_url, page_id, page_list_url
+function setPageConfigs(incoming = {}) {
+    return Object.assign(configs, incoming);
+}
+
+var WYMeditor = window.WYMeditor;
+
+var editor = null;
+
+var CONTROLS = {
+    // Item types.
+    ITEM_HISTORY: "item_history",
+    ITEM_DATASET: "item_dataset",
+    ITEM_WORKFLOW: "item_workflow",
+    ITEM_PAGE: "item_page",
+    ITEM_VISUALIZATION: "item_visualization",
+
+    // Link dialogs.
+    DIALOG_HISTORY_LINK: "link_history",
+    DIALOG_DATASET_LINK: "link_dataset",
+    DIALOG_WORKFLOW_LINK: "link_workflow",
+    DIALOG_PAGE_LINK: "link_page",
+    DIALOG_VISUALIZATION_LINK: "link_visualization",
+
+    // Embed dialogs.
+    DIALOG_EMBED_HISTORY: "embed_history",
+    DIALOG_EMBED_DATASET: "embed_dataset",
+    DIALOG_EMBED_WORKFLOW: "embed_workflow",
+    DIALOG_EMBED_PAGE: "embed_page",
+    DIALOG_EMBED_VISUALIZATION: "embed_visualization"
+};
+
+// Based on the dialog type, return a dictionary of information about an item
+function get_item_info(dialog_type) {
+    var item_singular;
+    var item_plural;
+    var item_controller;
+    var item_class;
+    switch (dialog_type) {
+        case CONTROLS.ITEM_HISTORY:
+            item_singular = "History";
+            item_plural = "Histories";
+            item_controller = "history";
+            item_class = "History";
+            break;
+        case CONTROLS.ITEM_DATASET:
+            item_singular = "Dataset";
+            item_plural = "Datasets";
+            item_controller = "dataset";
+            item_class = "HistoryDatasetAssociation";
+            break;
+        case CONTROLS.ITEM_WORKFLOW:
+            item_singular = "Workflow";
+            item_plural = "Workflows";
+            item_controller = "workflow";
+            item_class = "StoredWorkflow";
+            break;
+        case CONTROLS.ITEM_PAGE:
+            item_singular = "Page";
+            item_plural = "Pages";
+            item_controller = "page";
+            item_class = "Page";
+            break;
+        case CONTROLS.ITEM_VISUALIZATION:
+            item_singular = "Visualization";
+            item_plural = "Visualizations";
+            item_controller = "visualization";
+            item_class = "Visualization";
+            break;
+    }
+
+    // Build ajax URL that lists items for selection.
+    var item_list_action = `list_${item_plural.toLowerCase()}_for_selection`;
+    var ajax_url = configs.list_objects_url.replace("LIST_ACTION", item_list_action);
+
+    // Set up and return dict.
+    return {
+        singular: item_singular,
+        plural: item_plural,
+        controller: item_controller,
+        iclass: item_class,
+        list_ajax_url: ajax_url
+    };
+}
+
+// Make an item importable.
+function make_item_importable(item_controller, item_id, item_type) {
+    var ajax_url = configs.set_accessible_url.replace("ITEM_CONTROLLER", item_controller);
+    $.ajax({
+        type: "POST",
+        url: ajax_url,
+        data: { id: item_id, accessible: "True" },
+        error: function() {
+            alert(`Making ${item_type} accessible failed`);
+        }
+    });
+}
+
+// Completely replace WYM's dialog handling
+WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtml) {
+    var wym = this;
+    var sStamp = wym.uniqueStamp();
+    var selected = wym.selected();
+
+    // Swap out URL attribute for id/name attribute in link creation to enable anchor creation in page.
+    function set_link_id() {
+        // When "set link id" link clicked, update UI.
+        $("#set_link_id").click(function() {
+            // Set label.
+            $("#link_attribute_label").text("ID/Name");
+
+            // Set input elt class, value.
+            var attribute_input = $(".wym_href");
+            attribute_input.addClass("wym_id").removeClass("wym_href");
+            if (selected) attribute_input.val($(selected).attr("id"));
+
+            // Remove link.
+            $(this).remove();
+        });
+    }
+
+    // LINK DIALOG
+    if (dialogType == WYMeditor.DIALOG_LINK) {
+        if (selected) {
+            $(wym._options.hrefSelector).val($(selected).attr(WYMeditor.HREF));
+            $(wym._options.srcSelector).val($(selected).attr(WYMeditor.SRC));
+            $(wym._options.titleSelector).val($(selected).attr(WYMeditor.TITLE));
+            $(wym._options.altSelector).val($(selected).attr(WYMeditor.ALT));
+        }
+
+        // Get current URL, title.
+        var curURL;
+
+        var curTitle;
+        if (selected) {
+            curURL = $(selected).attr("href");
+            if (curURL == undefined) curURL = "";
+            curTitle = $(selected).attr("title");
+            if (curTitle == undefined) curTitle = "";
+        }
+        show_modal(
+            "Create Link",
+            `<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='${curURL}' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='${curTitle}' size='40' /></div><div>`,
+            {
+                "Make link": function() {
+                    // Get URL, name/title.
+                    var sUrl = $(wym._options.hrefSelector).val() || "";
+
+                    var sId = $(".wym_id").val() || "";
+                    var sName = $(wym._options.titleSelector).val() || "";
+
+                    if (sUrl || sId) {
+                        // Create link.
+                        wym._exec(WYMeditor.CREATE_LINK, sStamp);
+
+                        // Set link attributes.
+                        var link = $(`a[href=${sStamp}]`, wym._doc.body);
+                        link.attr(WYMeditor.HREF, sUrl)
+                            .attr(WYMeditor.TITLE, sName)
+                            .attr("id", sId);
+
+                        // If link's text is default (wym-...), change it to the title.
+                        if (link.text().indexOf("wym-") === 0) {
+                            link.text(sName);
+                        }
+                    }
+                    hide_modal();
+                },
+                Cancel: function() {
+                    hide_modal();
+                }
+            },
+            {},
+            set_link_id
+        );
+    }
+
+    // IMAGE DIALOG
+    if (dialogType == WYMeditor.DIALOG_IMAGE) {
+        if (wym._selected_image) {
+            $(`${wym._options.dialogImageSelector} ${wym._options.srcSelector}`).val(
+                $(wym._selected_image).attr(WYMeditor.SRC)
+            );
+            $(`${wym._options.dialogImageSelector} ${wym._options.titleSelector}`).val(
+                $(wym._selected_image).attr(WYMeditor.TITLE)
+            );
+            $(`${wym._options.dialogImageSelector} ${wym._options.altSelector}`).val(
+                $(wym._selected_image).attr(WYMeditor.ALT)
+            );
+        }
+        show_modal(
+            "Image",
+            "<div class='row'>" +
+                "<label>URL</label><br>" +
+                "<input type='text' class='wym_src' value='' size='40' />" +
+                "</div>" +
+                "<div class='row'>" +
+                "<label>Alt text</label><br>" +
+                "<input type='text' class='wym_alt' value='' size='40' />" +
+                "</div>" +
+                "<div class='row'>" +
+                "<label>Title</label><br>" +
+                "<input type='text' class='wym_title' value='' size='40' />" +
+                "</div>",
+            {
+                Insert: function() {
+                    var sUrl = $(wym._options.srcSelector).val();
+                    if (sUrl.length > 0) {
+                        wym._exec(WYMeditor.INSERT_IMAGE, sStamp);
+                        $(`img[src$=${sStamp}]`, wym._doc.body)
+                            .attr(WYMeditor.SRC, sUrl)
+                            .attr(WYMeditor.TITLE, $(wym._options.titleSelector).val())
+                            .attr(WYMeditor.ALT, $(wym._options.altSelector).val());
+                    }
+                    hide_modal();
+                },
+                Cancel: function() {
+                    hide_modal();
+                }
+            }
+        );
+        return;
+    }
+
+    // TABLE DIALOG
+    if (dialogType == WYMeditor.DIALOG_TABLE) {
+        show_modal(
+            "Table",
+            "<div class='row'>" +
+                "<label>Caption</label><br>" +
+                "<input type='text' class='wym_caption' value='' size='40' />" +
+                "</div>" +
+                "<div class='row'>" +
+                "<label>Summary</label><br>" +
+                "<input type='text' class='wym_summary' value='' size='40' />" +
+                "</div>" +
+                "<div class='row'>" +
+                "<label>Number Of Rows<br></label>" +
+                "<input type='text' class='wym_rows' value='3' size='3' />" +
+                "</div>" +
+                "<div class='row'>" +
+                "<label>Number Of Cols<br></label>" +
+                "<input type='text' class='wym_cols' value='2' size='3' />" +
+                "</div>",
+            {
+                Insert: function() {
+                    var iRows = $(wym._options.rowsSelector).val();
+                    var iCols = $(wym._options.colsSelector).val();
+
+                    if (iRows > 0 && iCols > 0) {
+                        var table = wym._doc.createElement(WYMeditor.TABLE);
+                        var newRow = null;
+
+                        var sCaption = $(wym._options.captionSelector).val();
+
+                        //we create the caption
+                        var newCaption = table.createCaption();
+                        newCaption.innerHTML = sCaption;
+
+                        //we create the rows and cells
+                        for (var x = 0; x < iRows; x++) {
+                            newRow = table.insertRow(x);
+                            for (var y = 0; y < iCols; y++) {
+                                newRow.insertCell(y);
+                            }
+                        }
+
+                        //set the summary attr
+                        $(table).attr("summary", $(wym._options.summarySelector).val());
+
+                        //append the table after the selected container
+                        var node = $(wym.findUp(wym.container(), WYMeditor.MAIN_CONTAINERS)).get(0);
+                        if (!node || !node.parentNode) $(wym._doc.body).append(table);
+                        else $(node).after(table);
+                    }
+                    hide_modal();
+                },
+                Cancel: function() {
+                    hide_modal();
+                }
+            }
+        );
+    }
+
+    // INSERT "GALAXY ITEM" LINK DIALOG
+    if (
+        dialogType == CONTROLS.DIALOG_HISTORY_LINK ||
+        dialogType == CONTROLS.DIALOG_DATASET_LINK ||
+        dialogType == CONTROLS.DIALOG_WORKFLOW_LINK ||
+        dialogType == CONTROLS.DIALOG_PAGE_LINK ||
+        dialogType == CONTROLS.DIALOG_VISUALIZATION_LINK
+    ) {
+        // Based on item type, set useful vars.
+        var item_info;
+        switch (dialogType) {
+            case CONTROLS.DIALOG_HISTORY_LINK:
+                item_info = get_item_info(CONTROLS.ITEM_HISTORY);
+                break;
+            case CONTROLS.DIALOG_DATASET_LINK:
+                item_info = get_item_info(CONTROLS.ITEM_DATASET);
+                break;
+            case CONTROLS.DIALOG_WORKFLOW_LINK:
+                item_info = get_item_info(CONTROLS.ITEM_WORKFLOW);
+                break;
+            case CONTROLS.DIALOG_PAGE_LINK:
+                item_info = get_item_info(CONTROLS.ITEM_PAGE);
+                break;
+            case CONTROLS.DIALOG_VISUALIZATION_LINK:
+                item_info = get_item_info(CONTROLS.ITEM_VISUALIZATION);
+                break;
+        }
+
+        var grid = new GridView({
+            url_base: item_info.list_ajax_url,
+            embedded: true
+        });
+        const Galaxy = getGalaxyInstance();
+        Galaxy.modal.show({
+            title: `Insert Link to ${item_info.singular}`,
+            body: $("<div/>")
+                .append(grid.$el)
+                .append(
+                    $("<div/>")
+                        .append('<input id="make-importable" type="checkbox" checked/>')
+                        .append(
+                            `Make the selected ${item_info.plural.toLowerCase()} accessible so that they can viewed by everyone.`
+                        )
+                ),
+            closing_events: true,
+            buttons: {
+                Insert: function() {
+                    // Make selected items accessible (importable) ?
+                    var make_importable = false;
+                    if ($("#make-importable:checked").val() != null) make_importable = true;
+
+                    // Insert links to history for each checked item.
+                    grid.$("input[name=id]:checked").each(function() {
+                        var item_id = $(this).val();
+
+                        // Make item importable?
+                        if (make_importable) make_item_importable(item_info.controller, item_id, item_info.singular);
+
+                        // Insert link(s) to item(s). This is done by getting item info and then manipulating wym.
+                        var url_template = configs.get_name_and_link_url + item_id;
+                        var ajax_url = url_template.replace("ITEM_CONTROLLER", item_info.controller);
+                        $.getJSON(ajax_url, returned_item_info => {
+                            // Get link text.
+                            wym._exec(WYMeditor.CREATE_LINK, sStamp);
+                            var link_text = $(`a[href=${sStamp}]`, wym._doc.body).text();
+
+                            // Insert link: need to do different actions depending on link text.
+                            if (
+                                link_text == "" || // Firefox.
+                                link_text == sStamp // Safari
+                            ) {
+                                // User selected no text; create link from scratch and use default text.
+                                wym.insert(
+                                    `<a href='${returned_item_info.link}'>${item_info.singular} '${
+                                        returned_item_info.name
+                                    }'</a>`
+                                );
+                            } else {
+                                // Link created from selected text; add href and title.
+                                $(`a[href=${sStamp}]`, wym._doc.body)
+                                    .attr(WYMeditor.HREF, returned_item_info.link)
+                                    .attr(WYMeditor.TITLE, item_info.singular + item_id);
+                            }
+                        });
+                    });
+                    Galaxy.modal.hide();
+                },
+                Close: function() {
+                    Galaxy.modal.hide();
+                }
+            }
+        });
+    }
+    // EMBED GALAXY OBJECT DIALOGS
+    if (
+        dialogType == CONTROLS.DIALOG_EMBED_HISTORY ||
+        dialogType == CONTROLS.DIALOG_EMBED_DATASET ||
+        dialogType == CONTROLS.DIALOG_EMBED_WORKFLOW ||
+        dialogType == CONTROLS.DIALOG_EMBED_PAGE ||
+        dialogType == CONTROLS.DIALOG_EMBED_VISUALIZATION
+    ) {
+        // Based on item type, set useful vars.
+        let item_info;
+        switch (dialogType) {
+            case CONTROLS.DIALOG_EMBED_HISTORY:
+                item_info = get_item_info(CONTROLS.ITEM_HISTORY);
+                break;
+            case CONTROLS.DIALOG_EMBED_DATASET:
+                item_info = get_item_info(CONTROLS.ITEM_DATASET);
+                break;
+            case CONTROLS.DIALOG_EMBED_WORKFLOW:
+                item_info = get_item_info(CONTROLS.ITEM_WORKFLOW);
+                break;
+            case CONTROLS.DIALOG_EMBED_PAGE:
+                item_info = get_item_info(CONTROLS.ITEM_PAGE);
+                break;
+            case CONTROLS.DIALOG_EMBED_VISUALIZATION:
+                item_info = get_item_info(CONTROLS.ITEM_VISUALIZATION);
+                break;
+        }
+
+        const grid = new GridView({
+            url_base: item_info.list_ajax_url,
+            embedded: true
+        });
+        const Galaxy = getGalaxyInstance();
+        Galaxy.modal.show({
+            title: `Insert Link to ${item_info.singular}`,
+            body: $("<div/>")
+                .append(grid.$el)
+                .append(
+                    $("<div/>")
+                        .append('<input id="make-importable" type="checkbox" checked/>')
+                        .append(
+                            `Make the selected ${item_info.plural.toLowerCase()} accessible so that they can viewed by everyone.`
+                        )
+                ),
+            closing_events: true,
+            extra_class: "pages-embed",
+            buttons: {
+                Embed: function() {
+                    // Make selected items accessible (importable) ?
+                    var make_importable = false;
+                    if ($("#make-importable:checked").val() != null) make_importable = true;
+
+                    grid.$("input[name=id]:checked").each(function() {
+                        var elt = $(this);
+                        // Get item ID and name.
+                        var item_id = elt.val();
+                        // Use ':first' because there are many labels in table; the first one is the item name.
+                        var item_name = elt
+                            .closest("td")
+                            .next("td")
+                            .find("label")
+                            .text();
+
+                        if (make_importable) make_item_importable(item_info.controller, item_id, item_info.singular);
+
+                        // Embedded item HTML; item class is embedded in div container classes; this is necessary because the editor strips
+                        // all non-standard attributes when it returns its content (e.g. it will not return an element attribute of the form
+                        // item_class='History').
+                        var item_elt_id = `${item_info.iclass}-${item_id}`;
+                        var item_embed_html = [
+                            "<div id='",
+                            item_elt_id,
+                            "' class='embedded-item ",
+                            item_info.singular.toLowerCase(),
+                            " placeholder'>",
+                            "<p class='title'>",
+                            "Embedded Galaxy ",
+                            item_info.singular,
+                            " '",
+                            item_name,
+                            "'",
+                            "</p>",
+                            "<p class='content'>",
+                            "[Do not edit this block; Galaxy will fill it in with the annotated ",
+                            item_info.singular.toLowerCase(),
+                            " when it is displayed.]",
+                            "</p>",
+                            "</div>"
+                        ].join("");
+
+                        // Insert embedded item into document.
+                        wym.insert(item_embed_html);
+                    });
+                    Galaxy.modal.hide();
+                },
+                Close: function() {
+                    Galaxy.modal.hide();
+                }
+            }
+        });
+    }
+};
+
+function renderEditorWithContent(pageId, content) {
+    const appRoot = getAppRoot();
+    const pageConfigs = {
+        page_id: pageId,
+        page_list_url: `${appRoot}pages/list`,
+        list_objects_url: `${appRoot}page/LIST_ACTION`,
+        set_accessible_url: `${appRoot}ITEM_CONTROLLER/set_accessible_async`,
+        get_name_and_link_url: `${appRoot}ITEM_CONTROLLER/get_name_and_link_async?id=`,
+        editor_base_path: `${appRoot}static/wymeditor/`,
+        iframe_base_path: `${appRoot}static/wymeditor/iframe/galaxy/`
+    };
+    setPageConfigs(pageConfigs);
+
+    // Generic error handling
+    $(document).ajaxError((e, x) => {
+        // console.log( e, x );
+        var message = x.responseText || x.statusText || "Could not connect to server";
+        show_modal("Server error", message, { "Ignore error": hide_modal });
+        return false;
+    });
+    // Create editor
+    $("[name=page_content]")
+        .val(content)
+        .wymeditor({
+            skin: "galaxy",
+            basePath: configs.editor_base_path,
+            iframeBasePath: configs.iframe_base_path,
+            // + WYMeditor.HTML
+            boxHtml: `<table class='wym_box' width='100%' height='100%'><tr><td><div class='wym_area_top'>${
+                WYMeditor.TOOLS
+            }</div></td></tr><tr height='100%'><td><div class='wym_area_main' style='height: 100%;'>${
+                // + WYMeditor.HTML
+                WYMeditor.IFRAME
+            }${WYMeditor.STATUS}</div></div></td></tr></table>`,
+            toolsItems: [
+                { name: "Bold", title: "Strong", css: "wym_tools_strong" },
+                { name: "Italic", title: "Emphasis", css: "wym_tools_emphasis" },
+                {
+                    name: "Superscript",
+                    title: _l("Superscript"),
+                    css: "wym_tools_superscript"
+                },
+                {
+                    name: "Subscript",
+                    title: _l("Subscript"),
+                    css: "wym_tools_subscript"
+                },
+                {
+                    name: "InsertOrderedList",
+                    title: "Ordered_List",
+                    css: "wym_tools_ordered_list"
+                },
+                {
+                    name: "InsertUnorderedList",
+                    title: "Unordered_List",
+                    css: "wym_tools_unordered_list"
+                },
+                { name: "Indent", title: "Indent", css: "wym_tools_indent" },
+                { name: "Outdent", title: "Outdent", css: "wym_tools_outdent" },
+                { name: "Undo", title: "Undo", css: "wym_tools_undo" },
+                { name: "Redo", title: "Redo", css: "wym_tools_redo" },
+                { name: "CreateLink", title: "Link", css: "wym_tools_link" },
+                { name: "Unlink", title: "Unlink", css: "wym_tools_unlink" },
+                { name: "InsertImage", title: "Image", css: "wym_tools_image" },
+                { name: "InsertTable", title: "Table", css: "wym_tools_table" }
+            ]
+        });
+    // Get the editor object
+    editor = $.wymeditors(0);
+
+    //
+    // Containers, Galaxy style
+    //
+    var containers_menu = $(
+        "<div class='galaxy-page-editor-button'><a id='insert-galaxy-link' class='action-button popup' href='#'>Paragraph type</a></div>"
+    );
+    $(".wym_area_top").append(containers_menu);
+
+    // Add menu options.
+    var items = {};
+    $.each(editor._options.containersItems, (k, v) => {
+        var tagname = v.name;
+        items[v.title.replace("_", " ")] = () => {
+            editor.container(tagname);
+        };
+    });
+    make_popupmenu(containers_menu, items);
+
+    //
+    // Create 'Insert Link to Galaxy Object' menu.
+    //
+
+    // Add menu button.
+    var insert_link_menu_button = $(
+        "<div><a id='insert-galaxy-link' class='action-button popup' href='#'>Insert Link to Galaxy Object</a></div>"
+    ).addClass("galaxy-page-editor-button");
+    $(".wym_area_top").append(insert_link_menu_button);
+
+    // Add menu options.
+    make_popupmenu(insert_link_menu_button, {
+        "Insert History Link": function() {
+            editor.dialog(CONTROLS.DIALOG_HISTORY_LINK);
+        },
+        "Insert Dataset Link": function() {
+            editor.dialog(CONTROLS.DIALOG_DATASET_LINK);
+        },
+        "Insert Workflow Link": function() {
+            editor.dialog(CONTROLS.DIALOG_WORKFLOW_LINK);
+        },
+        "Insert Page Link": function() {
+            editor.dialog(CONTROLS.DIALOG_PAGE_LINK);
+        },
+        "Insert Visualization Link": function() {
+            editor.dialog(CONTROLS.DIALOG_VISUALIZATION_LINK);
+        }
+    });
+
+    //
+    // Create 'Embed Galaxy Object' menu.
+    //
+
+    // Add menu button.
+    var embed_object_button = $(
+        "<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>"
+    ).addClass("galaxy-page-editor-button");
+    $(".wym_area_top").append(embed_object_button);
+
+    // Add menu options.
+    make_popupmenu(embed_object_button, {
+        "Embed History": function() {
+            editor.dialog(CONTROLS.DIALOG_EMBED_HISTORY);
+        },
+        "Embed Dataset": function() {
+            editor.dialog(CONTROLS.DIALOG_EMBED_DATASET);
+        },
+        "Embed Workflow": function() {
+            editor.dialog(CONTROLS.DIALOG_EMBED_WORKFLOW);
+        },
+        "Embed Visualization": function() {
+            editor.dialog(CONTROLS.DIALOG_EMBED_VISUALIZATION);
+        }
+        //"Embed Page": function() {
+        //    editor.dialog(CONTROLS.DIALOG_EMBED_PAGE);
+        //}
+    });
+}
+
+export default {
+    props: {
+        pageId: {
+            required: true,
+            type: String
+        },
+        content: {
+            type: String
+        }
+    },
+    created: function() {
+        this.$nextTick(() => {
+            renderEditorWithContent(this.pageId, this.content);
+        });
+    },
+    methods: {
+        saveContent: function() {
+            save(this.pageId, editor.xhtml());
+        }
+    }
+};
+</script>
+
+<style lang="scss">
+@import "embed_item";
+.galaxy-page-editor-button {
+    position: relative;
+    float: left;
+    padding: 0.2em;
+}
+</style>
diff --git a/client/galaxy/scripts/components/PageEditor/index.js b/client/galaxy/scripts/components/PageEditor/index.js
new file mode 100644
index 00000000000..326ba8fc57f
--- /dev/null
+++ b/client/galaxy/scripts/components/PageEditor/index.js
@@ -0,0 +1 @@
+export { default as PageEditor } from "./PageEditor.vue";
diff --git a/client/galaxy/scripts/components/PageEditor/util.js b/client/galaxy/scripts/components/PageEditor/util.js
new file mode 100644
index 00000000000..5339f5172f6
--- /dev/null
+++ b/client/galaxy/scripts/components/PageEditor/util.js
@@ -0,0 +1,24 @@
+import $ from "jquery";
+import _l from "utils/localization";
+import { getAppRoot } from "onload/loadConfig";
+import { show_modal, hide_modal } from "layout/modal";
+
+export const save = (pageId, content) => {
+    console.log(`content is ${content}`);
+
+    show_modal(_l("Saving page"), _l("progress"));
+
+    // Do save.
+    $.ajax({
+        url: `${getAppRoot()}page/save`,
+        type: "POST",
+        data: {
+            id: pageId,
+            content: content,
+            _: "true"
+        },
+        success: function() {
+            hide_modal();
+        }
+    });
+};
diff --git a/client/galaxy/scripts/components/PluginList.vue b/client/galaxy/scripts/components/PluginList.vue
index ae55e131fa5..7acf1ff0533 100644
--- a/client/galaxy/scripts/components/PluginList.vue
+++ b/client/galaxy/scripts/components/PluginList.vue
@@ -73,9 +73,9 @@ export default {
         };
     },
     created() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         let url = `${getAppRoot()}api/plugins`;
-        let dataset_id = Galaxy.params.dataset_id;
+        const dataset_id = Galaxy.params.dataset_id;
         if (dataset_id) {
             this.fixed = true;
             this.selected = dataset_id;
@@ -95,8 +95,8 @@ export default {
             if (this.fixed) {
                 this.create(plugin);
             } else {
-                let Galaxy = getGalaxyInstance();
-                let history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
+                const Galaxy = getGalaxyInstance();
+                const history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
                 if (history_id) {
                     axios
                         .get(`${getAppRoot()}api/plugins/${plugin.name}?history_id=${history_id}`)
@@ -116,7 +116,7 @@ export default {
             }
         },
         create: function(plugin) {
-            let href = `${plugin.href}?dataset_id=${this.selected}`;
+            const href = `${plugin.href}?dataset_id=${this.selected}`;
             if (plugin.target == "_top") {
                 window.location.href = href;
             } else {
@@ -131,7 +131,7 @@ export default {
             );
         },
         _errorMessage: function(e) {
-            let message = e && e.response && e.response.data && e.response.data.err_msg;
+            const message = e && e.response && e.response.data && e.response.data.err_msg;
             return message || "Request failed for an unknown reason.";
         }
     }
diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index dccaac7e71a..fccb9d37f3b 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -670,7 +670,7 @@ const ColumnSelector = {
                 return colHeaders;
             }
             const remaining = {};
-            for (let key in colHeaders) {
+            for (const key in colHeaders) {
                 if (this.target.indexOf(parseInt(key)) === -1) {
                     remaining[key] = colHeaders[key];
                 }
@@ -685,7 +685,7 @@ const ColumnSelector = {
         handleInput(value) {
             if (this.multiple) {
                 // https://stackoverflow.com/questions/262427/why-does-parseint-yield-nan-with-arraymap
-                let val = value.map(idx => parseInt(idx));
+                const val = value.map(idx => parseInt(idx));
                 this.$emit("update:target", val);
             } else {
                 let val = parseInt(value);
@@ -951,7 +951,7 @@ export default {
                 if (this.initialElements !== null) {
                     const collectionType = this.initialElements.collection_type;
                     const collectionTypeRanks = collectionType.split(":");
-                    for (let index in collectionTypeRanks) {
+                    for (const index in collectionTypeRanks) {
                         rules.push({
                             type: "add_column_metadata",
                             value: "identifier" + index
@@ -1187,7 +1187,7 @@ export default {
         },
         mappedTargets() {
             const targets = [];
-            for (let mapping of this.mapping) {
+            for (const mapping of this.mapping) {
                 targets.push(mapping.type);
             }
             return targets;
@@ -1195,7 +1195,7 @@ export default {
         unmappedTargets() {
             const targets = [];
             const mappedTargets = this.mappedTargets;
-            for (let target in MAPPING_TARGETS) {
+            for (const target in MAPPING_TARGETS) {
                 const targetModes = MAPPING_TARGETS[target].modes;
 
                 if (targetModes && targetModes.indexOf(this.elementsType) < 0) {
@@ -1217,16 +1217,16 @@ export default {
             return targets;
         },
         colHeaders() {
-            let { data, columns } = this.hotData;
+            const { data, columns } = this.hotData;
             return RuleDefs.colHeadersFor(data, columns);
         },
         colHeadersDisplay() {
             const formattedHeaders = [];
-            for (let colIndex in this.colHeaders) {
+            for (const colIndex in this.colHeaders) {
                 const colHeader = this.colHeaders[colIndex];
                 formattedHeaders[colIndex] = `<b>${_.escape(colHeader)}</b>`;
                 const mappingDisplay = [];
-                for (let mapping of this.mapping) {
+                for (const mapping of this.mapping) {
                     if (mapping.columns.indexOf(parseInt(colIndex)) !== -1) {
                         const mappingDef = MAPPING_TARGETS[mapping.type];
                         mappingDisplay.push(`<i>${_.escape(mappingDef.columnHeader || mappingDef.label)}</i>`);
@@ -1245,7 +1245,7 @@ export default {
         },
         mappingAsDict() {
             const asDict = {};
-            for (let mapping of this.mapping) {
+            for (const mapping of this.mapping) {
                 asDict[mapping.type] = mapping;
             }
             return asDict;
@@ -1261,7 +1261,7 @@ export default {
                     collectionType = "list:list:list:paired";
                 }
                 const collectionTypeRanks = collectionType.split(":");
-                for (let index in collectionTypeRanks) {
+                for (const index in collectionTypeRanks) {
                     const collectionTypeRank = collectionTypeRanks[index];
                     if (collectionTypeRank == "list") {
                         // TODO: drop the numeral at the end if only flat list
@@ -1323,7 +1323,7 @@ export default {
             if (requiresSourceColumn && !mappingAsDict.ftp_path && !mappingAsDict.url) {
                 valid = false;
             }
-            for (var rule of this.rules) {
+            for (const rule of this.rules) {
                 if (rule.error) {
                     valid = false;
                 }
@@ -1487,7 +1487,7 @@ export default {
             this.mapping.splice(index, 1);
         },
         refreshAndWait(response) {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel) {
                 Galaxy.currHistoryPanel.refreshContents();
             }
@@ -1506,7 +1506,7 @@ export default {
                         "Unknown error encountered while running your upload job, this could be a server issue or a problem with the upload definition.";
                     this.doFullJobCheck(jobId);
                 } else {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     const history = Galaxy && Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model;
                     history.refresh();
                     this.oncreate();
@@ -1592,13 +1592,13 @@ export default {
                     this.oncreate();
                 }
             } else {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 const historyId = Galaxy.currHistoryPanel.model.id;
                 let elements, targets;
                 if (collectionType) {
                     targets = [];
                     const elementsByCollectionName = this.creationElementsForFetch();
-                    for (let collectionName in elementsByCollectionName) {
+                    for (const collectionName in elementsByCollectionName) {
                         const target = {
                             destination: { type: "hdca" },
                             elements: elementsByCollectionName[collectionName],
@@ -1656,11 +1656,11 @@ export default {
             const collectionType = this.collectionType;
             const elementsByName = {};
 
-            let dataByCollection = {};
+            const dataByCollection = {};
             const collectionNameMap = this.mappingAsDict.collection_name;
             if (collectionNameMap) {
                 const collectionNameTarget = collectionNameMap.columns[0];
-                for (let dataIndex in data) {
+                for (const dataIndex in data) {
                     const row = data[dataIndex];
                     const name = row[collectionNameTarget];
                     if (!dataByCollection[name]) {
@@ -1673,11 +1673,11 @@ export default {
                 dataByCollection[this.collectionName] = data;
             }
 
-            for (let collectionName in dataByCollection) {
+            for (const collectionName in dataByCollection) {
                 const elements = [];
                 const identifiers = [];
 
-                for (let dataIndex in dataByCollection[collectionName]) {
+                for (const dataIndex in dataByCollection[collectionName]) {
                     const rowData = data[dataIndex];
 
                     // For each row, find place in depth for this element.
@@ -1724,7 +1724,7 @@ export default {
                                 .slice(1)
                                 .join(":");
                             let found = false;
-                            for (let element of elementsAtDepth) {
+                            for (const element of elementsAtDepth) {
                                 if (element["name"] == identifier) {
                                     elementsAtDepth = element[subElementProp];
                                     identifiersAtDepth = identifiersAtDepth[identifier];
@@ -1795,7 +1795,7 @@ export default {
 
             const datasets = [];
 
-            for (let dataIndex in data) {
+            for (const dataIndex in data) {
                 const res = this._datasetFor(dataIndex, data, mappingAsDict);
                 datasets.push(res);
             }
@@ -1806,7 +1806,7 @@ export default {
             const parentIdentifiers = parentIdentifiers_ ? parentIdentifiers_ : [];
             let data = [];
             let sources = [];
-            for (let element of elements) {
+            for (const element of elements) {
                 const elementObject = element.object;
                 const identifiers = parentIdentifiers.concat([element.element_identifier]);
                 const collectionTypeLevelSepIndex = collectionType.indexOf(":");
@@ -1818,7 +1818,7 @@ export default {
                     sources.push(source);
                 } else {
                     const restCollectionType = collectionType.slice(collectionTypeLevelSepIndex + 1);
-                    let elementObj = this.populateElementsFromCollectionDescription(
+                    const elementObj = this.populateElementsFromCollectionDescription(
                         elementObject.elements,
                         restCollectionType,
                         identifiers
@@ -1892,14 +1892,14 @@ export default {
             const tags = [];
             if (mappingAsDict.tags) {
                 const tagColumns = mappingAsDict.tags.columns;
-                for (var tagColumn of tagColumns) {
+                for (const tagColumn of tagColumns) {
                     const tag = data[dataIndex][tagColumn];
                     tags.push(tag);
                 }
             }
             if (mappingAsDict.group_tags) {
                 const groupTagColumns = mappingAsDict.group_tags.columns;
-                for (var groupTagColumn of groupTagColumns) {
+                for (const groupTagColumn of groupTagColumns) {
                     const tag = data[dataIndex][groupTagColumn];
                     tags.push("group:" + tag);
                 }
@@ -1919,7 +1919,7 @@ export default {
         if (this.elementsType !== "collection_contents") {
             let columnCount = null;
             if (this.elementsType == "datasets") {
-                for (let element of this.initialElements) {
+                for (const element of this.initialElements) {
                     if (element.history_content_type == "dataset_collection") {
                         this.errorMessage =
                             "This component can only be used with datasets, you have specified one or more collections.";
@@ -1927,7 +1927,7 @@ export default {
                     }
                 }
             } else {
-                for (let row of this.initialElements) {
+                for (const row of this.initialElements) {
                     if (columnCount == null) {
                         columnCount = row.length;
                     } else {
diff --git a/client/galaxy/scripts/components/Select2.js b/client/galaxy/scripts/components/Select2.js
index 639511faeaf..66629b348b8 100644
--- a/client/galaxy/scripts/components/Select2.js
+++ b/client/galaxy/scripts/components/Select2.js
@@ -6,7 +6,7 @@ export default {
     props: ["options", "value", "placeholder"],
     template: `<select><slot></slot></select>`,
     mounted: function() {
-        var vm = this;
+        const vm = this;
         $(this.$el)
             // init select2
             .select2({ data: this.options, placeholder: this.placeholder, allowClear: this.placeholder })
diff --git a/client/galaxy/scripts/components/Sharing.vue b/client/galaxy/scripts/components/Sharing.vue
index 002c90a3f6e..84ffbde9e3c 100644
--- a/client/galaxy/scripts/components/Sharing.vue
+++ b/client/galaxy/scripts/components/Sharing.vue
@@ -25,7 +25,9 @@
                         <span id="item-url-text" style="display: none">
                             {{ item_url_parts[0] }}<span id="item-identifier">{{ item_url_parts[1] }}</span>
                         </span>
-                        <a href="#" id="edit-identifier"><img :src="pencil_url"/></a>
+                        <a href="javascript:void(0)" id="edit-identifier"
+                            ><img :src="pencil_url" alt="Edit Share Url"
+                        /></a>
                     </blockquote>
                     <div v-if="item.published">
                         <p>
@@ -170,13 +172,14 @@ export default {
             return this.item.published ? "accessible via link and published" : "accessible via link";
         },
         item_url() {
-            return `${window.location.protocol}//${window.location.hostname}:${window.location.port}${getAppRoot()}${
+            const port = window.location.port ? `:${window.location.port}` : "";
+            return `${window.location.protocol}//${window.location.hostname}${port}${getAppRoot()}${
                 this.item.username_and_slug
             }`;
         },
         item_url_parts() {
-            let str = this.item_url;
-            let index = str.lastIndexOf("/");
+            const str = this.item_url;
+            const index = str.lastIndexOf("/");
             return [str.substring(0, index + 1), str.substring(index + 1)];
         },
         published_url() {
@@ -196,7 +199,7 @@ export default {
         }
     },
     data() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         return {
             ready: false,
             has_username: Galaxy.user.get("username"),
@@ -232,7 +235,7 @@ export default {
                 .catch(error => (this.err_msg = error.response.data.err_msg));
         },
         setUsername: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             axios
                 .put(`${getAppRoot()}api/users/${Galaxy.user.id}/information/inputs`, {
                     username: this.new_username || ""
@@ -245,7 +248,7 @@ export default {
                 .catch(error => (this.err_msg = error.response.data.err_msg));
         },
         setSharing: function(action, user_id) {
-            let data = {
+            const data = {
                 action: action,
                 user_id: user_id
             };
@@ -263,7 +266,7 @@ export default {
                 .catch(error => (this.err_msg = error.response.data.err_msg));
         },
         createSlugHandler: function() {
-            var on_start = function(text_elt) {
+            const on_start = function(text_elt) {
                 // Replace URL with URL text.
                 $("#item-url").hide();
                 $("#item-url-text").show();
@@ -279,14 +282,14 @@ export default {
                     );
                 });
             };
-            var on_finish = function(text_elt) {
+            const on_finish = function(text_elt) {
                 // Replace URL text with URL.
                 $("#item-url-text").hide();
                 $("#item-url").show();
 
                 // Set URL to new value.
-                var new_url = $("#item-url-text").text();
-                var item_url_obj = $("#item-url");
+                const new_url = $("#item-url-text").text();
+                const item_url_obj = $("#item-url");
                 item_url_obj.attr("href", new_url);
                 item_url_obj.text(new_url);
             };
diff --git a/client/galaxy/scripts/components/Tags/StatelessTags.vue b/client/galaxy/scripts/components/Tags/StatelessTags.vue
index 8cbaac11041..c45ab737cdd 100644
--- a/client/galaxy/scripts/components/Tags/StatelessTags.vue
+++ b/client/galaxy/scripts/components/Tags/StatelessTags.vue
@@ -44,7 +44,7 @@ export default {
     },
     data() {
         // initialize toggle value
-        let isClosed = this.useToggleLink && this.value.length > this.maxVisibleTags;
+        const isClosed = this.useToggleLink && this.value.length > this.maxVisibleTags;
 
         return {
             tagText: "",
@@ -92,13 +92,13 @@ export default {
         },
         beforeAddingTag($event) {
             if (!this.emitHookEvent("before-adding-tag", $event)) {
-                let { tag, addTag } = $event;
+                const { tag, addTag } = $event;
                 addTag(tag);
             }
         },
         beforeDeletingTag($event) {
             if (!this.emitHookEvent("before-deleting-tag", $event)) {
-                let { tag, deleteTag } = $event;
+                const { tag, deleteTag } = $event;
                 deleteTag(tag);
             }
         },
diff --git a/client/galaxy/scripts/components/Tags/backboneTagService.js b/client/galaxy/scripts/components/Tags/backboneTagService.js
index 7b162b5fd1c..60912fa3d62 100644
--- a/client/galaxy/scripts/components/Tags/backboneTagService.js
+++ b/client/galaxy/scripts/components/Tags/backboneTagService.js
@@ -12,7 +12,7 @@ export class BackboneTagService extends TagService {
     }
 
     async save(rawTag) {
-        let tag = createTag(rawTag);
+        const tag = createTag(rawTag);
         if (!tag.valid) {
             throw new Error("Invalid tag");
         }
@@ -27,7 +27,7 @@ export class BackboneTagService extends TagService {
     }
 
     async delete(rawTag) {
-        let tag = createTag(rawTag);
+        const tag = createTag(rawTag);
 
         let tags = new Set(this.model.attributes.tags);
         tags.delete(tag.text);
diff --git a/client/galaxy/scripts/components/Tags/model.js b/client/galaxy/scripts/components/Tags/model.js
index 2449e22ce0e..a9dd7c68eae 100644
--- a/client/galaxy/scripts/components/Tags/model.js
+++ b/client/galaxy/scripts/components/Tags/model.js
@@ -21,9 +21,9 @@ function TagModel(props = {}) {
         enumerable: true,
         get: function() {
             if (this.text.startsWith("name:")) {
-                let { primary, contrasting, darker } = keyedColorScheme(this.text);
+                const { primary, contrasting, darker } = keyedColorScheme(this.text);
 
-                let styles = {
+                const styles = {
                     "background-color": primary,
                     color: contrasting,
                     "border-color": darker
@@ -82,7 +82,7 @@ export function createTag(data) {
 // Returns tags in "newTags" that aren't present in "existingTags"
 
 export const diffTags = (newTags, existingTags) => {
-    let newModels = newTags.map(createTag);
-    let existingModels = existingTags.map(createTag);
+    const newModels = newTags.map(createTag);
+    const existingModels = existingTags.map(createTag);
     return newModels.filter(tag => !existingModels.some(st => st.equals(tag)));
 };
diff --git a/client/galaxy/scripts/components/Tags/mounts.js b/client/galaxy/scripts/components/Tags/mounts.js
index ae502d87e9b..2ac287cdcc4 100644
--- a/client/galaxy/scripts/components/Tags/mounts.js
+++ b/client/galaxy/scripts/components/Tags/mounts.js
@@ -14,17 +14,17 @@ import { BackboneTagService } from "./backboneTagService";
  * by the tagging_common.mako file
  */
 export const mountMakoTags = (options = {}, el) => {
-    let { id, itemClass, tags = [], disabled = false, context = "unspecified" } = options;
+    const { id, itemClass, tags = [], disabled = false, context = "unspecified" } = options;
 
-    let propData = {
+    const propData = {
         storeKey: `${itemClass}-${id}`,
         tagService: new TagService({ id, itemClass, context }),
         tags,
         disabled
     };
 
-    let fn = mountVueComponent(Tags);
-    let vm = fn(propData, el);
+    const fn = mountVueComponent(Tags);
+    const vm = fn(propData, el);
     vm.$on("tag-click", makoClickHandler(options, vm));
     return vm;
 };
@@ -40,15 +40,13 @@ const makoClickHandler = (options, vm) =>
             return;
         }
 
-        let { tagClickFn = "none", clickUrl } = options;
+        const { tagClickFn = "none", clickUrl } = options;
 
         switch (tagClickFn) {
-            // I made this match the existing behavior, but I am not clear on
-            // the reason why this link redirects to a raw json page
             case "community_tag_click":
                 if (undefined !== clickUrl) {
-                    let suffix = tag.value ? `:${tag.value}` : "";
-                    let href = `${clickUrl}?f-tags=${tag.text}${suffix}`;
+                    const suffix = tag.value ? `:${tag.value}` : "";
+                    const href = `${clickUrl}?f-tags=${tag.text}${suffix}`;
                     redirectToUrl(href);
                 }
                 break;
@@ -63,22 +61,22 @@ const makoClickHandler = (options, vm) =>
  * Mount function when a backbone model is provided.
  */
 export const mountModelTags = (options = {}, el) => {
-    let { model, disabled = false, context = "unspecified" } = options;
+    const { model, disabled = false, context = "unspecified" } = options;
 
     if (!model) {
         console.warn("Missing model in mountModelTags");
         return;
     }
 
-    let { id, model_class: itemClass, tags = [] } = model.attributes;
+    const { id, model_class: itemClass, tags = [] } = model.attributes;
 
-    let propData = {
+    const propData = {
         storeKey: `${itemClass}-${id}`,
         tagService: new BackboneTagService({ id, itemClass, context, model }),
         tags,
         disabled
     };
 
-    let fn = mountVueComponent(Tags);
+    const fn = mountVueComponent(Tags);
     return fn(propData, el);
 };
diff --git a/client/galaxy/scripts/components/Tags/tagService.js b/client/galaxy/scripts/components/Tags/tagService.js
index 9a0e6f36228..496c0d4726e 100644
--- a/client/galaxy/scripts/components/Tags/tagService.js
+++ b/client/galaxy/scripts/components/Tags/tagService.js
@@ -52,13 +52,13 @@ export class TagService {
      * @returns Promise yielding new tag model
      */
     async save(rawTag) {
-        let { id, itemClass, context } = this;
-        let tag = createTag(rawTag);
+        const { id, itemClass, context } = this;
+        const tag = createTag(rawTag);
         if (!tag.valid) {
             throw new Error("Invalid tag");
         }
-        let url = `/tag/add_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&new_tag=${tag.text}`;
-        let response = await axios.get(url);
+        const url = `/tag/add_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&new_tag=${tag.text}`;
+        const response = await axios.get(url);
         if (response.status !== 200) {
             throw new Error(`Unable to save tag: ${tag}`);
         }
@@ -71,10 +71,12 @@ export class TagService {
      * @returns Promise yielding deleted tag model
      */
     async delete(rawTag) {
-        let { id, itemClass, context } = this;
-        let tag = createTag(rawTag);
-        let url = `/tag/remove_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&tag_name=${tag.text}`;
-        let response = await axios.get(url);
+        const { id, itemClass, context } = this;
+        const tag = createTag(rawTag);
+        const url = `/tag/remove_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&tag_name=${
+            tag.text
+        }`;
+        const response = await axios.get(url);
         if (response.status !== 200) {
             throw new Error(`Unable to delete tag: ${tag}`);
         }
@@ -87,9 +89,9 @@ export class TagService {
      * @returns Promise yielding an array of tag models
      */
     async autocomplete(searchText) {
-        let { id, itemClass } = this;
-        let url = `/tag/tag_autocomplete_data?item_id=${id}&item_class=${itemClass}&q=${searchText}`;
-        let response = await axios.get(url);
+        const { id, itemClass } = this;
+        const url = `/tag/tag_autocomplete_data?item_id=${id}&item_class=${itemClass}&q=${searchText}`;
+        const response = await axios.get(url);
         if (response.status !== 200) {
             throw new Error(`Unable to retrieve autocomplete tags for search string: ${searchText}`);
         }
diff --git a/client/galaxy/scripts/components/Tags/tagService.test.js b/client/galaxy/scripts/components/Tags/tagService.test.js
index 82169efd590..ee4b3d77c2f 100644
--- a/client/galaxy/scripts/components/Tags/tagService.test.js
+++ b/client/galaxy/scripts/components/Tags/tagService.test.js
@@ -132,7 +132,7 @@ describe("Tags/tagService.js", () => {
             );
 
             // spam a bunch of key inputs
-            for (var i = 0; i < spamCount; i++) svc.autocompleteSearchText = new String(Math.random());
+            for (let i = 0; i < spamCount; i++) svc.autocompleteSearchText = new String(Math.random());
             svc.autocompleteSearchText = searchString;
         });
     });
diff --git a/client/galaxy/scripts/components/Toolshed/Categories.vue b/client/galaxy/scripts/components/Toolshed/Categories.vue
new file mode 100644
index 00000000000..fce86dabae7
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/Categories.vue
@@ -0,0 +1,67 @@
+<template>
+    <div>
+        <div v-if="loading">
+            <span class="fa fa-spinner fa-spin mb-4 mr-1" />
+            <span>Loading categories...</span>
+        </div>
+        <b-table v-else striped :items="categories" :fields="fields">
+            <template slot="name" slot-scope="data">
+                <b-link href="#" class="font-weight-bold" @click="onCategory(data.value)">
+                    {{ data.value }}
+                </b-link>
+            </template>
+        </b-table>
+    </div>
+</template>
+<script>
+import { Services } from "./services.js";
+export default {
+    props: ["toolshedUrl", "loading"],
+    data() {
+        return {
+            categories: [],
+            fields: {
+                name: {
+                    label: "Category",
+                    sortable: true
+                },
+                description: {
+                    sortable: false
+                },
+                repositories: {
+                    sortable: true
+                }
+            }
+        };
+    },
+    created() {
+        this.services = new Services();
+        this.load();
+    },
+    watch: {
+        toolshedUrl() {
+            this.load();
+        }
+    },
+    methods: {
+        load() {
+            this.$emit("onLoading", true);
+            this.services
+                .getCategories(this.toolshedUrl)
+                .then(categories => {
+                    this.categories = categories;
+                    const reducer = (value, entry) => value + entry.repositories;
+                    this.$emit("onTotal", this.categories.reduce(reducer, 0));
+                    this.$emit("onLoading", false);
+                })
+                .catch(errorMessage => {
+                    this.$emit("onError", errorMessage);
+                    this.$emit("onLoading", false);
+                });
+        },
+        onCategory(category) {
+            this.$emit("onCategory", category);
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/Toolshed/Index.vue b/client/galaxy/scripts/components/Toolshed/Index.vue
new file mode 100644
index 00000000000..c5788beb546
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/Index.vue
@@ -0,0 +1,118 @@
+<template>
+    <div class="overflow-auto h-100 p-1" @scroll="onScroll">
+        <div v-if="error" class="alert alert-danger">{{ error }}</div>
+        <div v-else>
+            <b-input
+                class="mb-3"
+                placeholder="search repositories"
+                v-model="queryInput"
+                @input="delayQuery"
+                @change="setQuery"
+            />
+            <serverselection
+                :toolshedUrl="toolshedUrl"
+                :toolshedUrls="toolshedUrls"
+                :total="total"
+                :loading="loading"
+                @onToolshed="setToolshed"
+            />
+            <repositories
+                :query="query"
+                :scrolled="scrolled"
+                :toolshedUrl="toolshedUrl"
+                @onError="setError"
+                v-if="!queryEmpty"
+            />
+            <categories
+                :toolshedUrl="toolshedUrl"
+                :loading="loading"
+                @onCategory="setQuery"
+                @onTotal="setTotal"
+                @onError="setError"
+                @onLoading="setLoading"
+                v-show="queryEmpty"
+            />
+        </div>
+    </div>
+</template>
+<script>
+import { getGalaxyInstance } from "app";
+import Categories from "./Categories.vue";
+import Repositories from "./Repositories.vue";
+import ServerSelection from "./ServerSelection.vue";
+export default {
+    components: {
+        categories: Categories,
+        repositories: Repositories,
+        serverselection: ServerSelection
+    },
+    data() {
+        return {
+            toolshedUrl: null,
+            toolshedUrls: [],
+            queryInput: null,
+            queryDelay: 1000,
+            queryTimer: null,
+            queryLength: 3,
+            query: null,
+            scrolled: false,
+            loading: false,
+            total: 0,
+            error: null
+        };
+    },
+    created() {
+        this.configureToolsheds();
+    },
+    computed: {
+        queryEmpty() {
+            return !this.query || this.query.length < this.queryLength;
+        }
+    },
+    methods: {
+        configureToolsheds() {
+            const galaxy = getGalaxyInstance();
+            this.toolshedUrls = galaxy.config.tool_shed_urls;
+            if (!this.toolshedUrls || this.toolshedUrls.length == 0) {
+                this.setError("Toolshed registry is empty, no servers found.");
+            } else {
+                this.toolshedUrl = this.toolshedUrls[0];
+            }
+        },
+        clearTimer() {
+            if (this.queryTimer) {
+                clearTimeout(this.queryTimer);
+            }
+        },
+        delayQuery(query) {
+            this.clearTimer();
+            if (query) {
+                this.queryTimer = setTimeout(() => {
+                    this.setQuery(query);
+                }, this.queryDelay);
+            } else {
+                this.setQuery(query);
+            }
+        },
+        setError(error) {
+            this.error = error;
+        },
+        setQuery(query) {
+            this.clearTimer();
+            this.query = this.queryInput = query;
+        },
+        setToolshed(url) {
+            this.toolshedUrl = url;
+        },
+        setTotal(total) {
+            this.total = total;
+        },
+        setLoading(loading) {
+            this.loading = loading;
+        },
+        onScroll: function({ target: { scrollTop, clientHeight, scrollHeight } }) {
+            this.scrolled = scrollTop + clientHeight >= scrollHeight;
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/Toolshed/InstallationButton.vue b/client/galaxy/scripts/components/Toolshed/InstallationButton.vue
new file mode 100644
index 00000000000..8176cd0360f
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/InstallationButton.vue
@@ -0,0 +1,45 @@
+<template>
+    <div>
+        <b-button v-if="installState" :class="buttonClass" variant="primary" @click="onInstall">
+            Install
+        </b-button>
+        <div v-else>
+            <b-button v-if="uninstallState" :class="buttonClass" variant="danger" @click="onUninstall">
+                Uninstall
+            </b-button>
+            <b-button v-else :class="buttonClass" @click="onUninstall">
+                <span v-if="!errorState" class="fa fa-spinner fa-spin" />
+                <span>{{ status }}</span>
+            </b-button>
+        </div>
+    </div>
+</template>
+<script>
+export default {
+    props: ["installed", "status"],
+    data() {
+        return {
+            buttonClass: "btn-sm text-nowrap"
+        };
+    },
+    computed: {
+        installState() {
+            return !this.status || this.status == "Uninstalled";
+        },
+        uninstallState() {
+            return this.status == "Installed";
+        },
+        errorState() {
+            return this.status == "Error";
+        }
+    },
+    methods: {
+        onInstall() {
+            this.$emit("onInstall");
+        },
+        onUninstall() {
+            this.$emit("onUninstall");
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/Toolshed/InstallationSettings.vue b/client/galaxy/scripts/components/Toolshed/InstallationSettings.vue
new file mode 100644
index 00000000000..41673819f71
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/InstallationSettings.vue
@@ -0,0 +1,138 @@
+<template>
+    <b-modal v-model="modalShow" @ok="onOk" @hide="onHide">
+        <template slot="modal-header">
+            <h4 class="m-0">
+                {{ modalTitle }}
+            </h4>
+        </template>
+        <div class="mb-1">
+            {{ repo.long_description || repo.description }}
+        </div>
+        <div class="text-muted small mb-3">{{ repo.repo_owner_username }} rev. {{ changesetRevision }}</div>
+        <b-form-group
+            v-if="requiresPanel"
+            label="Target Section:"
+            description="Choose an existing tool panel section or create a new section to contain the installed tools (optional)."
+        >
+            <b-form-input list="sectionSelect" v-model="toolSection" />
+            <datalist id="sectionSelect">
+                <option v-for="section in toolSections" :key="section.name">
+                    {{ section.name }}
+                </option>
+            </datalist>
+        </b-form-group>
+        <b-link variant="primary" @click="onAdvanced"> {{ advancedTitle }} advanced settings. </b-link>
+        <b-collapse id="advanced-collapse" v-model="advancedShow" class="mt-2">
+            <b-card>
+                <b-form-group v-if="showConfig" label="Tool Configuration:" description="Choose a tool configuration.">
+                    <b-form-radio
+                        v-for="filename in toolConfigs"
+                        v-model="toolConfig"
+                        :value="filename"
+                        :key="filename"
+                    >
+                        {{ filename }}
+                    </b-form-radio>
+                </b-form-group>
+                <b-form-group label="Dependencies:" description="Choose how to handle dependencies.">
+                    <b-form-checkbox v-model="installResolverDependencies">
+                        Install resolvable dependencies
+                    </b-form-checkbox>
+                    <b-form-checkbox v-model="installRepositoryDependencies">
+                        Install repository dependencies
+                    </b-form-checkbox>
+                    <b-form-checkbox v-model="installToolDependencies">
+                        Install tool dependencies
+                    </b-form-checkbox>
+                </b-form-group>
+            </b-card>
+        </b-collapse>
+    </b-modal>
+</template>
+<script>
+import { getGalaxyInstance } from "app";
+import { Services } from "./services.js";
+export default {
+    props: ["repo", "changesetRevision", "requiresPanel", "toolshedUrl"],
+    data() {
+        return {
+            modalShow: true,
+            advancedShow: false,
+            installToolDependencies: true,
+            installRepositoryDependencies: true,
+            installResolverDependencies: true,
+            toolConfigs: [],
+            toolConfig: null,
+            toolSections: [],
+            toolSection: null
+        };
+    },
+    computed: {
+        advancedTitle() {
+            return this.advancedShow ? "Hide" : "Show";
+        },
+        modalTitle() {
+            return `Installing '${this.repo.name}'`;
+        },
+        showConfig() {
+            return this.toolConfigs.length > 1;
+        }
+    },
+    created() {
+        this.services = new Services();
+        this.loadConfig();
+    },
+    methods: {
+        findSection: function(name) {
+            const result = ['', ''];
+            if (name) {
+                const found = this.toolSections.find(s => {
+                    return s.name.toLowerCase().trim() == name.toLowerCase().trim();
+                });
+                if (found) {
+                    result[0] = found.id;
+                } else {
+                    result[1] = name;
+                }
+            }
+            return result;
+        },
+        loadConfig: function() {
+            const galaxy = getGalaxyInstance();
+            const sections = galaxy.config.toolbox_in_panel;
+            this.toolSections = sections.filter(x => x.model_class == "ToolSection");
+            this.toolConfigs = galaxy.config.tool_dynamic_configs || [];
+            if (this.toolConfigs.length > 0) {
+                this.toolConfig = this.toolConfigs[0];
+            }
+        },
+        onAdvanced: function() {
+            this.advancedShow = !this.advancedShow;
+        },
+        onOk: function() {
+            const [sectionId, sectionLabel] = this.findSection(this.toolSection);
+            this.services
+                .installRepository({
+                    tool_shed_url: this.toolshedUrl,
+                    name: this.repo.name,
+                    owner: this.repo.repo_owner_username,
+                    changeset_revision: this.changesetRevision,
+                    new_tool_panel_section_label: sectionLabel,
+                    tool_panel_section_id: sectionId,
+                    shed_tool_conf: this.toolConfig,
+                    install_resolver_dependencies: this.installResolverDependencies,
+                    install_tool_dependencies: this.installToolDependencies,
+                    install_repository_dependencies: this.installRepositoryDependencies
+                })
+                .then(response => {
+                    window.console.log(response);
+                    this.$emit("ok");
+                })
+                .catch(error => {});
+        },
+        onHide: function() {
+            this.$emit("hide");
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/Toolshed/Repositories.vue b/client/galaxy/scripts/components/Toolshed/Repositories.vue
new file mode 100644
index 00000000000..f70d611ea4d
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/Repositories.vue
@@ -0,0 +1,102 @@
+<template>
+    <div>
+        <b-table striped :items="repositories" :fields="fields">
+            <template slot="name" slot-scope="row">
+                <b-link href="#" class="font-weight-bold" @click="row.toggleDetails">
+                    {{ row.item.name }}
+                </b-link>
+            </template>
+            <template slot="row-details" slot-scope="row">
+                <repositorydetails :repo="row.item" :toolshedUrl="toolshedUrl" />
+            </template>
+        </b-table>
+        <div v-if="noResultsFound">
+            No matching repositories found.
+        </div>
+        <div v-if="pageLoading">
+            <span class="fa fa-spinner fa-spin mb-4" />
+            <span>Loading repositories...</span>
+        </div>
+    </div>
+</template>
+<script>
+import RepositoryDetails from "./RepositoryDetails.vue";
+import { Services } from "./services.js";
+const READY = 0;
+const LOADING = 1;
+const COMPLETE = 2;
+export default {
+    components: {
+        repositorydetails: RepositoryDetails
+    },
+    props: ["query", "scrolled", "toolshedUrl"],
+    data() {
+        return {
+            repositories: [],
+            fields: [
+                { key: "name" },
+                { key: "description" },
+                { key: "last_updated", label: "Updated" },
+                { key: "repo_owner_username", label: "Owner" },
+                { key: "times_downloaded", label: "Downloaded" }
+            ],
+            page: 1,
+            pageSize: 10,
+            pageState: READY,
+            error: null
+        };
+    },
+    watch: {
+        toolshedUrl() {
+            this.load();
+        },
+        query() {
+            this.load();
+        },
+        scrolled() {
+            if (this.scrolled && this.pageState === READY) {
+                this.load(this.page + 1);
+            }
+        }
+    },
+    computed: {
+        pageLoading() {
+            return this.pageState === LOADING;
+        },
+        noResultsFound() {
+            return this.repositories.length === 0 && !this.pageLoading;
+        }
+    },
+    created() {
+        this.services = new Services();
+        this.load();
+    },
+    methods: {
+        load(page = 1) {
+            this.page = page;
+            this.pageState = LOADING;
+            if (page == 1) {
+                this.repositories = [];
+            }
+            this.services
+                .getRepositories({
+                    tool_shed_url: this.toolshedUrl,
+                    q: this.query,
+                    page: this.page,
+                    page_size: this.pageSize
+                })
+                .then(incoming => {
+                    this.repositories = this.repositories.concat(incoming);
+                    if (incoming.length < this.pageSize) {
+                        this.pageState = COMPLETE;
+                    } else {
+                        this.pageState = READY;
+                    }
+                })
+                .catch(errorMessage => {
+                    this.$emit("onError", errorMessage);
+                });
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryDetails.vue b/client/galaxy/scripts/components/Toolshed/RepositoryDetails.vue
new file mode 100644
index 00000000000..a79d9216d5e
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryDetails.vue
@@ -0,0 +1,177 @@
+<template>
+    <b-card>
+        <div class="mb-1">{{ repo.long_description }}</div>
+        <div class="mb-3">
+            <b-link :href="repo.repository_url" target="_blank">Show additional details and dependencies.</b-link>
+        </div>
+        <div>
+            <span v-if="loading">
+                <span class="fa fa-spinner fa-spin" />
+                Loading repository details...
+            </span>
+            <div v-else>
+                <b-alert v-if="error" variant="danger" show>
+                    {{ error }}
+                </b-alert>
+                <div v-else class="border rounded">
+                    <b-table borderless :items="repoTable" :fields="repoFields" class="text-center m-0">
+                        <template slot="numeric_revision" slot-scope="data">
+                            <span class="font-weight-bold">{{ data.value }}</span>
+                        </template>
+                        <template slot="tools" slot-scope="data">
+                            <repositorytools :tools="data.value" />
+                        </template>
+                        <template slot="profile" slot-scope="data">
+                            {{ data.value ? `+${data.value}` : "-" }}
+                        </template>
+                        <template slot="missing_test_components" slot-scope="data">
+                            <span v-if="!data.value" :class="repoChecked" />
+                            <span v-else :class="repoUnchecked" />
+                        </template>
+                        <template slot="actions" slot-scope="row">
+                            <installationbutton
+                                :installed="row.item.installed"
+                                :status="row.item.status"
+                                @onInstall="setupRepository(row.item)"
+                                @onUninstall="uninstallRepository(row.item)"
+                            />
+                        </template>
+                    </b-table>
+                    <installationsettings
+                        v-if="showSettings"
+                        :repo="repo"
+                        :toolshedUrl="toolshedUrl"
+                        :changesetRevision="selectedChangeset"
+                        :requiresPanel="selectedRequiresPanel"
+                        @hide="onHide"
+                        @ok="onOk"
+                    />
+                </div>
+            </div>
+        </div>
+    </b-card>
+</template>
+<script>
+import { Services } from "./services.js";
+import InstallationSettings from "./InstallationSettings.vue";
+import InstallationButton from "./InstallationButton.vue";
+import RepositoryTools from "./RepositoryTools.vue";
+export default {
+    components: {
+        installationsettings: InstallationSettings,
+        installationbutton: InstallationButton,
+        repositorytools: RepositoryTools
+    },
+    props: ["repo", "toolshedUrl"],
+    data() {
+        return {
+            repoChecked: "fa fa-check text-success",
+            repoUnchecked: "fa fa-times text-danger",
+            selectedChangeset: null,
+            selectedRequiresPanel: false,
+            repoTable: [],
+            repoFields: {
+                numeric_revision: {
+                    label: "Revision"
+                },
+                tools: {
+                    label: "Tools and Versions"
+                },
+                profile: {
+                    label: "Requires"
+                },
+                missing_test_components: {
+                    label: "Tests"
+                },
+                actions: {
+                    label: ""
+                }
+            },
+            showSettings: false,
+            error: null,
+            loading: true,
+            delay: 2000
+        };
+    },
+    created() {
+        this.services = new Services();
+        this.loadDetails();
+    },
+    destroyed() {
+        this.clearTimeout();
+    },
+    methods: {
+        clearTimeout() {
+            if (this.timeout) {
+                clearTimeout(this.timeout);
+            }
+        },
+        loadDetails() {
+            this.services
+                .getDetails(this.toolshedUrl, this.repo.id)
+                .then(response => {
+                    this.repoTable = response;
+                    this.loadInstalledRepositories();
+                })
+                .catch(error => {
+                    this.error = error;
+                    this.loading = false;
+                });
+        },
+        listenInstalledRepositories() {
+            this.clearTimeout();
+            this.timeout = setTimeout(() => {
+                this.loadInstalledRepositories();
+            }, this.delay);
+        },
+        loadInstalledRepositories() {
+            this.services
+                .getInstalledRepositories(this.repo)
+                .then(revisions => {
+                    let changed = false;
+                    this.repoTable.forEach(x => {
+                        const revision = revisions[x.changeset_revision];
+                        if (revision && revision.status !== x.status) {
+                            x.status = revision.status;
+                            x.installed = revision.installed;
+                            changed = true;
+                            return false;
+                        }
+                    });
+                    if (changed) {
+                        this.repoTable = [...this.repoTable];
+                    }
+                    this.listenInstalledRepositories();
+                    this.loading = false;
+                })
+                .catch(error => {
+                    this.error = error;
+                    this.loading = false;
+                });
+        },
+        onOk: function() {
+            this.showSettings = false;
+        },
+        onHide: function() {
+            this.showSettings = false;
+        },
+        setupRepository: function(details) {
+            this.selectedChangeset = details.changeset_revision;
+            this.selectedRequiresPanel = details.includes_tools_for_display_in_tool_panel || details.repository.type == "repository_suite_definition";
+            this.showSettings = true;
+        },
+        uninstallRepository: function(details) {
+            this.services
+                .uninstallRepository({
+                    tool_shed_url: this.toolshedUrl,
+                    name: this.repo.name,
+                    owner: this.repo.repo_owner_username,
+                    changeset_revision: details.changeset_revision
+                })
+                .catch(error => {
+                    this.error = error;
+                });
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/Toolshed/RepositoryTools.vue b/client/galaxy/scripts/components/Toolshed/RepositoryTools.vue
new file mode 100644
index 00000000000..3db30cb03ca
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/RepositoryTools.vue
@@ -0,0 +1,67 @@
+<template>
+    <table v-if="tools" class="table table-borderless">
+        <tbody>
+            <tr v-if="canExpand && expanded" class="bg-transparent">
+                <td :class="clsFirstColumn">
+                    <a href="#" @click.stop.prevent="onExpand">
+                        <span class="fa fa-angle-double-up" />
+                        <span>Show less</span>
+                    </a>
+                </td>
+                <td :class="clsSecondColumn" />
+            </tr>
+            <tr v-for="tool in visibleTools" :key="tool.guid" :class="clsRow">
+                <td :class="clsFirstColumn">
+                    {{ tool.id }}
+                </td>
+                <td :class="clsSecondColumn">
+                    {{ tool.version }}
+                </td>
+            </tr>
+            <tr v-if="canExpand && !expanded" class="bg-transparent">
+                <td :class="clsFirstColumn">
+                    <a href="#" @click.stop.prevent="onExpand">
+                        <span class="fa fa-angle-double-down" />
+                        <span>Show more</span>
+                    </a>
+                </td>
+                <td :class="clsSecondColumn" />
+            </tr>
+        </tbody>
+    </table>
+    <span v-else>-</span>
+</template>
+<script>
+export default {
+    props: ["tools"],
+    data() {
+        return {
+            clsExpanded: "bg-transparent border-bottom",
+            clsCollapsed: "bg-transparent",
+            clsFirstColumn: "p-0 w-50 text-left",
+            clsSecondColumn: "p-0 w-50 text-center",
+            expanded: false,
+            preview: 2
+        };
+    },
+    computed: {
+        clsRow() {
+            return this.expanded ? this.clsExpanded : this.clsCollapsed;
+        },
+        canExpand() {
+            return this.tools && this.tools.length > this.preview;
+        },
+        visibleTools() {
+            if (this.canExpand && !this.expanded) {
+                return this.tools.slice(0, this.preview);
+            }
+            return this.tools;
+        }
+    },
+    methods: {
+        onExpand() {
+            this.expanded = !this.expanded;
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/Toolshed/ServerSelection.vue b/client/galaxy/scripts/components/Toolshed/ServerSelection.vue
new file mode 100644
index 00000000000..abd24b8d522
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/ServerSelection.vue
@@ -0,0 +1,40 @@
+<template>
+    <div v-if="!loading" class="m-1 text-muted">
+        {{ total }} repositories available at
+        <span v-if="showDropdown" class="dropdown">
+            <b-link id="dropdownToolshedUrl" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+                {{ toolshedUrl }}
+            </b-link>
+            <div class="dropdown-menu" aria-labelledby="dropdownToolshedUrl">
+                <a
+                    v-for="url in toolshedUrls"
+                    :key="url"
+                    class="dropdown-item"
+                    href="#"
+                    @click.prevent="onToolshed(url)"
+                    >{{ url }}</a
+                >
+            </div>
+        </span>
+        <span v-else>
+            <b-link :href="toolshedUrl" target="_blank">
+                {{ toolshedUrl }}
+            </b-link>
+        </span>
+    </div>
+</template>
+<script>
+export default {
+    props: ["toolshedUrl", "toolshedUrls", "loading", "total"],
+    computed: {
+        showDropdown() {
+            return this.toolshedUrls.length > 1;
+        }
+    },
+    methods: {
+        onToolshed(url) {
+            this.$emit("onToolshed", url);
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/Toolshed/services.js b/client/galaxy/scripts/components/Toolshed/services.js
new file mode 100644
index 00000000000..a1a7551e459
--- /dev/null
+++ b/client/galaxy/scripts/components/Toolshed/services.js
@@ -0,0 +1,110 @@
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+
+/** Request repositories, categories etc from toolshed server **/
+export class Services {
+    async getCategories(toolshedUrl) {
+        const paramString = `tool_shed_url=${toolshedUrl}&controller=categories`;
+        const url = `${getAppRoot()}api/tool_shed/request?${paramString}`;
+        try {
+            const response = await axios.get(url);
+            return response.data;
+        } catch (e) {
+            return this._errorMessage(e);
+        }
+    }
+    async getRepositories(params) {
+        params["controller"] = "repositories";
+        const paramString = this._getParamString(params);
+        const url = `${getAppRoot()}api/tool_shed/request?${paramString}`;
+        try {
+            const response = await axios.get(url);
+            const data = response.data;
+            const incoming = data.hits.map(x => x.repository);
+            incoming.forEach(x => {
+                x.times_downloaded = this._formatCount(x.times_downloaded);
+                x.repository_url = `${data.hostname}repository?repository_id=${x.id}`;
+            });
+            return incoming;
+        } catch (e) {
+            return this._errorMessage(e);
+        }
+    }
+    async getDetails(toolshedUrl, repository_id) {
+        const paramString = `tool_shed_url=${toolshedUrl}&id=${repository_id}&controller=repositories&action=metadata`;
+        const url = `${getAppRoot()}api/tool_shed/request?${paramString}`;
+        try {
+            const response = await axios.get(url);
+            const data = response.data;
+            const table = Object.keys(data).map(key => data[key]);
+            table.sort((a, b) => b.numeric_revision - a.numeric_revision);
+            table.forEach(x => {
+                if (Array.isArray(x.tools)) {
+                    x.profile = x.tools.reduce(
+                        (value, current) => (current.profile > value ? current.profile : value),
+                        null
+                    );
+                }
+            });
+            return table;
+        } catch (e) {
+            return `${this._errorMessage(e)}, ${url}`;
+        }
+    }
+    async getInstalledRepositories(repo) {
+        const paramsString = `name=${repo.name}&owner=${repo.repo_owner_username}`;
+        const url = `${getAppRoot()}api/tool_shed_repositories?${paramsString}`;
+        try {
+            const response = await axios.get(url);
+            const data = response.data;
+            const result = {};
+            data.forEach(x => {
+                const d = {
+                    status: x.status,
+                    installed: !x.deleted && !x.uninstalled
+                };
+                result[x.changeset_revision] = result[x.installed_changeset_revision] = d;
+            });
+            return result;
+        } catch (e) {
+            this._errorMessage(e);
+        }
+    }
+    async installRepository(payload) {
+        const url = `${getAppRoot()}api/tool_shed_repositories`;
+        try {
+            const response = await axios.post(url, payload);
+            return response.data;
+        } catch (e) {
+            return this._errorMessage(e);
+        }
+    }
+    async uninstallRepository(params) {
+        const paramsString = Object.keys(params).reduce(function(previous, key) {
+            return `${previous}${key}=${params[key]}&`;
+        }, "");
+        const url = `${getAppRoot()}api/tool_shed_repositories?${paramsString}`;
+        try {
+            const response = await axios.delete(url);
+            return response.data;
+        } catch (e) {
+            return this._errorMessage(e);
+        }
+    }
+    _formatCount(value) {
+        if (value > 1000) return `>${Math.floor(value / 1000)}k`;
+        return value;
+    }
+    _errorMessage(e) {
+        let message = "Request failed.";
+        if (e.response) {
+            message = e.response.data.err_msg || `${e.response.statusText} (${e.response.status})`;
+        }
+        return message;
+    }
+    _getParamString(params) {
+        return Object.keys(params).reduce(function(previous, key) {
+            return `${previous}${key}=${params[key]}&`;
+        }, "");
+    }
+}
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.test.js b/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.test.js
new file mode 100644
index 00000000000..7d930f4e2e8
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.test.js
@@ -0,0 +1,87 @@
+import sinon from "sinon";
+import flushPromises from "flush-promises";
+import { shallowMount, createLocalVue } from "@vue/test-utils";
+
+import { default as CloudAuth, __RewireAPI__ as rewire } from "./CloudAuth";
+import CloudAuthItem from "./CloudAuthItem";
+import { Credential } from "./model";
+
+import _l from "utils/localization";
+import BootstrapVue from "bootstrap-vue";
+
+// test data
+import listCredentials from "./testdata/listCredentials.json";
+
+const localVue = createLocalVue();
+localVue.use(BootstrapVue);
+localVue.filter("localize", value => _l(value));
+
+describe("CloudAuth component", () => {
+    let stub, wrapper;
+
+    let mockSvc = {
+        listCredentials: async () => null
+    };
+
+    rewire.__Rewire__("svc", mockSvc);
+
+    beforeEach(async () => {
+        let creds = listCredentials.map(Credential.create);
+        stub = sinon.stub(mockSvc, "listCredentials").resolves(creds);
+        wrapper = shallowMount(CloudAuth, { localVue });
+        await flushPromises();
+    });
+
+    afterEach(() => {
+        if (stub) {
+            stub.restore();
+        }
+    });
+
+    describe("initialization", () => {
+        it("should render the initial list", () => {
+            assert(wrapper);
+            assert(wrapper.contains(CloudAuthItem));
+            assert(wrapper.vm.items.length == 2);
+            assert(wrapper.vm.filteredItems.length == 2);
+        });
+    });
+
+    describe("text filter", () => {
+        it("should show filter result by text match", () => {
+            let results;
+
+            wrapper.vm.filter = "aws";
+            results = wrapper.vm.filteredItems;
+            assert(wrapper.contains(CloudAuthItem));
+            assert(results.length == 1, `Wrong number of items: ${results.length}`);
+
+            wrapper.vm.filter = "azure";
+            results = wrapper.vm.filteredItems;
+            assert(results.length == 1, `Wrong number of items: ${results.length}`);
+
+            wrapper.vm.filter = "";
+            results = wrapper.vm.filteredItems;
+            assert(results.length == 2, `Wrong number of items: ${results.length}`);
+        });
+    });
+
+    describe("create button", () => {
+        it("clicking create button should add a blank key", () => {
+            let results = wrapper.vm.filteredItems;
+            assert(wrapper.contains(CloudAuthItem));
+            assert(results.length == 2, `Wrong number of items: ${results.length}`);
+
+            let button = wrapper.find("button[name=createNewKey]");
+            assert(button);
+            button.trigger("click");
+
+            results = wrapper.vm.filteredItems;
+            assert(results.length == 3, `Wrong number of items: ${results.length}`);
+
+            let blank = results.find(i => i.id == null);
+            assert(blank, "missing blank key");
+            assert(blank.id == null);
+        });
+    });
+});
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.vue b/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.vue
new file mode 100644
index 00000000000..74bc81e5592
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/CloudAuth.vue
@@ -0,0 +1,378 @@
+<template>
+    <section class="cloud-auth">
+        <header>
+            <b-alert dismissible fade variant="warning" :show="errorMessage !== null" @dismissed="errorMessage = null">
+                {{ errorMessage }}
+            </b-alert>
+
+            <hgroup class="cloud-auth-title">
+                <h1>Manage Cloud Authorization</h1>
+                <nav class="operations">
+                    <ul>
+                        <li class="cloudKeyHelp">
+                            <a
+                                :class="{ active: showHelp }"
+                                @click.prevent="showHelp = !showHelp"
+                                v-b-tooltip.hover
+                                aria-label="Instructions"
+                                title="Instructions"
+                            >
+                                <span>Instructions</span>
+                            </a>
+                        </li>
+                        <li class="cloudKeyFilter">
+                            <a
+                                :class="{ active: showFilter }"
+                                @click.prevent="showFilter = !showFilter"
+                                v-b-tooltip.hover
+                                aria-label="Filter Results"
+                                title="Filter Results"
+                            >
+                                <span>Filter</span>
+                            </a>
+                        </li>
+                        <li class="createCloudKey">
+                            <a
+                                @click.prevent="onCreate"
+                                v-b-tooltip.hover
+                                aria-label="Create New Key"
+                                title="Create New Key"
+                            >
+                                <span>Create New Key</span>
+                            </a>
+                        </li>
+                    </ul>
+                </nav>
+            </hgroup>
+
+            <transition name="fade">
+                <hgroup v-if="showHelp">
+                    <p>See the online <a href="https://galaxyproject.org/cloud/authnz/">Documentation</a>.</p>
+                </hgroup>
+            </transition>
+
+            <transition name="fade">
+                <hgroup v-if="showFilter">
+                    <b-form-group :description="filterDescription">
+                        <b-form-input type="text" placeholder="Filter" v-model="filter" />
+                    </b-form-group>
+                </hgroup>
+            </transition>
+
+            <b-button-group class="mb-4">
+                <button name="createNewKey" @click="onCreate">
+                    Create New Authorization Key
+                </button>
+            </b-button-group>
+        </header>
+
+        <div class="scroll-container">
+            <b-list-group>
+                <transition-group name="fade">
+                    <cloud-auth-item
+                        v-for="credential in filteredItems"
+                        :key="credential.counter"
+                        :credential="credential"
+                        class="mb-1"
+                        @delete="onDelete"
+                        @save="onSave"
+                        @expand="expand(credential, $event)"
+                    />
+                </transition-group>
+            </b-list-group>
+        </div>
+
+        <b-modal
+            v-model="hasDoomed"
+            centered
+            id="deleteCredentialModal"
+            ref="deleteModal"
+            title="Delete Key?"
+            size="sm"
+            @ok="deleteKey"
+            @cancel="doomedItem = null"
+        >
+        </b-modal>
+    </section>
+</template>
+
+<script>
+import Vue from "vue";
+import BootstrapVue from "bootstrap-vue";
+import CloudAuthItem from "./CloudAuthItem";
+import { Credential } from "./model";
+import svc from "./model/service";
+
+Vue.use(BootstrapVue);
+
+export default {
+    components: {
+        CloudAuthItem
+    },
+    data() {
+        return {
+            items: [],
+            filter: "",
+            showHelp: true,
+            showFilter: false,
+            loading: false,
+            doomedItem: null,
+            errorMessage: null
+        };
+    },
+    computed: {
+        filteredItems() {
+            return this.items.filter(o => o.match(this.filter));
+        },
+        filterDescription() {
+            return `${this.filteredItems.length} matches out of ${this.items.length} items`;
+        },
+        deleteButtonVariant() {
+            return this.showDeleted ? "primary" : "secondary";
+        },
+        hasDoomed: {
+            get() {
+                return this.doomedItem !== null;
+            },
+            // This setter is here because vue-bootstrap modal
+            // tries to set this property for unfathomable reasons
+            set() {}
+        }
+    },
+    watch: {
+        showDeleted(deleted) {
+            this.loadCredentials({ deleted });
+        }
+    },
+    methods: {
+        loadCredentials(params = {}) {
+            this.loading = true;
+            svc.listCredentials(params)
+                .then(items => (this.items = items))
+                .catch(this.setError("Unable to load cloud keys."))
+                .finally(() => (this.loading = false));
+        },
+        onCreate() {
+            const newItem = Credential.create({ expanded: true });
+            this.addItem(newItem);
+        },
+        onSave(item) {
+            if (!item.valid) {
+                return;
+            }
+            item.loading = true;
+            svc.saveCredential(item)
+                .then(result => {
+                    item.id = result.id;
+                    item.updateState();
+                })
+                .catch(this.setError("Unable to save key."))
+                .finally(() => (item.loading = false));
+        },
+        onDelete(doomed) {
+            this.doomedItem = doomed;
+            if (doomed.id) {
+                this.$refs.deleteModal.show();
+            } else {
+                this.removeItem(doomed);
+                this.doomedItem = null;
+            }
+        },
+        deleteKey() {
+            // Called when the modal is closed with an "OK"
+            svc.deleteCredential(this.doomedItem)
+                .then(() => this.removeItem(this.doomedItem))
+                .catch(this.setError("Unable to delete cloud key."))
+                .finally(() => {
+                    this.doomedItem = null;
+                });
+        },
+        expand(credential, { expanded }) {
+            credential.expanded = expanded;
+            if (expanded) {
+                this.items.filter(i => i !== credential).forEach(i => (i.expanded = false));
+            }
+        },
+        addItem(item) {
+            this.items = [...this.items, item];
+        },
+        removeItem(item) {
+            this.items = this.items.filter(o => o !== item);
+        },
+        setError(msg) {
+            return err => {
+                this.errorMessage = msg;
+                console.warn(err);
+            };
+        }
+    },
+    created() {
+        this.loadCredentials();
+    }
+};
+</script>
+
+<style lang="scss">
+@import "~bootstrap/scss/functions";
+@import "~bootstrap/scss/variables";
+@import "~bootstrap/scss/mixins";
+@import "~bootstrap/scss/utilities/spacing";
+
+@import "scss/theme/blue.scss";
+@import "scss/mixins";
+
+// TODO: build reusable icon menu? Maybe make into a component?
+// The existing one has lots of reusability problems
+
+.operations {
+    margin-bottom: 0;
+
+    ul {
+        @include list_reset();
+        display: flex;
+        li:not(:first-child) {
+            @extend .ml-2;
+        }
+    }
+}
+
+// General Layout
+
+.cloud-auth {
+    // header sticks, bottom part scrolls
+    @include scrollingListLayout("header", ".scroll-container");
+
+    // title left, icons right
+    .cloud-auth-title {
+        display: flex;
+        flex-direction: row;
+        justify-content: space-between;
+        align-items: center;
+
+        // top icon menu
+        .operations {
+            li {
+                a,
+                a::before {
+                    font-size: 1rem;
+                    color: $gray-400;
+                }
+                a.active::before,
+                a:hover::before {
+                    color: $brand-primary;
+                }
+            }
+
+            .cloudKeyHelp a {
+                @include fontawesome($fa-var-info-circle);
+            }
+            .cloudKeyFilter a {
+                @include fontawesome($fa-var-filter);
+            }
+            .createCloudKey a {
+                @include fontawesome($fa-var-plus);
+            }
+        }
+    }
+}
+
+// Single list item
+
+.cloud-auth-key {
+    header hgroup {
+        display: flex;
+        flex-direction: row;
+        justify-content: space-between;
+        align-items: center;
+        cursor: pointer;
+        user-select: none;
+
+        > * {
+            margin-bottom: 0;
+        }
+    }
+
+    form {
+        @extend .my-3;
+        @extend .pt-3;
+
+        // removes wierd double arrows on select
+        .custom-select {
+            background: none;
+        }
+
+        // Undo butchering from base.css so side-by-side labels work
+        .form-row {
+            display: flex;
+            input,
+            select {
+                max-width: none;
+            }
+            label {
+                font-weight: 400;
+            }
+        }
+
+        // button list at bottom of form
+        footer {
+            display: flex;
+            flex-direction: row;
+            justify-content: flex-end;
+            @extend .pt-3;
+
+            button:not(:first-child) {
+                @extend .ml-1;
+            }
+        }
+    }
+
+    // icon menu
+
+    .operations {
+        .save a {
+            @include fontawesome($fa-var-save);
+        }
+        .delete a {
+            @include fontawesome($fa-var-times);
+        }
+        .details a {
+            @include fontawesome($fa-var-window-minimize);
+            &:hover {
+                @include fontawesome($fa-var-window-maximize);
+            }
+        }
+    }
+
+    // reverse icons when key is expanded
+
+    &.expanded .details a {
+        @include fontawesome($fa-var-window-maximize);
+        &:hover {
+            @include fontawesome($fa-var-window-minimize);
+        }
+    }
+}
+
+// Transitions
+
+.fade-enter-active,
+.fade-leave-active {
+    transition: opacity 0.5s;
+}
+
+.fade-enter,
+.fade-leave-to {
+    opacity: 0;
+}
+
+// Delete modal
+
+#deleteCredentialModal {
+    .modal-body {
+        display: none;
+    }
+    .modal-dialog {
+        max-width: 300px;
+    }
+}
+</style>
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CloudAuthItem.vue b/client/galaxy/scripts/components/User/CloudAuth/CloudAuthItem.vue
new file mode 100644
index 00000000000..39d8c43f7d5
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/CloudAuthItem.vue
@@ -0,0 +1,95 @@
+<template>
+    <b-list-group-item class="cloud-auth-key" :class="statusClasses" :variant="variant" :button="!expanded">
+        <header>
+            <hgroup>
+                <h4 @click.prevent="expand()">{{ credential.title }}</h4>
+                <nav class="operations">
+                    <ul>
+                        <transition name="fade">
+                            <li class="save" v-if="expanded && credential.dirty">
+                                <a
+                                    @click.prevent="$emit('save', credential)"
+                                    v-b-tooltip.hover
+                                    aria-label="Save Key"
+                                    title="Save Key"
+                                >
+                                    <span>Save Key</span>
+                                </a>
+                            </li>
+                        </transition>
+                        <li class="delete">
+                            <a
+                                @click.prevent="$emit('delete', credential)"
+                                v-b-tooltip.hover
+                                aria-label="Delete Key"
+                                title="Delete Key"
+                            >
+                                <span>Delete Key</span>
+                            </a>
+                        </li>
+                        <li class="details">
+                            <a
+                                @click.prevent="expand()"
+                                v-b-tooltip.hover
+                                aria-label="Show Details"
+                                title="Show Details"
+                            >
+                                <span>Details</span>
+                            </a>
+                        </li>
+                    </ul>
+                </nav>
+            </hgroup>
+        </header>
+
+        <credential-form
+            v-if="expanded"
+            class="border-top"
+            v-model="credential"
+            @click.self="expand()"
+            @save="$emit('save', credential)"
+            @delete="$emit('delete', credential)"
+        />
+    </b-list-group-item>
+</template>
+
+<script>
+import { Credential } from "./model";
+import CredentialForm from "./CredentialForm";
+
+export default {
+    components: {
+        CredentialForm
+    },
+    props: {
+        credential: { type: Credential, required: true }
+    },
+    computed: {
+        statusClasses() {
+            const { expanded, valid, dirty, loading } = this.credential;
+            return { loading, expanded, valid, dirty, collapsed: !expanded };
+        },
+        variant() {
+            if (this.expanded) {
+                return "";
+            }
+            if (this.credential.dirty) {
+                return "warning";
+            }
+            if (!this.credential.valid) {
+                return "danger";
+            }
+            return "primary";
+        },
+        expanded() {
+            return this.credential.expanded;
+        }
+    },
+    methods: {
+        expand(forceState) {
+            const expanded = forceState !== undefined ? forceState : !this.expanded;
+            this.$emit("expand", { expanded });
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CredentialConfig.vue b/client/galaxy/scripts/components/User/CloudAuth/CredentialConfig.vue
new file mode 100644
index 00000000000..8314cb93bb8
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/CredentialConfig.vue
@@ -0,0 +1,44 @@
+<template>
+    <div>
+        <b-form-group
+            v-for="(field, fieldName) in fieldDefs"
+            :key="fieldName"
+            :label="field.label || fieldName"
+            :label-for="'config-' + fieldName"
+            label-cols-lg="3"
+            :state="config.fieldValid(fieldName)"
+            :invalid-feedback="config.errorMessage(fieldName)"
+        >
+            <masked-input
+                :id="'config-' + fieldName"
+                v-model="config[fieldName]"
+                :mask="field.mask"
+                :placeholder="field.placeholder"
+                :maxlength="field.maxlength || Math.Infinity"
+                :state="config.fieldValid(fieldName)"
+                trim
+            />
+        </b-form-group>
+    </div>
+</template>
+
+<script>
+import MaskedInput from "components/MaskedInput";
+
+export default {
+    components: {
+        MaskedInput
+    },
+    props: {
+        value: { type: Object, required: true }
+    },
+    computed: {
+        config() {
+            return this.value;
+        },
+        fieldDefs() {
+            return this.value.constructor.fields;
+        }
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/User/CloudAuth/CredentialForm.vue b/client/galaxy/scripts/components/User/CloudAuth/CredentialForm.vue
new file mode 100644
index 00000000000..0dd4d16a332
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/CredentialForm.vue
@@ -0,0 +1,108 @@
+<template>
+    <b-form :validated="credential.isValid">
+        <!-- user label -->
+        <b-form-group label="Description" label-for="credentialDescription" label-cols-lg="3">
+            <b-form-input
+                id="credentialDescription"
+                v-model="credential.description"
+                :state="credential.fieldValid('description')"
+                placeholder="Description (optional)"
+                trim
+            />
+        </b-form-group>
+
+        <!-- google-openidconnect -->
+        <b-form-group
+            label="Identity Provider"
+            label-for="identityProvider"
+            label-cols-lg="3"
+            v-if="identityProviders.length > 1"
+        >
+            <b-form-select
+                id="identityProvider"
+                v-model="credential.authn_id"
+                :state="credential.fieldValid('authn_id')"
+                :options="identityProviders"
+            />
+        </b-form-group>
+
+        <!-- aws/azure, etc -->
+        <b-form-group label="Resource Provider" label-for="resourceProvider" label-cols-lg="3">
+            <b-form-select
+                id="resourceProvider"
+                v-model="credential.resourceProvider"
+                :state="credential.fieldValid('provider')"
+                :options="resourceProviderOptions"
+            />
+        </b-form-group>
+
+        <credential-config v-model="credential.config" />
+
+        <footer class="border-top">
+            <b-button variant="secondary" @click.prevent="$emit('delete', credential)">
+                Delete Key
+            </b-button>
+            <b-button
+                aria-label="Save Key"
+                :variant="saveButtonVariant"
+                :disabled="saveButtonDisabled"
+                @click.prevent="$emit('save', credential)"
+            >
+                {{ saveButtonTitle }}
+            </b-button>
+        </footer>
+    </b-form>
+</template>
+
+<script>
+import { Credential, ResourceProviders } from "./model";
+import { getIdentityProviders } from "./model/service";
+import CredentialConfig from "./CredentialConfig";
+
+export default {
+    components: {
+        CredentialConfig
+    },
+    props: {
+        value: { type: Credential, required: true }
+    },
+    data() {
+        return {
+            identityProviders: []
+        };
+    },
+    computed: {
+        credential() {
+            return this.value;
+        },
+        // transformed for bootstrap component
+        resourceProviderOptions() {
+            return Array.from(ResourceProviders.entries()).map(([value, o]) => ({ value, text: o.label }));
+        },
+        config() {
+            return this.credential.config;
+        },
+        loading() {
+            return this.credential.loading;
+        },
+        saveButtonDisabled() {
+            return !(this.credential.valid && this.credential.dirty);
+        },
+        saveButtonVariant() {
+            return this.saveButtonDisabled ? "secondary" : "primary";
+        },
+        saveButtonTitle() {
+            return this.loading ? "Saving Key..." : "Save Key";
+        }
+    },
+    created() {
+        getIdentityProviders().then(result => {
+            if (!this.credential.authn_id && result.length == 1) {
+                this.credential.authn_id = result[0].authn_id;
+                this.credential.updateState();
+            }
+            this.identityProviders = result;
+        });
+    }
+};
+</script>
diff --git a/client/galaxy/scripts/components/User/CloudAuth/index.js b/client/galaxy/scripts/components/User/CloudAuth/index.js
new file mode 100644
index 00000000000..3e5bd9184df
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/index.js
@@ -0,0 +1 @@
+export { default as CloudAuth } from "./CloudAuth.vue";
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.js b/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.js
new file mode 100644
index 00000000000..269d75578a3
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.js
@@ -0,0 +1,27 @@
+import { safeAssign } from "utils/safeAssign";
+import { BaseModel } from "./BaseModel";
+
+export class AwsConfig extends BaseModel {
+    constructor(props = {}) {
+        super();
+        this.role_arn = "";
+        safeAssign(this, props);
+        this.updateState();
+    }
+}
+
+AwsConfig.setValidator(function(model) {
+    const errors = {};
+    if (!model.role_arn.length) {
+        errors.role_arn = "Missing role_arn";
+    }
+    return errors;
+});
+
+AwsConfig.fields = {
+    role_arn: {
+        label: "Role ARN",
+        description: "The Amazon resource name (ARN) of the role to be assumed by Galaxy.",
+        placeholder: "arn:aws:iam::XXXXXXXXXXXX:role/XXXXXXXXXXX"
+    }
+};
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.test.js b/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.test.js
new file mode 100644
index 00000000000..462683198e2
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/AwsConfig.test.js
@@ -0,0 +1,22 @@
+import { AwsConfig } from "./AwsConfig";
+
+describe("AwsConfig", () => {
+    it("should instantiate", () => {
+        let instance = new AwsConfig();
+        assert(instance);
+        assert(!instance.dirty);
+        assert(!instance.valid);
+    });
+
+    it("should validate role_arn", () => {
+        let instance = new AwsConfig();
+        instance.role_arn = "abc";
+        assert(instance.fieldValid("role_arn"));
+    });
+
+    it("should invalidate role_arn", () => {
+        let instance = new AwsConfig();
+        instance.role_arn = "";
+        assert(!instance.fieldValid("role_arn"));
+    });
+});
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.js b/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.js
new file mode 100644
index 00000000000..7cee6dacf06
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.js
@@ -0,0 +1,61 @@
+import { safeAssign } from "utils/safeAssign";
+import { BaseModel } from "./BaseModel";
+
+export class AzureConfig extends BaseModel {
+    constructor(props = {}) {
+        super();
+        this.tenant_id = "";
+        this.client_id = "";
+        this.client_secret = "";
+        safeAssign(this, props);
+        this.updateState();
+    }
+}
+
+AzureConfig.setValidator(function(model) {
+    const errors = {};
+
+    if (model.tenant_id.length < 36) {
+        errors.tenant_id = "Tenant ID too short";
+    }
+    if (!model.tenant_id) {
+        errors.tenant_id = "Missing Tenant ID";
+    }
+
+    if (model.client_id.length < 36) {
+        errors.client_id = "Client ID too short";
+    }
+    if (!model.client_id) {
+        errors.client_id = "Missing client ID";
+    }
+
+    if (!model.client_secret) {
+        errors.client_secret = "Missing secret";
+    }
+
+    return errors;
+});
+
+AzureConfig.fields = {
+    tenant_id: {
+        label: "Tenant ID",
+        mask: "********-****-****-****-************",
+        placeholder: "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx",
+        maxlength: 36,
+        description: "Your Tenant ID (or Directory ID) on Azure."
+    },
+    client_id: {
+        label: "Client ID",
+        mask: "********-****-****-****-************",
+        placeholder: "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx",
+        maxlength: 36,
+        description: "The Client ID (or Application ID) you defined for Galaxy on your Azure directory."
+    },
+    client_secret: {
+        label: "Client Secret",
+        mask: "",
+        placeholder: "Client Secret",
+        description:
+            "A secret string you obtained from Azure portal that Galaxy can use to prove its identity when requesting tokens to access your resources."
+    }
+};
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.test.js b/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.test.js
new file mode 100644
index 00000000000..cc90a205bd6
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/AzureConfig.test.js
@@ -0,0 +1,58 @@
+import { AzureConfig } from "./AzureConfig";
+
+describe("AzureConfig", () => {
+    it("should instantiate", () => {
+        let instance = new AzureConfig();
+        assert(instance);
+        assert(!instance.dirty);
+        assert(!instance.valid);
+    });
+
+    describe("client_secret", () => {
+        it("should validate client_secret", () => {
+            let instance = new AzureConfig();
+            instance.client_secret = "abc";
+            assert(instance.fieldValid("client_secret"));
+        });
+
+        it("should invalidate client_secret", () => {
+            let instance = new AzureConfig();
+            instance.client_secret = "";
+            assert(!instance.fieldValid("client_secret"));
+        });
+    });
+
+    describe("tenant_id", () => {
+        it("should validate tenant_id", () => {
+            let validTenantId = "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx";
+            let instance = new AzureConfig();
+            instance.tenant_id = validTenantId;
+            assert(instance.fieldValid("tenant_id"));
+        });
+
+        it("should invalidate tenant_id", () => {
+            let instance = new AzureConfig();
+            instance.tenant_id = "";
+            assert(!instance.fieldValid("tenant_id"));
+            instance.tenant_id = "asdfa";
+            assert(!instance.fieldValid("tenant_id"));
+        });
+    });
+
+    describe("client_id", () => {
+        it("should validate client_id", () => {
+            let validClientId = "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx";
+            let instance = new AzureConfig();
+            instance.client_id = validClientId;
+            assert(instance.fieldValid("client_id"));
+        });
+
+        it("should invalidate client_id", () => {
+            let instance = new AzureConfig();
+            instance.client_id = "";
+            assert(!instance.fieldValid("client_id"));
+            instance.client_id = "asdf";
+            assert(!instance.fieldValid("client_id"));
+        });
+    });
+});
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/BaseModel.js b/client/galaxy/scripts/components/User/CloudAuth/model/BaseModel.js
new file mode 100644
index 00000000000..651ce0d0ab1
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/BaseModel.js
@@ -0,0 +1,102 @@
+const lastState = new WeakMap();
+const validators = new WeakMap();
+const transients = new WeakMap();
+const counter = new WeakMap();
+
+// Helps with Vue for-loop keys
+let instanceCounter = 0;
+
+export class BaseModel {
+    constructor() {
+        counter.set(this, instanceCounter++);
+    }
+
+    /* object ID */
+
+    get counter() {
+        return counter.get(this);
+    }
+
+    /* Dirty state tracking */
+
+    get dirty() {
+        return lastState.get(this) != this.state;
+    }
+
+    get clean() {
+        return !this.dirty;
+    }
+
+    get state() {
+        // build state JSON ignoring transient fields
+        const tFields = this.transientFields;
+        return JSON.stringify(this, function(key) {
+            if (!tFields.has(key)) {
+                return this[key];
+            }
+            return undefined;
+        });
+    }
+
+    get lastState() {
+        return lastState.get(this);
+    }
+
+    get transientFields() {
+        const key = this.constructor;
+        if (!transients.has(key)) {
+            transients.set(key, new Set());
+        }
+        return transients.get(key);
+    }
+
+    updateState() {
+        lastState.set(this, this.state);
+    }
+
+    // Setting a property name as transient for a class means its
+    // state will be caclulated without regard to that propety
+    static setTransient(...fieldNames) {
+        const klass = this; // this will be a class
+        if (!transients.has(klass)) {
+            transients.set(klass, new Set());
+        }
+
+        const fields = transients.get(klass);
+        fieldNames.forEach(fieldName => fields.add(fieldName));
+        transients.set(klass, fields);
+    }
+
+    /* Validation */
+
+    get valid() {
+        return Object.keys(this.validationErrors).length == 0;
+    }
+
+    get validationErrors() {
+        return this.constructor.validate(this);
+    }
+
+    errorMessage(field) {
+        if (field in this.validationErrors) {
+            return this.validationErrors[field];
+        }
+        return "errmessage";
+    }
+
+    fieldValid(fieldName) {
+        return !(fieldName in this.validationErrors);
+    }
+
+    static validate(model) {
+        if (validators.has(this)) {
+            const validator = validators.get(this);
+            return validator(model);
+        }
+        throw new Error("Missing validator");
+    }
+
+    static setValidator(validationFunction) {
+        validators.set(this, validationFunction);
+    }
+}
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/Credential.js b/client/galaxy/scripts/components/User/CloudAuth/model/Credential.js
new file mode 100644
index 00000000000..defa15e67df
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/Credential.js
@@ -0,0 +1,104 @@
+import { safeAssign } from "utils/safeAssign";
+import { ResourceProviders } from "./ResourceProviders";
+import { BaseModel } from "./BaseModel";
+
+export class Credential extends BaseModel {
+    constructor(props = {}) {
+        super();
+
+        this.id = null;
+        this.description = "";
+        this.authn_id = null; // identity provider
+        this.provider = null; // resource provider
+
+        // transient props, exclude from state
+        this.expanded = false;
+        this.loading = false;
+
+        // populate props
+        const options = Object.assign({}, Credential.defaults, props);
+        safeAssign(this, options);
+
+        // init nested config
+        this.config = new this.configClass(options.config);
+
+        // initialize state
+        this.updateState();
+    }
+
+    get title() {
+        return this.description.length ? this.description : this.provider;
+    }
+
+    get valid() {
+        return super.valid && this.config.valid;
+    }
+
+    // Alias for provider also changes config object when updated
+    // Set this when updating in the UI
+
+    get resourceProvider() {
+        return this.provider;
+    }
+
+    set resourceProvider(newProvider) {
+        this.provider = newProvider;
+        this.config = new this.configClass({});
+    }
+
+    // Polymorphic config class
+
+    get configClass() {
+        return ResourceProviders.get(this.provider).klass;
+    }
+
+    // Methods
+
+    match(searchText = "") {
+        // TODO: more robust object matching?
+        return searchText.length ? this.title.includes(searchText) : true;
+    }
+
+    // Statics
+
+    static get defaults() {
+        return {
+            authn_id: null,
+            provider: "aws",
+            expanded: false
+        };
+    }
+
+    static create(props = {}) {
+        return new Credential(props);
+    }
+}
+
+/**
+ * Transient fields do not factor into the state
+ * for purposes of dirty tracking
+ */
+Credential.setTransient("expanded", "loading");
+
+/**
+ * A validator function's job is to return an object
+ * where the keys are field names and the values are
+ * error messages.
+ */
+Credential.setValidator(function(model) {
+    const errors = {};
+
+    if (!model.provider) {
+        errors.provider = "Provider must be set";
+    }
+
+    if (!model.authn_id) {
+        errors.authn_id = "Please pick an identity provider";
+    }
+
+    if (!model.config.valid) {
+        errors.config = "Invalid config object";
+    }
+
+    return errors;
+});
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/Credential.test.js b/client/galaxy/scripts/components/User/CloudAuth/model/Credential.test.js
new file mode 100644
index 00000000000..ee2be51b315
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/Credential.test.js
@@ -0,0 +1,106 @@
+import { Credential } from "./Credential";
+
+describe("Credential model", () => {
+    describe("basic model props", () => {
+        it("should exist", () => {
+            assert(Credential);
+        });
+
+        it("should build with defaults", () => {
+            let instance = new Credential();
+            assert(instance);
+        });
+
+        it("should build with props", () => {
+            let description = "i am the test description";
+            let props = { description };
+            let instance = new Credential(props);
+            assert(instance);
+            assert(instance.description == description);
+        });
+
+        it("default config object should be AWS", () => {
+            let instance = new Credential();
+            assert("role_arn" in instance.config, "Missing role_arn prop");
+            assert(instance.config.constructor.name == "AwsConfig");
+        });
+
+        it("should load a different config object given the right provider", () => {
+            let provider = "azure";
+            let props = { provider };
+            let instance = new Credential(props);
+            assert(instance.provider == provider);
+            assert(instance.config.constructor.name == "AzureConfig");
+        });
+
+        it("should dynamically switch config objects as resourceProvider is changed", () => {
+            let instance = new Credential();
+            assert(instance.provider == "aws", "Should default to AWS config' ");
+            instance.resourceProvider = "azure";
+            assert(instance.config.constructor.name == "AzureConfig", "Should have been AzureConfig");
+            instance.resourceProvider = "aws";
+            assert(instance.config.constructor.name == "AwsConfig", "Should be AWS Config again");
+        });
+    });
+
+    describe("dirty state", () => {
+        it("should flag as dirty when a prop is changed", () => {
+            let instance = new Credential();
+            instance.description = "foo";
+            assert(instance.dirty);
+        });
+
+        it("should flag as clean when a prop is restored", () => {
+            let instance = new Credential();
+            instance.description = "foo";
+            assert(instance.dirty);
+            instance.description = "";
+            assert(!instance.dirty);
+        });
+
+        it("should not flag as dirty when a transient prop is changed", () => {
+            let instance = new Credential();
+            instance.loading = true;
+            assert(!instance.dirty);
+        });
+    });
+
+    describe("validation", () => {
+        it("a new object should be invalid", () => {
+            let instance = new Credential();
+            assert(!instance.valid);
+        });
+
+        it("it should become valid when props are assigned", () => {
+            let instance = new Credential();
+            instance.authn_id = "floob";
+            instance.resourceProvider = "aws";
+            instance.config.role_arn = "abc";
+            assert(instance.valid);
+        });
+
+        it("it should be valid when initialized with correct props", () => {
+            let props = {
+                authn_id: "asdfasdf",
+                provider: "aws",
+                config: {
+                    role_arn: "floobar"
+                }
+            };
+            let instance = new Credential(props);
+            assert(instance.valid);
+        });
+
+        it("should be invalid when bad props assigned", () => {
+            let props = {
+                authn_id: "asdfasdf",
+                provider: "aws",
+                config: {
+                    role_arn: ""
+                }
+            };
+            let instance = new Credential(props);
+            assert(!instance.valid);
+        });
+    });
+});
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/IdentityProvider.js b/client/galaxy/scripts/components/User/CloudAuth/model/IdentityProvider.js
new file mode 100644
index 00000000000..7c0974fc50b
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/IdentityProvider.js
@@ -0,0 +1,29 @@
+import { safeAssign } from "utils/safeAssign";
+
+export class IdentityProvider {
+    constructor(props = {}) {
+        this.id = "";
+        this.provider = "";
+        safeAssign(this, props);
+    }
+
+    // Aliases
+
+    get authn_id() {
+        return this.id;
+    }
+
+    get text() {
+        return this.provider;
+    }
+
+    get value() {
+        return this.id;
+    }
+
+    // Statics
+
+    static create(props = {}) {
+        return new IdentityProvider(props);
+    }
+}
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/ResourceProviders.js b/client/galaxy/scripts/components/User/CloudAuth/model/ResourceProviders.js
new file mode 100644
index 00000000000..965e254b2f1
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/ResourceProviders.js
@@ -0,0 +1,14 @@
+import { AwsConfig } from "./AwsConfig";
+import { AzureConfig } from "./AzureConfig";
+
+export const ResourceProviders = new Map();
+
+ResourceProviders.set("aws", {
+    klass: AwsConfig,
+    label: "Amazon Web Services (AWS)"
+});
+
+ResourceProviders.set("azure", {
+    klass: AzureConfig,
+    label: "Microsoft Azure"
+});
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/index.js b/client/galaxy/scripts/components/User/CloudAuth/model/index.js
new file mode 100644
index 00000000000..24f019b67c5
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/index.js
@@ -0,0 +1,3 @@
+export { Credential } from "./Credential";
+export { IdentityProvider } from "./IdentityProvider";
+export { ResourceProviders } from "./ResourceProviders";
diff --git a/client/galaxy/scripts/components/User/CloudAuth/model/service.js b/client/galaxy/scripts/components/User/CloudAuth/model/service.js
new file mode 100644
index 00000000000..28e6339b8c0
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/model/service.js
@@ -0,0 +1,78 @@
+/**
+ * Data retrieval/storage for the auth keys
+ */
+
+import axios from "axios";
+import { Credential, IdentityProvider } from "./index";
+import { getRootFromIndexLink } from "onload";
+
+const getUrl = path => getRootFromIndexLink() + path;
+
+export async function listCredentials() {
+    const url = getUrl("api/cloud/authz");
+    const response = await axios.get(url);
+    if (response.status != 200) {
+        throw new Error("Unexpected response from listing.");
+    }
+    return response.data.map(Credential.create);
+}
+
+export async function getCredential(id) {
+    const url = getUrl("api/cloud/authz/${id}");
+    const response = await axios.get(url);
+    if (response.status != 200) {
+        throw new Error("Unexpected response loading key.");
+    }
+    return Credential.create(response.data);
+}
+
+export async function saveCredential(newItem) {
+    const model = Credential.create(newItem);
+    const response = await saveOrUpdate(model);
+    if (response.status != 200) {
+        throw new Error("Save failure.");
+    }
+    return Credential.create(response.data);
+}
+
+async function saveOrUpdate(model) {
+    return model.id
+        ? axios.put(getUrl(`api/cloud/authz/${model.id}`), model)
+        : axios.post(getUrl("api/cloud/authz"), model);
+}
+
+export async function deleteCredential(doomed) {
+    const model = Credential.create(doomed);
+    if (model.id) {
+        const url = getUrl(`api/cloud/authz/${doomed.id}`);
+        const response = await axios.delete(url);
+        if (response.status != 200) {
+            throw new Error("Delete failure.");
+        }
+    }
+    return model;
+}
+
+// Memoize results (basically never changes)
+
+let identityProviders;
+
+export async function getIdentityProviders() {
+    if (!identityProviders) {
+        const url = getUrl("authnz");
+        const response = await axios.get(url);
+        if (response.status != 200) {
+            throw new Error("Unable to load identity providers");
+        }
+        identityProviders = response.data.map(IdentityProvider.create);
+    }
+    return identityProviders;
+}
+
+export default {
+    listCredentials,
+    getCredential,
+    saveCredential,
+    deleteCredential,
+    getIdentityProviders
+};
diff --git a/client/galaxy/scripts/components/User/CloudAuth/testdata/listCredentials.json b/client/galaxy/scripts/components/User/CloudAuth/testdata/listCredentials.json
new file mode 100644
index 00000000000..82973dc3a7f
--- /dev/null
+++ b/client/galaxy/scripts/components/User/CloudAuth/testdata/listCredentials.json
@@ -0,0 +1,32 @@
+[
+    {
+        "authn_id": "f2db41e1fa331b3e",
+        "user_id": "f2db41e1fa331b3e",
+        "description": "aws description",
+        "last_update": "2019-04-04 09:13:16.135032",
+        "last_activity": "2019-04-04 09:13:16.135042",
+        "create_time": "2019-04-04 16:13:16.135755",
+        "provider": "aws",
+        "model_class": "CloudAuthz",
+        "config": {
+            "role_arn": "floobadooba"
+        },
+        "id": "a7db2fac67043c7e"
+    },
+    {
+        "authn_id": "f2db41e1fa331b3e",
+        "user_id": "f2db41e1fa331b3e",
+        "description": "azure description",
+        "last_update": "2019-04-03 20:21:51.350748",
+        "last_activity": "2019-04-03 20:21:51.350804",
+        "create_time": "2019-04-04 03:21:51.351508",
+        "provider": "azure",
+        "model_class": "CloudAuthz",
+        "config": {
+            "client_secret": "dannon likes Nickleback",
+            "client_id": "22222222-2222-2222-2222-222222222222",
+            "tenant_id": "11111111-1111-1111-1111-111111111111"
+        },
+        "id": "b472e2eb553fa0d1"
+    }
+]
\ No newline at end of file
diff --git a/client/galaxy/scripts/components/WorkflowImport.vue b/client/galaxy/scripts/components/WorkflowImport.vue
index c202ebd5c2b..bd621e881e4 100644
--- a/client/galaxy/scripts/components/WorkflowImport.vue
+++ b/client/galaxy/scripts/components/WorkflowImport.vue
@@ -31,7 +31,7 @@ Vue.use(BootstrapVue);
 
 export default {
     data() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         return {
             sourceFile: null,
             sourceURL: null,
@@ -52,7 +52,7 @@ export default {
             if (!this.sourceFile && !this.sourceURL) {
                 this.errorMessage = "You must provide a workflow archive URL or file.";
             } else {
-                let formData = new FormData();
+                const formData = new FormData();
                 formData.append("archive_file", this.sourceFile);
                 formData.append("archive_source", this.sourceURL);
                 axios
@@ -63,7 +63,7 @@ export default {
                         }&status=success`;
                     })
                     .catch(error => {
-                        let message = error.response.data && error.response.data.err_msg;
+                        const message = error.response.data && error.response.data.err_msg;
                         this.errorMessage = message || "Import failed for an unknown reason.";
                     });
             }
diff --git a/client/galaxy/scripts/components/admin/AdminServices.js b/client/galaxy/scripts/components/admin/AdminServices.js
index 22c0c1c2e33..64701d52816 100644
--- a/client/galaxy/scripts/components/admin/AdminServices.js
+++ b/client/galaxy/scripts/components/admin/AdminServices.js
@@ -2,16 +2,16 @@ import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 
 export function getErrorStack() {
-    let url = `${getAppRoot()}api/tools/error_stack`;
+    const url = `${getAppRoot()}api/tools/error_stack`;
     return axios.get(url);
 }
 
 export function getDisplayApplications() {
-    let url = `${getAppRoot()}api/display_applications`;
+    const url = `${getAppRoot()}api/display_applications`;
     return axios.get(url);
 }
 
 export function reloadDisplayApplications(ids) {
-    let url = `${getAppRoot()}api/display_applications/reload`;
+    const url = `${getAppRoot()}api/display_applications/reload`;
     return axios.post(url, { ids: ids });
 }
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManager.vue b/client/galaxy/scripts/components/admin/DataManager/DataManager.vue
index 52251caaa16..5f60232b00f 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManager.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManager.vue
@@ -6,18 +6,10 @@
         <div v-else-if="dataManagers && !dataManagers.length">
             <Alert variant="primary">
                 <h4 class="alert-heading">None installed</h4>
-                You do not currently have any Data Managers installed
-            </Alert>
-            <Alert variant="info">
-                Data Managers can be installed from a
-                <ToolShedButton />
+                You do not currently have any Data Managers installed.
             </Alert>
         </div>
         <div v-else-if="dataManagers && dataTables">
-            <Alert variant="secondary" dismissible>
-                Choose your data managing option from below. You may install additional Data Managers from a
-                <ToolShedButton />
-            </Alert>
             <b-container fluid>
                 <b-row>
                     <b-col md="6">
@@ -37,7 +29,7 @@
                 </b-row>
             </b-container>
             <b-card-group columns>
-                <b-card no-body header="<h4>Data Managers</h4>" id="data-managers-card">
+                <b-card no-body header="Installed Data Managers" id="data-managers-card">
                     <b-list-group flush>
                         <b-list-group-item v-for="(dataManager, index) in dataManagersFiltered" :key="index">
                             <b-button-group vertical>
@@ -65,7 +57,7 @@
                         </b-list-group-item>
                     </b-list-group>
                 </b-card>
-                <b-card no-body header="<h4>Tool Data Tables</h4>">
+                <b-card no-body header="Tool Data Tables">
                     <b-list-group flush>
                         <b-list-group-item
                             v-for="(dataTable, index) in dataTablesFiltered"
@@ -91,19 +83,9 @@ import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 import Alert from "components/Alert.vue";
 
-var ToolShedButton = {
-    template: `
-  <b-link href="/admin_toolshed/browse_tool_sheds"
-          target="galaxy_main"
-          class="alert-link">
-  ToolShed
-  </b-link>`
-};
-
 export default {
     components: {
-        Alert,
-        ToolShedButton
+        Alert
     },
     data() {
         return {
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
index 87bf41802de..156e3208c0d 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
@@ -133,7 +133,7 @@ export default {
             ];
         },
         tableFields() {
-            let tableFields = this.fields.slice(0);
+            const tableFields = this.fields.slice(0);
             if (this.showCommandLine) {
                 tableFields.splice(5, 0, {
                     key: "commandLine",
@@ -143,9 +143,9 @@ export default {
             return tableFields;
         },
         tableItems() {
-            let tableItems = this.jobs.slice(0);
+            const tableItems = this.jobs.slice(0);
 
-            for (let item of tableItems) {
+            for (const item of tableItems) {
                 // Nicer time formatting
                 item["updateTime"] = item["updateTime"].replace("T", "\n");
 
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
index a49800d81d3..55cbf0ed008 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
@@ -1,11 +1,26 @@
 <template>
     <div>
-        <h2 class="mb-3">
-            <span id="data-managers-title">Data Manager</span>
-            <b-badge href="https://galaxyproject.org/admin/tools/data-managers/" target="_blank" variant="secondary"
-                >Wiki</b-badge
-            >
-        </h2>
+        <span class="mb-3">
+            <h2 id="data-managers-title">Local Data</h2>
+            <p>
+                Data Managers are used to manage Galaxy's local data. They can be installed manually, or via the
+                <b-link :href="toolShedLink" target="galaxy_main">ToolShed</b-link>. For more
+                comprehensive information
+                <b-link href="https://galaxyproject.org/admin/tools/data-managers/" target="_blank">See the Wiki</b-link
+                >.
+            </p>
+        </span>
         <router-view />
     </div>
 </template>
+<script>
+import { getAppRoot } from "onload/loadConfig";
+
+export default {
+    computed:{
+        toolShedLink() {
+            return `${getAppRoot()}admin_toolshed/browse_tool_sheds`
+        }
+    }
+}
+</script>
diff --git a/client/galaxy/scripts/components/admin/DataTypes.vue b/client/galaxy/scripts/components/admin/DataTypes.vue
index 263139c02b2..e4e84f2b98c 100644
--- a/client/galaxy/scripts/components/admin/DataTypes.vue
+++ b/client/galaxy/scripts/components/admin/DataTypes.vue
@@ -56,20 +56,20 @@ export default {
         // Return predefined column headers merged
         // with all other column headers returned by the api
         columns() {
-            var columns = this.prettyColumns();
+            let columns = this.prettyColumns();
             // We have keys to look at
             if (this.keys.length > 0) {
                 // Additional column headers only when option is selected
                 if (this.showAllColumns) {
-                    var keys = this.keys;
+                    let keys = this.keys;
                     // Filter out the predefined column headers
-                    for (var c of columns) {
+                    for (const c of columns) {
                         keys = keys.filter(k => k !== c["dataIndex"]);
                     }
                     // Create column headers from each remaining key and merge
                     // with predefined column headers
                     columns = keys.reduce(function(m, k) {
-                        var text = k[0].toUpperCase();
+                        let text = k[0].toUpperCase();
                         text += k.slice(1).replace(/_/g, " ");
                         m.push({
                             text: text,
diff --git a/client/galaxy/scripts/components/admin/DisplayApplications.vue b/client/galaxy/scripts/components/admin/DisplayApplications.vue
index db9fe8e191f..3f751410fff 100644
--- a/client/galaxy/scripts/components/admin/DisplayApplications.vue
+++ b/client/galaxy/scripts/components/admin/DisplayApplications.vue
@@ -58,15 +58,15 @@ export default {
     },
     computed: {
         applicationsIndex: function() {
-            let result = {};
-            for (let app of this.applications) {
+            const result = {};
+            for (const app of this.applications) {
                 result[app.id] = app;
             }
             return result;
         },
         applicationsAll: function() {
-            let result = [];
-            for (let app of this.applications) {
+            const result = [];
+            for (const app of this.applications) {
                 result.push(app.id);
             }
             return result;
@@ -99,8 +99,8 @@ export default {
             this._reload([id]);
         },
         reloadAll: function() {
-            let ids = [];
-            for (let app of this.applications) {
+            const ids = [];
+            for (const app of this.applications) {
                 ids.push(app.id);
             }
             this._reload(ids);
@@ -119,15 +119,15 @@ export default {
                 });
         },
         _highlightRows: function(appList, status) {
-            for (let appIndex of appList) {
-                let app = this.applicationsIndex[appIndex];
+            for (const appIndex of appList) {
+                const app = this.applicationsIndex[appIndex];
                 if (app) {
                     app._rowVariant = status;
                 }
             }
         },
         _errorMessage: function(e) {
-            let message = e && e.response && e.response.data && e.response.data.err_msg;
+            const message = e && e.response && e.response.data && e.response.data.err_msg;
             this.messageText = message || "Request failed for an unknown reason.";
             this.messageVariant = "danger";
         }
diff --git a/client/galaxy/scripts/components/admin/ErrorStack.vue b/client/galaxy/scripts/components/admin/ErrorStack.vue
index b466213cf70..b83043c7caa 100644
--- a/client/galaxy/scripts/components/admin/ErrorStack.vue
+++ b/client/galaxy/scripts/components/admin/ErrorStack.vue
@@ -40,7 +40,7 @@ export default {
                 this.errorStackLoaded = true;
             })
             .catch(e => {
-                let message = e && e.response && e.response.data && e.response.data.err_msg;
+                const message = e && e.response && e.response.data && e.response.data.err_msg;
                 this.messageText = message || "Request failed for an unknown reason.";
             });
     }
diff --git a/client/galaxy/scripts/components/admin/Jobs.vue b/client/galaxy/scripts/components/admin/Jobs.vue
new file mode 100644
index 00000000000..f3500e08676
--- /dev/null
+++ b/client/galaxy/scripts/components/admin/Jobs.vue
@@ -0,0 +1,370 @@
+<template>
+    <div>
+        <h2 class="mb-3">
+            <span id="jobs-title">Jobs</span>
+        </h2>
+        <b-alert v-if="this.message !== ''" :variant="galaxyKwdToBootstrap(status)" show>
+            {{ message }}
+        </b-alert>
+        <b-alert variant="info" show>
+            <p>
+                Unfinished and recently finished jobs are displayed on this page. The 'cutoff' input box will do two
+                things -- it will limit the display of unfinished jobs to only those jobs that have not had their job
+                state updated recently, and it will limit the recently finished jobs list to only displaying jobs that
+                have finished since the cutoff.
+            </p>
+            If any jobs are displayed, you may choose to stop them. Your stop message will be displayed to the user as:
+            "This job was stopped by an administrator: <strong>&lt;YOUR MESSAGE&gt;</strong> For more information or
+            help, report this error".
+        </b-alert>
+        <b-alert v-if="loading" variant="info" show>
+            Waiting for data
+        </b-alert>
+        <div v-else>
+            <b-container class="mb-3">
+                <b-row>
+                    <b-col md="6">
+                        <b-form name="jobs" @submit.prevent="onRefresh">
+                            <b-form-group
+                                id="cutoff"
+                                label="Update Jobs"
+                                label-for="cutoff-seconds"
+                                description="Cutoff in seconds"
+                            >
+                                <b-input-group>
+                                    <b-form-input id="cutoff" type="number" placeholder="180" v-model="cutoff">
+                                    </b-form-input>
+                                    <b-input-group-append>
+                                        <b-btn type="submit">Refresh</b-btn>
+                                    </b-input-group-append>
+                                </b-input-group>
+                            </b-form-group>
+                        </b-form>
+                    </b-col>
+                    <b-col>
+                        <b-form-group label="Administrative Job Lock" label-for="prevent-job-dispatching">
+                            <b-form-checkbox id="prevent-job-dispatching" v-model="jobLock" switch>
+                                Job dispatching is currently
+                                <strong>{{ jobLockDisplay ? "locked" : "unlocked" }}</strong>
+                            </b-form-checkbox>
+                        </b-form-group>
+                    </b-col>
+                </b-row>
+                <b-row>
+                    <b-col md="6">
+                        <b-form-group
+                            label="Filter Jobs"
+                            label-for="filter-regex"
+                            description="Search for strings or regular expressions"
+                        >
+                            <b-input-group id="filter-regex">
+                                <b-form-input
+                                    v-model="filter"
+                                    placeholder="Type to Search"
+                                    @keyup.esc.native="filter = ''"
+                                />
+                                <b-input-group-append>
+                                    <b-btn :disabled="!filter" @click="filter = ''">Clear (esc)</b-btn>
+                                </b-input-group-append>
+                            </b-input-group>
+                        </b-form-group>
+                        <b-button :pressed.sync="showCommandLine" variant="outline-secondary">
+                            {{ showCommandLine ? "Hide" : "Show" }} Command Line
+                        </b-button>
+                    </b-col>
+                    <b-col>
+                        <b-card v-if="jobsItemsComputed.length" header="Stop Selected Jobs">
+                            <b-form @submit.prevent="onStopJobs">
+                                <b-form-group label-for="stop-message" description="will be displayed to the user">
+                                    <b-input-group>
+                                        <b-form-input
+                                            id="stop-message"
+                                            v-model="stopMessage"
+                                            placeholder="Stop message"
+                                            required
+                                        >
+                                        </b-form-input>
+                                        <b-input-group-append>
+                                            <b-btn type="submit">Submit</b-btn>
+                                        </b-input-group-append>
+                                    </b-input-group>
+                                </b-form-group>
+                            </b-form>
+                        </b-card>
+                    </b-col>
+                </b-row>
+            </b-container>
+            <b-alert v-if="!jobsItemsComputed.length" variant="secondary" show>
+                There are no unfinished jobs to show with current cutoff time.
+            </b-alert>
+            <b-table
+                v-else
+                :fields="jobsFieldsComputed"
+                :items="jobsItemsComputed"
+                v-model="jobsItemsModel"
+                :filter="filter"
+                hover
+                responsive
+                striped
+                caption-top
+                @row-clicked="showRowDetails"
+                :busy="busy"
+            >
+                <template slot="table-caption">
+                    Unfinished Jobs: These jobs are unfinished and have had their state updated in the previous
+                    {{ cutoffDisplay }} seconds.
+                </template>
+                <!-- Enable cell formatting for the command line column -->
+                <span slot="html" slot-scope="data" v-html="data.value" />
+                <template slot="HEAD_selected">
+                    <b-form-checkbox
+                        v-model="allSelected"
+                        :indeterminate="indeterminate"
+                        @change="toggleAll"
+                    ></b-form-checkbox>
+                </template>
+                <template slot="selected" slot-scope="data">
+                    <b-form-checkbox
+                        v-model="selectedStopJobIds"
+                        :checked="allSelected"
+                        :key="data.index"
+                        :value="data.item['job_info']['id']"
+                    ></b-form-checkbox>
+                </template>
+                <template slot="job_info" slot-scope="data">
+                    <b-link :href="data.value['info_url']" target="galaxy_main">
+                        {{ data.value["id"] }}
+                    </b-link>
+                </template>
+                <template slot="row-details" slot-scope="row">
+                    <b-card>
+                        <h5>Command Line</h5>
+                        <pre
+                            class="text-white bg-dark"
+                        ><code class="break-word">{{ row.item.command_line }}</code></pre>
+                    </b-card>
+                </template>
+            </b-table>
+            <b-alert v-if="!recentJobsItemsComputed.length" variant="secondary" show>
+                There are no recently finished jobs to show with current cutoff time.
+            </b-alert>
+            <b-table
+                v-else
+                :fields="recentJobsFieldsComputed"
+                :items="recentJobsItemsComputed"
+                :filter="filter"
+                hover
+                responsive
+                striped
+                caption-top
+                @row-clicked="showRowDetails"
+                :busy="busy"
+            >
+                <template slot="table-caption">
+                    Recent Jobs: These jobs have completed in the previous {{ cutoffDisplay }} seconds.
+                </template>
+                <!-- Enable cell formatting for the command line column -->
+                <span slot="html" slot-scope="data" v-html="data.value" />
+                <template slot="job_info" slot-scope="data">
+                    <b-link :href="data.value['info_url']" target="galaxy_main">
+                        {{ data.value["id"] }}
+                    </b-link>
+                </template>
+                <template slot="row-details" slot-scope="row">
+                    <b-card>
+                        <h5>Command Line</h5>
+                        <pre
+                            class="text-white bg-dark"
+                        ><code class="break-word">{{ row.item.command_line }}</code></pre>
+                    </b-card>
+                </template>
+            </b-table>
+        </div>
+    </div>
+</template>
+
+<script>
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+export default {
+    data() {
+        return {
+            jobsItems: [],
+            jobsItemsModel: [],
+            recentJobsItems: [],
+            jobsFields: [
+                { key: "job_info", label: "Job ID", sortable: true },
+                { key: "user" },
+                { key: "tool_id", label: "Tool", tdClass: ["break-word"] },
+                { key: "state" },
+                { key: "input_dataset", label: "Inputs" },
+                { key: "job_runner_name", label: "Job Runner" },
+                { key: "job_runner_external_id", label: "PID/Cluster ID", sortable: true }
+            ],
+            showCommandLine: false,
+            cutoff: 180,
+            cutoffDisplay: 180,
+            jobLock: false,
+            jobLockDisplay: false,
+            selectedStopJobIds: [],
+            allSelected: false,
+            indeterminate: false,
+            stopMessage: "",
+            filter: "",
+            message: "",
+            status: "",
+            loading: true,
+            busy: true
+        };
+    },
+    watch: {
+        jobLock(newVal) {
+            axios
+                .get(`${getAppRoot()}admin/jobs_control?job_lock=${this.jobLock}`)
+                .then(response => {
+                    this.jobLock = response.data.job_lock;
+                    this.jobLockDisplay = response.data.job_lock;
+                })
+                .catch(error => {
+                    console.error(error);
+                });
+        },
+        selectedStopJobIds(newVal) {
+            if (newVal.length === 0) {
+                this.indeterminate = false;
+                this.allSelected = false;
+            } else if (newVal.length === this.jobsItemsModel.length) {
+                this.indeterminate = false;
+                this.allSelected = true;
+            } else {
+                this.indeterminate = true;
+                this.allSelected = false;
+            }
+        }
+    },
+    methods: {
+        update() {
+            this.busy = true;
+            let params = [];
+            params.push(`cutoff=${this.cutoff}`);
+            params.push(`stop_msg=${this.stopMessage}`);
+            params.push(`stop=${this.selectedStopJobIds.join()}`);
+            params = params.join("&");
+            axios
+                .get(`${getAppRoot()}admin/jobs_list?${params}`)
+                .then(response => {
+                    this.jobsItems = response.data.jobs;
+                    this.recentJobsItems = response.data.recent_jobs;
+                    this.cutoffDisplay = response.data.cutoff;
+                    this.message = response.data.message;
+                    this.status = response.data.status;
+                    this.jobLock = response.data.job_lock;
+                    this.jobLockDisplay = response.data.job_lock;
+                    this.loading = false;
+                    this.busy = false;
+                })
+                .catch(error => {
+                    this.message = error.response.data.err_msg;
+                    this.status = "error";
+                    console.log(error.response);
+                });
+        },
+        onRefresh() {
+            this.update();
+        },
+        onStopJobs() {
+            this.update();
+            this.selectedStopJobIds = [];
+            this.stopMessage = "";
+        },
+        showRowDetails(row, index, e) {
+            if (e.target.nodeName != "A") {
+                row._showDetails = !row._showDetails;
+            }
+        },
+        translateState(state) {
+            const translateDict = {
+                ok: "success",
+                error: "danger",
+                new: "primary",
+                queued: "secondary",
+                running: "info",
+                upload: "dark"
+            };
+            return translateDict[state] || "primary";
+        },
+        computeItems(items) {
+            return items.map(job => {
+                return {
+                    ...job,
+                    _showDetails: false,
+                    _cellVariants: { state: this.translateState(job.state) }
+                };
+            });
+        },
+        computeFields(fields) {
+            const f = Array.from(fields).slice(0);
+            if (this.showCommandLine) {
+                f.splice(6, 0, {
+                    key: "command_line",
+                    tdClass: ["text-white", "bg-dark", "break-word"]
+                });
+            }
+            return f;
+        },
+        toggleAll(checked) {
+            this.selectedStopJobIds = checked
+                ? this.jobsItemsModel.reduce((acc, j) => [...acc, j["job_info"]["id"]], [])
+                : [];
+        },
+        galaxyKwdToBootstrap(status) {
+            let variant = "info";
+            if (status !== "") {
+                variant = status;
+            }
+            const galaxyKwdToBoostrapDict = {
+                done: "success",
+                info: "info",
+                warning: "warning",
+                error: "danger"
+            };
+            if (variant in galaxyKwdToBoostrapDict) {
+                return galaxyKwdToBoostrapDict[variant];
+            } else {
+                return variant;
+            }
+        }
+    },
+    computed: {
+        jobsItemsComputed() {
+            return this.computeItems(this.jobsItems);
+        },
+        recentJobsItemsComputed() {
+            return this.computeItems(this.recentJobsItems);
+        },
+        jobsFieldsComputed() {
+            const f = this.jobsFields.slice(0);
+            f.splice(0, 0, { key: "selected", label: "" });
+            f.splice(2, 0, { key: "update_time", label: "Last Update", sortable: true });
+            return this.computeFields(f);
+        },
+        recentJobsFieldsComputed() {
+            const f = this.jobsFields.slice(0);
+            f.splice(2, 0, { key: "update_time", label: "Finished", sortable: true });
+            return this.computeFields(f);
+        }
+    },
+    created() {
+        this.update();
+    }
+};
+</script>
+
+<style>
+/* Can not be scoped because of command line tdClass */
+.break-word {
+    white-space: pre-wrap;
+    word-break: break-word;
+}
+</style>
diff --git a/client/galaxy/scripts/components/login/Index.vue b/client/galaxy/scripts/components/login/Index.vue
index aaa5a784f62..a166bdc0253 100644
--- a/client/galaxy/scripts/components/login/Index.vue
+++ b/client/galaxy/scripts/components/login/Index.vue
@@ -7,7 +7,7 @@
             <register
                 :registration_warning_message="registration_warning_message"
                 :mailing_join_addr="mailing_join_addr"
-                :smtp_server="smtp_server"
+                :server_mail_configured="server_mail_configured"
             />
         </template>
     </div>
@@ -57,8 +57,8 @@ export default {
             type: String,
             required: false
         },
-        smtp_server: {
-            type: String,
+        server_mail_configured: {
+            type: Boolean,
             required: false
         }
     }
diff --git a/client/galaxy/scripts/components/login/Login.vue b/client/galaxy/scripts/components/login/Login.vue
index e2c0ad2eb40..149251ea0c7 100644
--- a/client/galaxy/scripts/components/login/Login.vue
+++ b/client/galaxy/scripts/components/login/Login.vue
@@ -6,7 +6,7 @@
                 <b-form id="login" @submit.prevent="submitGalaxyLogin()">
                     <b-card no-body header="Welcome to Galaxy, please log in">
                         <b-card-body>
-                            <b-form-group label="Username or Email Address">
+                            <b-form-group label="Public name or Email Address">
                                 <b-form-input name="login" type="text" v-model="login" />
                             </b-form-group>
                             <b-form-group label="Password">
@@ -20,12 +20,19 @@
                         </b-card-body>
                         <b-card-footer>
                             Don't have an account?
-                            <a id="register-toggle" href="#" @click.prevent="toggleLogin">Register here.</a>
+                            <span v-if="allowUserCreation">
+                                <a id="register-toggle" href="#" @click.prevent="toggleLogin">Register here.</a>
+                            </span>
+                            <span v-else>
+                                Registration for this Galaxy instance is disabled. Please contact an administrator for
+                                assistance.
+                            </span>
                         </b-card-footer>
                     </b-card>
                 </b-form>
                 <b-button v-for="idp in oidc_idps" :key="idp" class="d-block mt-3" @click="submitOIDCLogin(idp)">
-                    <i v-bind:class="oidc_idps_icons[idp]" /> Sign in with {{ idp.charAt(0).toUpperCase() + idp.slice(1) }}
+                    <i v-bind:class="oidc_idps_icons[idp]" /> Sign in with
+                    {{ idp.charAt(0).toUpperCase() + idp.slice(1) }}
                 </b-button>
             </div>
             <div v-if="show_welcome_with_login" class="col">
@@ -55,14 +62,18 @@ export default {
         }
     },
     data() {
-        let galaxy = getGalaxyInstance();
-        let oidc_idps = galaxy.config.oidc;
+        const galaxy = getGalaxyInstance();
+        const oidc_idps = galaxy.config.oidc;
         // Icons to use for each IdP
-        let oidc_idps_icons = {'google': 'fa fa-google'};
+        const oidc_idps_icons = { google: "fa fa-google" };
         // Add default icons to IdPs without icons
-        oidc_idps.filter(function(key) { return oidc_idps_icons[key] === undefined; }).forEach(function(idp) {
-             oidc_idps_icons[idp] = 'fa fa-id-card'
-        });
+        oidc_idps
+            .filter(function(key) {
+                return oidc_idps_icons[key] === undefined;
+            })
+            .forEach(function(idp) {
+                oidc_idps_icons[idp] = "fa fa-id-card";
+            });
         return {
             login: null,
             password: null,
@@ -70,12 +81,12 @@ export default {
             provider: null,
             messageText: null,
             messageVariant: null,
+            allowUserCreation: galaxy.config.allow_user_creation,
             redirect: galaxy.params.redirect,
             session_csrf_token: galaxy.session_csrf_token,
             enable_oidc: galaxy.config.enable_oidc,
             oidc_idps: oidc_idps,
             oidc_idps_icons: oidc_idps_icons
-
         };
     },
     computed: {
@@ -90,7 +101,7 @@ export default {
             }
         },
         submitGalaxyLogin: function(method) {
-            let rootUrl = getAppRoot();
+            const rootUrl = getAppRoot();
             axios
                 .post(`${rootUrl}user/login`, this.$data)
                 .then(response => {
@@ -107,12 +118,12 @@ export default {
                 })
                 .catch(error => {
                     this.messageVariant = "danger";
-                    let message = error.response.data && error.response.data.err_msg;
+                    const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Login failed for an unknown reason.";
                 });
         },
         submitOIDCLogin: function(idp) {
-            let rootUrl = getAppRoot();
+            const rootUrl = getAppRoot();
             axios
                 .post(`${rootUrl}authnz/${idp}/login`)
                 .then(response => {
@@ -123,12 +134,12 @@ export default {
                 })
                 .catch(error => {
                     this.messageVariant = "danger";
-                    let message = error.response.data && error.response.data.err_msg;
+                    const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Login failed for an unknown reason.";
                 });
         },
         reset: function(ev) {
-            let rootUrl = getAppRoot();
+            const rootUrl = getAppRoot();
             ev.preventDefault();
             axios
                 .post(`${rootUrl}user/reset_password`, { email: this.login })
@@ -138,7 +149,7 @@ export default {
                 })
                 .catch(error => {
                     this.messageVariant = "danger";
-                    let message = error.response.data && error.response.data.err_msg;
+                    const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Password reset failed for an unknown reason.";
                 });
         }
diff --git a/client/galaxy/scripts/components/login/Password.vue b/client/galaxy/scripts/components/login/Password.vue
index 9d25aa38ffd..f50b6a6afb1 100644
--- a/client/galaxy/scripts/components/login/Password.vue
+++ b/client/galaxy/scripts/components/login/Password.vue
@@ -22,7 +22,7 @@ Vue.use(BootstrapVue);
 
 export default {
     data() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         return {
             token: Galaxy.params.token,
             user: Galaxy.params.expired_user,
@@ -40,7 +40,7 @@ export default {
     },
     methods: {
         submit: function(ev) {
-            let urlRoot = getAppRoot();
+            const urlRoot = getAppRoot();
             ev.preventDefault();
             axios
                 .post(`${urlRoot}user/change_password`, {
@@ -55,7 +55,7 @@ export default {
                 })
                 .catch(error => {
                     this.messageVariant = "danger";
-                    let message = error.response.data && error.response.data.err_msg;
+                    const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Password change failed for an unknown reason.";
                 });
         }
diff --git a/client/galaxy/scripts/components/login/Register.vue b/client/galaxy/scripts/components/login/Register.vue
index 2009c783a1f..588e2251ec9 100644
--- a/client/galaxy/scripts/components/login/Register.vue
+++ b/client/galaxy/scripts/components/login/Register.vue
@@ -1,7 +1,7 @@
 <template>
     <div class="container">
         <div class="row justify-content-md-center">
-            <div class="col col-lg-6">
+            <div class="col" :class="{ 'col-lg-6': !isAdmin }">
                 <b-alert :show="registration_warning_message" variant="danger">
                     {{ registration_warning_message }}
                 </b-alert>
@@ -27,12 +27,12 @@
                                     ('.', '_', '-').</b-form-text
                                 >
                             </b-form-group>
-                            <b-form-group v-if="mailing_join_addr && smtp_server" label="Subscribe to mailing list">
+                            <b-form-group v-if="mailing_join_addr && server_mail_configured" label="Subscribe to mailing list">
                                 <input name="subscribe" type="checkbox" v-model="subscribe" />
                             </b-form-group>
-                            <b-button name="create" type="submit">Create</b-button>
+                            <b-button name="create" type="submit" :disabled="disableCreate">Create</b-button>
                         </b-card-body>
-                        <b-card-footer>
+                        <b-card-footer v-if="!isAdmin">
                             Already have an account?
                             <a id="login-toggle" href="#" @click.prevent="toggleLogin">Log in here.</a>
                         </b-card-footer>
@@ -57,8 +57,8 @@ export default {
             type: String,
             required: false
         },
-        smtp_server: {
-            type: String,
+        server_mail_configured: {
+            type: Boolean,
             required: false
         },
         mailing_join_addr: {
@@ -71,8 +71,9 @@ export default {
         }
     },
     data() {
-        let galaxy = getGalaxyInstance();
+        const galaxy = getGalaxyInstance();
         return {
+            disableCreate: false,
             email: null,
             password: null,
             username: null,
@@ -80,7 +81,8 @@ export default {
             subscribe: null,
             messageText: null,
             messageVariant: null,
-            session_csrf_token: galaxy.session_csrf_token
+            session_csrf_token: galaxy.session_csrf_token,
+            isAdmin: galaxy.user.isAdmin()
         };
     },
     computed: {
@@ -95,7 +97,8 @@ export default {
             }
         },
         submit: function(method) {
-            let rootUrl = getAppRoot();
+            this.disableCreate = true;
+            const rootUrl = getAppRoot();
             axios
                 .post(`${rootUrl}user/create`, this.$data)
                 .then(response => {
@@ -105,8 +108,9 @@ export default {
                     window.location = this.redirect || rootUrl;
                 })
                 .catch(error => {
+                    this.disableCreate = false;
                     this.messageVariant = "danger";
-                    let message = error.response.data && error.response.data.err_msg;
+                    const message = error.response.data && error.response.data.err_msg;
                     this.messageText = message || "Registration failed for an unknown reason.";
                 });
         }
diff --git a/client/galaxy/scripts/entry/admin/AdminRouter.js b/client/galaxy/scripts/entry/admin/AdminRouter.js
index 1eeae6a2138..ca0edba64fd 100644
--- a/client/galaxy/scripts/entry/admin/AdminRouter.js
+++ b/client/galaxy/scripts/entry/admin/AdminRouter.js
@@ -7,15 +7,17 @@ import QueryStringParsing from "utils/query-string-parsing";
 import Router from "layout/router";
 import DataTables from "components/admin/DataTables.vue";
 import DataTypes from "components/admin/DataTypes.vue";
+import Jobs from "components/admin/Jobs.vue";
 import DataManagerView from "components/admin/DataManager/DataManagerView.vue";
 import DataManagerRouter from "components/admin/DataManager/DataManagerRouter.vue";
 import Register from "components/login/Register.vue";
 import ErrorStack from "components/admin/ErrorStack.vue";
 import DisplayApplications from "components/admin/DisplayApplications.vue";
+import Toolshed from "components/Toolshed/Index.vue";
 import Vue from "vue";
 
 export const getAdminRouter = (Galaxy, options) => {
-    let galaxyRoot = getAppRoot();
+    const galaxyRoot = getAppRoot();
 
     return Router.extend({
         routes: {
@@ -24,6 +26,7 @@ export const getAdminRouter = (Galaxy, options) => {
             "(/)admin(/)users(/)create": "show_users_create",
             "(/)admin(/)roles": "show_roles",
             "(/)admin(/)groups": "show_groups",
+            "(/)admin(/)toolshed": "show_toolshed",
             "(/)admin(/)error_stack": "show_error_stack",
             "(/)admin(/)display_applications": "show_display_applications",
             "(/)admin(/)tool_versions": "show_tool_versions",
@@ -33,12 +36,13 @@ export const getAdminRouter = (Galaxy, options) => {
             "(/)admin(/)form(/)(:form_id)": "show_form",
             "(/)admin/data_tables": "show_data_tables",
             "(/)admin/data_types": "show_data_types",
+            "(/)admin/jobs": "show_jobs",
             "(/)admin/data_manager*path": "show_data_manager",
             "*notFound": "not_found"
         },
 
         authenticate: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             return Galaxy.user && Galaxy.user.id && Galaxy.user.get("is_admin");
         },
 
@@ -57,15 +61,15 @@ export const getAdminRouter = (Galaxy, options) => {
         },
 
         show_users_create: function() {
-            let instance = Vue.extend(Register);
-            let vm = document.createElement("div");
+            const instance = Vue.extend(Register);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new instance({
                 propsData: {
                     redirect: "/admin/users",
                     registration_warning_message: options.config.registration_warning_message,
                     mailing_join_addr: options.config.mailing_join_addr,
-                    smtp_server: options.config.smtp_server
+                    server_mail_configured: options.config.server_mail_configured
                 }
             }).$mount(vm);
         },
@@ -82,6 +86,10 @@ export const getAdminRouter = (Galaxy, options) => {
             this._show_grid_view("admin_toolshed/browse_repositories");
         },
 
+        show_toolshed: function() {
+            this._display_vue_helper(Toolshed);
+        },
+
         show_tool_versions: function() {
             this._show_grid_view("admin/tool_versions_list");
         },
@@ -91,7 +99,7 @@ export const getAdminRouter = (Galaxy, options) => {
         },
 
         _show_grid_view: function(urlSuffix) {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             this.page.display(
                 new GridView({
                     url_base: `${galaxyRoot}${urlSuffix}`,
@@ -101,8 +109,8 @@ export const getAdminRouter = (Galaxy, options) => {
         },
 
         _display_vue_helper: function(component, props) {
-            let instance = Vue.extend(component);
-            let vm = document.createElement("div");
+            const instance = Vue.extend(component);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new instance(props).$mount(vm);
         },
@@ -115,6 +123,10 @@ export const getAdminRouter = (Galaxy, options) => {
             this._display_vue_helper(DataTypes);
         },
 
+        show_jobs: function() {
+            this._display_vue_helper(Jobs);
+        },
+
         show_error_stack: function() {
             this._display_vue_helper(ErrorStack);
         },
@@ -124,9 +136,9 @@ export const getAdminRouter = (Galaxy, options) => {
         },
 
         show_data_manager: function(path) {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             console.log("show_data_manager");
-            let vueMount = document.createElement("div");
+            const vueMount = document.createElement("div");
             this.page.display(vueMount);
             // always set the route back to the base, i.e.
             // `${galaxyRoot}admin/data_manager`
@@ -140,8 +152,8 @@ export const getAdminRouter = (Galaxy, options) => {
         },
 
         show_form: function(form_id) {
-            var id = `?id=${QueryStringParsing.get("id")}`;
-            var form_defs = {
+            const id = `?id=${QueryStringParsing.get("id")}`;
+            const form_defs = {
                 reset_user_password: {
                     title: _l("Reset passwords"),
                     url: `admin/reset_user_password${id}`,
diff --git a/client/galaxy/scripts/entry/admin/index.js b/client/galaxy/scripts/entry/admin/index.js
index 570e68aa356..7268210f20d 100644
--- a/client/galaxy/scripts/entry/admin/index.js
+++ b/client/galaxy/scripts/entry/admin/index.js
@@ -11,7 +11,7 @@ addInitialization((Galaxy, { options }) => {
         active_view: "admin"
     });
 
-    let pageOptions = Object.assign({}, options, {
+    const pageOptions = Object.assign({}, options, {
         Left: AdminPanel,
         Router: getAdminRouter(Galaxy, options)
     });
diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
index 3fc93a5cb39..ddc58f00e5a 100644
--- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js
@@ -38,6 +38,7 @@ import DatasetEditAttributes from "mvc/dataset/dataset-edit-attributes";
 import Citations from "components/Citations.vue";
 import DisplayStructure from "components/DisplayStructured.vue";
 import Vue from "vue";
+import { CloudAuth } from "components/User/CloudAuth";
 
 /** Routes */
 export const getAnalysisRouter = Galaxy =>
@@ -47,6 +48,7 @@ export const getAnalysisRouter = Galaxy =>
             "(/)root*": "home",
             "(/)tours(/)(:tour_id)": "show_tours",
             "(/)user(/)": "show_user",
+            "(/)user(/)cloud_auth": "show_cloud_auth",
             "(/)user(/)(:form_id)": "show_user_form",
             "(/)pages(/)create(/)": "show_pages_create",
             "(/)pages(/)edit(/)": "show_pages_edit",
@@ -75,18 +77,19 @@ export const getAnalysisRouter = Galaxy =>
             "(/)datasets/error": "show_dataset_error"
         },
 
-        require_login: ["show_user", "show_user_form", "show_workflows"],
+        require_login: ["show_user", "show_user_form", "show_workflows", "show_cloud_auth"],
 
         authenticate: function(args, name) {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             return (Galaxy.user && Galaxy.user.id) || this.require_login.indexOf(name) == -1;
         },
 
-        _display_vue_helper: function(component, props) {
-            let instance = Vue.extend(component);
-            let vm = document.createElement("div");
-            this.page.display(vm);
-            new instance(props).$mount(vm);
+        _display_vue_helper: function(component, props = {}) {
+            const instance = Vue.extend(component);
+            const container = document.createElement("div");
+            this.page.display(container);
+            const vm = new instance(props).$mount(container);
+            return vm;
         },
 
         show_tours: function(tour_id) {
@@ -102,15 +105,19 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_user_form: function(form_id) {
-            let Galaxy = getGalaxyInstance();
-            var model = new UserPreferences.Model({
+            const Galaxy = getGalaxyInstance();
+            const model = new UserPreferences.Model({
                 user_id: Galaxy.params.id
             });
             this.page.display(new FormWrapper.View(_.extend(model.get(form_id), { active_tab: "user" })));
         },
 
+        show_cloud_auth: function() {
+            this._display_vue_helper(CloudAuth);
+        },
+
         show_visualizations: function(action_id) {
-            var activeTab = action_id == "list_published" ? "shared" : "user";
+            const activeTab = action_id == "list_published" ? "shared" : "user";
             this.page.display(
                 new GridShared.View({
                     action_id: action_id,
@@ -132,8 +139,8 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_visualizations_sharing: function() {
-            var sharingInstance = Vue.extend(Sharing);
-            var vm = document.createElement("div");
+            const sharingInstance = Vue.extend(Sharing);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new sharingInstance({
                 propsData: {
@@ -145,7 +152,7 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_workflows_published: function() {
-            var userFilter = QueryStringParsing.get("f-username");
+            const userFilter = QueryStringParsing.get("f-username");
             this.page.display(
                 new GridView({
                     url_base: `${getAppRoot()}workflow/list_published`,
@@ -158,27 +165,27 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_history_view: function() {
-            var historyInstance = Vue.extend(HistoryView);
-            var vm = document.createElement("div");
+            const historyInstance = Vue.extend(HistoryView);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new historyInstance({ propsData: { id: QueryStringParsing.get("id") } }).$mount(vm);
         },
 
         show_history_structure: function() {
-            let displayStructureInstance = Vue.extend(DisplayStructure);
-            let vm = document.createElement("div");
+            const displayStructureInstance = Vue.extend(DisplayStructure);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new displayStructureInstance({ propsData: { id: QueryStringParsing.get(" id: ") } }).$mount(vm);
         },
 
         show_histories: function(action_id) {
-            let view = new HistoryList.View({ action_id: action_id });
+            const view = new HistoryList.View({ action_id: action_id });
             this.page.display(view);
         },
 
         show_history_citations: function() {
-            var citationInstance = Vue.extend(Citations);
-            var vm = document.createElement("div");
+            const citationInstance = Vue.extend(Citations);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new citationInstance({ propsData: { id: QueryStringParsing.get("id"), source: "histories" } }).$mount(vm);
         },
@@ -193,8 +200,8 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_histories_sharing: function() {
-            var sharingInstance = Vue.extend(Sharing);
-            var vm = document.createElement("div");
+            const sharingInstance = Vue.extend(Sharing);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new sharingInstance({
                 propsData: {
@@ -228,7 +235,7 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_pages: function(action_id) {
-            var activeTab = action_id == "list_published" ? "shared" : "user";
+            const activeTab = action_id == "list_published" ? "shared" : "user";
             this.page.display(
                 new GridShared.View({
                     action_id: action_id,
@@ -260,8 +267,8 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_pages_sharing: function() {
-            var sharingInstance = Vue.extend(Sharing);
-            var vm = document.createElement("div");
+            const sharingInstance = Vue.extend(Sharing);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new sharingInstance({
                 propsData: {
@@ -273,8 +280,8 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_plugins: function() {
-            var pluginListInstance = Vue.extend(PluginList);
-            var vm = document.createElement("div");
+            const pluginListInstance = Vue.extend(PluginList);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new pluginListInstance().$mount(vm);
         },
@@ -298,14 +305,14 @@ export const getAnalysisRouter = Galaxy =>
         },
 
         show_workflows_import: function() {
-            var workflowImportInstance = Vue.extend(WorkflowImport);
-            var vm = document.createElement("div");
+            const workflowImportInstance = Vue.extend(WorkflowImport);
+            const vm = document.createElement("div");
             this.page.display(vm);
             new workflowImportInstance().$mount(vm);
         },
 
         show_custom_builds: function() {
-            var historyPanel = this.page.historyPanel.historyView;
+            const historyPanel = this.page.historyPanel.historyView;
             if (!historyPanel || !historyPanel.model || !historyPanel.model.id) {
                 window.setTimeout(() => {
                     this.show_custom_builds();
@@ -375,8 +382,8 @@ export const getAnalysisRouter = Galaxy =>
                     this.page.display(new ToolFormComposite.View(_.extend(response, { active_tab: "workflow" })));
                 },
                 error: response => {
-                    var error_msg = response.err_msg || "Error occurred while loading the resource.";
-                    var options = {
+                    const error_msg = response.err_msg || "Error occurred while loading the resource.";
+                    const options = {
                         message: error_msg,
                         status: "danger",
                         persistent: true,
diff --git a/client/galaxy/scripts/entry/analysis/index.js b/client/galaxy/scripts/entry/analysis/index.js
index a36a61c5a07..1bac19b9eb1 100644
--- a/client/galaxy/scripts/entry/analysis/index.js
+++ b/client/galaxy/scripts/entry/analysis/index.js
@@ -7,7 +7,7 @@ import Page from "layout/page";
 addInitialization((Galaxy, { options = {} }) => {
     console.log("Analysis custom page setup");
 
-    let pageOptions = Object.assign({}, options, {
+    const pageOptions = Object.assign({}, options, {
         config: Object.assign({}, options.config, {
             hide_panels: Galaxy.params.hide_panels,
             hide_masthead: Galaxy.params.hide_masthead
diff --git a/client/galaxy/scripts/entry/login/index.js b/client/galaxy/scripts/entry/login/index.js
index 151c5567210..572acadfd05 100644
--- a/client/galaxy/scripts/entry/login/index.js
+++ b/client/galaxy/scripts/entry/login/index.js
@@ -7,10 +7,10 @@ import Vue from "vue";
 export function initLoginView(Galaxy, { options }) {
     console.log("initLoginView");
     Galaxy.page = new Page.View(options);
-    var vm = document.createElement("div");
+    const vm = document.createElement("div");
     Galaxy.display(vm);
-    var component = Galaxy.params.token || Galaxy.params.expired_user ? Password : Index;
-    var loginInstance = Vue.extend(component);
+    const component = Galaxy.params.token || Galaxy.params.expired_user ? Password : Index;
+    const loginInstance = Vue.extend(component);
     new loginInstance({ propsData: options }).$mount(vm);
 }
 
diff --git a/client/galaxy/scripts/entry/panels/admin-panel.js b/client/galaxy/scripts/entry/panels/admin-panel.js
index 35fa5c21a4a..a91e6703a8e 100644
--- a/client/galaxy/scripts/entry/panels/admin-panel.js
+++ b/client/galaxy/scripts/entry/panels/admin-panel.js
@@ -4,9 +4,8 @@ import Backbone from "backbone";
 import _l from "utils/localization";
 import { getGalaxyInstance } from "app";
 
-var AdminPanel = Backbone.View.extend({
+const AdminPanel = Backbone.View.extend({
     initialize: function(page, options) {
-        var self = this;
         this.page = page;
         this.root = options.root;
         this.config = options.config;
@@ -39,6 +38,7 @@ var AdminPanel = Backbone.View.extend({
                     {
                         title: _l("Manage jobs"),
                         url: "admin/jobs",
+                        target: "__use_router__",
                         id: "admin-link-jobs"
                     },
                     {
@@ -62,7 +62,7 @@ var AdminPanel = Backbone.View.extend({
                         title: _l("Quotas"),
                         url: "admin/quotas",
                         target: "__use_router__",
-                        enabled: self.config.enable_quotas,
+                        enabled: this.config.enable_quotas,
                         id: "admin-link-quotas"
                     },
                     {
@@ -88,25 +88,26 @@ var AdminPanel = Backbone.View.extend({
                 title: _l("Tool Management"),
                 items: [
                     {
-                        title: "Install new tools",
-                        url: "admin_toolshed/browse_toolsheds",
-                        enabled: self.settings.is_tool_shed_installed
+                        title: _l("Install or Uninstall"),
+                        url: "admin/toolshed",
+                        target: "__use_router__",
+                        enabled: this.settings.is_tool_shed_installed
                     },
                     {
                         title: _l("Monitor installation"),
                         url: "admin_toolshed/monitor_repository_installation",
-                        enabled: self.settings.installing_repository_ids
+                        enabled: this.settings.installing_repository_ids
                     },
                     {
                         title: _l("Manage tools"),
                         url: "admin/repositories",
-                        enabled: self.settings.is_repo_installed,
+                        enabled: this.settings.is_repo_installed,
                         target: "__use_router__"
                     },
                     {
                         title: _l("Manage metadata"),
                         url: "admin_toolshed/reset_metadata_on_selected_installed_repositories",
-                        enabled: self.settings.is_repo_installed
+                        enabled: this.settings.is_repo_installed
                     },
                     {
                         title: _l("Manage whitelist"),
@@ -137,15 +138,14 @@ var AdminPanel = Backbone.View.extend({
     },
 
     render: function() {
-        var self = this;
         this.$el.empty();
         this.categories.each(category => {
-            var $section = $(self._templateSection(category.attributes));
-            var $entries = $section.find(".toolSectionBody");
+            const $section = $(this._templateSection(category.attributes));
+            const $entries = $section.find(".toolSectionBody");
             _.each(category.get("items"), item => {
                 if (item.enabled === undefined || item.enabled) {
-                    var $link = $("<a/>")
-                        .attr({ href: self.root + item.url })
+                    const $link = $("<a/>")
+                        .attr({ href: this.root + item.url })
                         .text(_l(item.title));
                     if (item.id) {
                         $link.attr("id", item.id);
@@ -153,7 +153,7 @@ var AdminPanel = Backbone.View.extend({
                     if (item.target == "__use_router__") {
                         $link.on("click", e => {
                             e.preventDefault();
-                            self.page.router.push(item.url);
+                            this.page.router.push(item.url);
                         });
                     } else {
                         $link.attr("target", "galaxy_main");
@@ -165,7 +165,7 @@ var AdminPanel = Backbone.View.extend({
                     );
                 }
             });
-            self.$el.append($section);
+            this.$el.append($section);
         });
     },
 
diff --git a/client/galaxy/scripts/entry/panels/history-panel.js b/client/galaxy/scripts/entry/panels/history-panel.js
index ac15e5b3c4d..95919e3cbc6 100644
--- a/client/galaxy/scripts/entry/panels/history-panel.js
+++ b/client/galaxy/scripts/entry/panels/history-panel.js
@@ -6,7 +6,7 @@ import historyOptionsMenu from "mvc/history/options-menu";
 import CurrentHistoryView from "mvc/history/history-view-edit-current";
 
 /** the right hand panel in the analysis page that shows the current history */
-var HistoryPanel = Backbone.View.extend({
+const HistoryPanel = Backbone.View.extend({
     initialize: function(page, options) {
         const Galaxy = getGalaxyInstance();
         const panelHeaderButtons = [];
@@ -38,7 +38,7 @@ var HistoryPanel = Backbone.View.extend({
         });
         panelHeaderButtons.push(this.buttonRefresh);
 
-        if (!this.userIsAnonymous){
+        if (!this.userIsAnonymous) {
             this.buttonNew = new Ui.ButtonLink({
                 id: "history-new-button",
                 title: _l("Create new history"),
diff --git a/client/galaxy/scripts/entry/panels/tool-panel.js b/client/galaxy/scripts/entry/panels/tool-panel.js
index 49b36eb9414..d3c134a77d0 100644
--- a/client/galaxy/scripts/entry/panels/tool-panel.js
+++ b/client/galaxy/scripts/entry/panels/tool-panel.js
@@ -9,23 +9,23 @@ import { getGalaxyInstance } from "app";
 import { getAppRoot } from "onload";
 import Buttons from "mvc/ui/ui-buttons";
 
-var ToolPanel = Backbone.View.extend({
+const ToolPanel = Backbone.View.extend({
     initialize: function(page, options) {
-        let Galaxy = getGalaxyInstance();
-        let appRoot = getAppRoot();
+        const Galaxy = getGalaxyInstance();
+        const appRoot = getAppRoot();
 
         // access configuration options
-        var config = options.config;
+        const config = options.config;
         this.root = options.root;
 
         /** @type {Object[]} descriptions of user's workflows to be shown in the tool menu */
         this.stored_workflow_menu_entries = config.stored_workflow_menu_entries || [];
 
         // create tool search, tool panel, and tool panel view.
-        var tool_search = new Tools.ToolSearch({
+        const tool_search = new Tools.ToolSearch({
             hidden: false
         });
-        var tools = new Tools.ToolCollection(config.toolbox);
+        const tools = new Tools.ToolCollection(config.toolbox);
         this.tool_panel = new Tools.ToolPanel({
             tool_search: tool_search,
             tools: tools,
@@ -43,26 +43,29 @@ var ToolPanel = Backbone.View.extend({
             default_genome: config.default_genome,
             default_extension: config.default_extension
         });
+        const panel_buttons = [this.upload_button];
 
         // add favorite filter button
-        this.favorite_button = new Buttons.ButtonLink({
-            cls: "panel-header-button",
-            title: _l("Show favorites"),
-            icon: "fa fa-star-o",
-            onclick: e => {
-                $("#tool-search-query")
-                    .val("#favorites")
-                    .trigger("change");
-            }
-        });
-
+        if (Galaxy.user && Galaxy.user.id) {
+            this.favorite_button = new Buttons.ButtonLink({
+                cls: "panel-header-button",
+                title: _l("Show favorites"),
+                icon: "fa fa-star-o",
+                onclick: e => {
+                    $("#tool-search-query")
+                        .val("#favorites")
+                        .trigger("change");
+                }
+            });
+            panel_buttons.push(this.favorite_button);
+        }
         // add uploader button to Galaxy object
         Galaxy.upload = this.upload_button;
 
         // components for panel definition
         this.model = new Backbone.Model({
             title: _l("Tools"),
-            buttons: [this.upload_button, this.favorite_button]
+            buttons: panel_buttons
         });
 
         // build body template
@@ -71,22 +74,21 @@ var ToolPanel = Backbone.View.extend({
 
     render: function() {
         // if there are tools, render panel and display everything
-        var self = this;
         if (this.tool_panel.get("layout").size() > 0) {
             this.$el.find(".toolMenu").replaceWith(this.tool_panel_view.$el);
             this.tool_panel_view.render();
         }
         // build the dom for the workflow portion of the tool menu
         // add internal workflow list
-        self.$("#internal-workflows").append(
-            self._templateAllWorkflow({
+        this.$("#internal-workflows").append(
+            this._templateAllWorkflow({
                 title: _l("All workflows"),
                 href: "workflows/list"
             })
         );
         _.each(this.stored_workflow_menu_entries, menu_entry => {
-            self.$("#internal-workflows").append(
-                self._templateWorkflowLink({
+            this.$("#internal-workflows").append(
+                this._templateWorkflowLink({
                     title: menu_entry.stored_workflow.name,
                     href: `workflows/run?id=${menu_entry.encoded_stored_workflow_id}`
                 })
@@ -96,7 +98,7 @@ var ToolPanel = Backbone.View.extend({
 
     /** build a link to one tool */
     _templateTool: function(tool) {
-        let appRoot = getAppRoot();
+        const appRoot = getAppRoot();
         return `<div class="toolTitle">
                     <a href="${appRoot}${tool.href}" target="galaxy_main">
                         ${tool.title}
@@ -106,7 +108,7 @@ var ToolPanel = Backbone.View.extend({
 
     /** build a link to 'All Workflows' */
     _templateAllWorkflow: function(tool) {
-        let appRoot = getAppRoot();
+        const appRoot = getAppRoot();
         return `<div class="toolTitle">
                     <a href="${appRoot}${tool.href}">
                         ${tool.title}
@@ -116,7 +118,7 @@ var ToolPanel = Backbone.View.extend({
 
     /** build links to workflows in toolpanel */
     _templateWorkflowLink: function(wf) {
-        let appRoot = getAppRoot();
+        const appRoot = getAppRoot();
         return `<div class="toolTitle">
                     <a class="${wf.cls}" href="${appRoot}${wf.href}">
                         ${_.escape(wf.title)}
diff --git a/client/galaxy/scripts/galaxy.interactive_environments.js b/client/galaxy/scripts/galaxy.interactive_environments.js
index 6ae025c5bb7..3f371508b09 100644
--- a/client/galaxy/scripts/galaxy.interactive_environments.js
+++ b/client/galaxy/scripts/galaxy.interactive_environments.js
@@ -1,6 +1,6 @@
-/* global $ */
-/* global toastr */
-// TODO: this file is transpiled and used directly without bundling; fix imports when that is no longer the case.
+import $ from "jquery";
+import { Toast } from "ui/toast";
+
 /**
  * Internal function to remove content from the main area and add the notebook.
  * Not idempotent
@@ -35,7 +35,7 @@ export function make_spin_state(
     sleep_step,
     log_attempts
 ) {
-    var s = {
+    return {
         type: typeof type !== "undefined" ? type : "GIE spin",
         ajax_timeout: typeof ajax_timeout_init !== "undefined" ? ajax_timeout_init : 2000,
         ajax_timeout_max: typeof ajax_timeout_max !== "undefined" ? ajax_timeout_max : 16000,
@@ -46,7 +46,6 @@ export function make_spin_state(
         log_attempts: typeof log_attempts !== "undefined" ? log_attempts : true,
         count: 0
     };
-    return s;
 }
 
 /* Log/display an error when spinning fails. */
@@ -54,8 +53,8 @@ export function spin_error(console_msg, user_msg, clear) {
     console.log(console_msg);
     if (clear) clear_main_area();
     if (typeof user_msg == "string") {
-        toastr.clear();
-        toastr.error(user_msg, "Error", {
+        Toast.clear();
+        Toast.error(user_msg, "Error", {
             closeButton: true,
             timeOut: 0,
             extendedTimeOut: 0,
@@ -112,7 +111,7 @@ export function spin(url, bool_response, success_callback, timeout_callback, err
                 }
             }
         };
-        if (bool_response) ajax_params["dataType"] = "json";
+        if (bool_response) ajax_params.dataType = "json";
         $.ajax(ajax_params);
     };
     console.log(`Setting up new spinner for ${spin_state.type} on ${url}`);
@@ -131,7 +130,7 @@ function spin_until(url, bool_response, messages, success_callback, spin_state)
     var message_once = (message, spin_state) => {
         if (spin_state.count == 1) {
             display_spinner();
-            toastr.info(message, null, {
+            Toast.info(message, null, {
                 closeButton: true,
                 timeOut: 0,
                 extendedTimeOut: 0,
@@ -141,22 +140,22 @@ function spin_until(url, bool_response, messages, success_callback, spin_state)
     };
     var wrapped_success = data => {
         if (!bool_response || (bool_response && data == true)) {
-            console.log(messages["success"]);
+            console.log(messages.success);
             clear_main_area();
-            toastr.clear();
+            Toast.clear();
             success_callback();
         } else if (bool_response && data == false) {
-            message_once(messages["not_ready"], spin_state);
+            message_once(messages.not_ready, spin_state);
             return false; // keep spinning
         } else {
-            spin_error(`Invalid response to ${spin_state.type} request`, messages["invalid_response"], true);
+            spin_error(`Invalid response to ${spin_state.type} request`, messages.invalid_response, true);
         }
         return true; // stop spinning
     };
     var timeout_error = (jqxhr, status, error) => {
-        message_once(messages["waiting"], spin_state);
+        message_once(messages.waiting, spin_state);
         if (spin_state.count == warn_at) {
-            toastr.warning(messages["wait_warn"], "Warning", {
+            Toast.warning(messages.wait_warn, "Warning", {
                 closeButton: true,
                 timeOut: 0,
                 extendedTimeOut: 0,
@@ -235,7 +234,7 @@ export function keepAlive(notebookAccessURL) {
                 if (request_count > 30) {
                     window.clearInterval(interval);
                     clear_main_area();
-                    toastr.error("Could not connect to IE, contact your administrator", "Error", {
+                    Toast.error("Could not connect to IE, contact your administrator", "Error", {
                         closeButton: true,
                         timeOut: 20000,
                         tapToDismiss: false
@@ -245,3 +244,15 @@ export function keepAlive(notebookAccessURL) {
         });
     }, 10000);
 }
+
+export default {
+    append_notebook,
+    clear_main_area,
+    display_spinner,
+    make_spin_state,
+    spin_error,
+    spin,
+    test_ie_availability,
+    load_when_ready,
+    keepAlive
+};
diff --git a/client/galaxy/scripts/galaxy.library.js b/client/galaxy/scripts/galaxy.library.js
index 3cf8fb8f63c..d1d9a9672b7 100644
--- a/client/galaxy/scripts/galaxy.library.js
+++ b/client/galaxy/scripts/galaxy.library.js
@@ -110,7 +110,7 @@ var GalaxyLibrary = Backbone.View.extend({
 
     initialize: function() {
         // This should go upstream in the js app once available
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (Galaxy.config.ga_code) {
             ((i, s, o, g, r, a, m) => {
                 i["GoogleAnalyticsObject"] = r;
diff --git a/client/galaxy/scripts/galaxy.pages.js b/client/galaxy/scripts/galaxy.pages.js
index d2f2d2888c2..fd31483c8cc 100644
--- a/client/galaxy/scripts/galaxy.pages.js
+++ b/client/galaxy/scripts/galaxy.pages.js
@@ -1,681 +1,31 @@
 import $ from "jquery";
-import _l from "utils/localization";
+import axios from "axios";
+import { Toast } from "ui/toast";
+import { getAppRoot } from "onload/loadConfig";
+import { PageEditor } from "components/PageEditor";
+import Vue from "vue";
 
-import GridView from "mvc/grid/grid-view";
-import { show_modal, hide_modal } from "layout/modal";
-import { make_popupmenu } from "ui/popupmenu";
-import { getGalaxyInstance } from "app";
-import { buildConfig } from "utils/genericConfig";
-
-// Built a generic config container for the properties that
-// are passed in from python then used (formerly) globally
-const configs = buildConfig();
-
-// Turn these window variables into config props list_objects_url,
-// set_accessible_url, get_name_and_link_url, editor_base_path,
-// iframe_base_path, save_url, page_id, page_list_url
-function setPageConfigs(incoming = {}) {
-    return Object.assign(configs, incoming);
-}
-
-var WYMeditor = window.WYMeditor;
-
-var CONTROLS = {
-    // Item types.
-    ITEM_HISTORY: "item_history",
-    ITEM_DATASET: "item_dataset",
-    ITEM_WORKFLOW: "item_workflow",
-    ITEM_PAGE: "item_page",
-    ITEM_VISUALIZATION: "item_visualization",
-
-    // Link dialogs.
-    DIALOG_HISTORY_LINK: "link_history",
-    DIALOG_DATASET_LINK: "link_dataset",
-    DIALOG_WORKFLOW_LINK: "link_workflow",
-    DIALOG_PAGE_LINK: "link_page",
-    DIALOG_VISUALIZATION_LINK: "link_visualization",
-
-    // Embed dialogs.
-    DIALOG_EMBED_HISTORY: "embed_history",
-    DIALOG_EMBED_DATASET: "embed_dataset",
-    DIALOG_EMBED_WORKFLOW: "embed_workflow",
-    DIALOG_EMBED_PAGE: "embed_page",
-    DIALOG_EMBED_VISUALIZATION: "embed_visualization"
-};
-
-// Based on the dialog type, return a dictionary of information about an item
-function get_item_info(dialog_type) {
-    var item_singular;
-    var item_plural;
-    var item_controller;
-    var item_class;
-    switch (dialog_type) {
-        case CONTROLS.ITEM_HISTORY:
-            item_singular = "History";
-            item_plural = "Histories";
-            item_controller = "history";
-            item_class = "History";
-            break;
-        case CONTROLS.ITEM_DATASET:
-            item_singular = "Dataset";
-            item_plural = "Datasets";
-            item_controller = "dataset";
-            item_class = "HistoryDatasetAssociation";
-            break;
-        case CONTROLS.ITEM_WORKFLOW:
-            item_singular = "Workflow";
-            item_plural = "Workflows";
-            item_controller = "workflow";
-            item_class = "StoredWorkflow";
-            break;
-        case CONTROLS.ITEM_PAGE:
-            item_singular = "Page";
-            item_plural = "Pages";
-            item_controller = "page";
-            item_class = "Page";
-            break;
-        case CONTROLS.ITEM_VISUALIZATION:
-            item_singular = "Visualization";
-            item_plural = "Visualizations";
-            item_controller = "visualization";
-            item_class = "Visualization";
-            break;
-    }
-
-    // Build ajax URL that lists items for selection.
-    var item_list_action = `list_${item_plural.toLowerCase()}_for_selection`;
-    var ajax_url = configs.list_objects_url.replace("LIST_ACTION", item_list_action);
-
-    // Set up and return dict.
-    return {
-        singular: item_singular,
-        plural: item_plural,
-        controller: item_controller,
-        iclass: item_class,
-        list_ajax_url: ajax_url
-    };
-}
-
-// Make an item importable.
-function make_item_importable(item_controller, item_id, item_type) {
-    var ajax_url = configs.set_accessible_url.replace("ITEM_CONTROLLER", item_controller);
-    $.ajax({
-        type: "POST",
-        url: ajax_url,
-        data: { id: item_id, accessible: "True" },
-        error: function() {
-            alert(`Making ${item_type} accessible failed`);
-        }
-    });
-}
-
-// Completely replace WYM's dialog handling
-WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtml) {
-    var wym = this;
-    var sStamp = wym.uniqueStamp();
-    var selected = wym.selected();
-
-    // Swap out URL attribute for id/name attribute in link creation to enable anchor creation in page.
-    function set_link_id() {
-        // When "set link id" link clicked, update UI.
-        $("#set_link_id").click(function() {
-            // Set label.
-            $("#link_attribute_label").text("ID/Name");
-
-            // Set input elt class, value.
-            var attribute_input = $(".wym_href");
-            attribute_input.addClass("wym_id").removeClass("wym_href");
-            if (selected) attribute_input.val($(selected).attr("id"));
-
-            // Remove link.
-            $(this).remove();
-        });
-    }
-
-    // LINK DIALOG
-    if (dialogType == WYMeditor.DIALOG_LINK) {
-        if (selected) {
-            $(wym._options.hrefSelector).val($(selected).attr(WYMeditor.HREF));
-            $(wym._options.srcSelector).val($(selected).attr(WYMeditor.SRC));
-            $(wym._options.titleSelector).val($(selected).attr(WYMeditor.TITLE));
-            $(wym._options.altSelector).val($(selected).attr(WYMeditor.ALT));
-        }
-
-        // Get current URL, title.
-        var curURL;
-
-        var curTitle;
-        if (selected) {
-            curURL = $(selected).attr("href");
-            if (curURL == undefined) curURL = "";
-            curTitle = $(selected).attr("title");
-            if (curTitle == undefined) curTitle = "";
-        }
-        show_modal(
-            "Create Link",
-            `<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='${curURL}' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='${curTitle}' size='40' /></div><div>`,
-            {
-                "Make link": function() {
-                    // Get URL, name/title.
-                    var sUrl = $(wym._options.hrefSelector).val() || "";
-
-                    var sId = $(".wym_id").val() || "";
-                    var sName = $(wym._options.titleSelector).val() || "";
-
-                    if (sUrl || sId) {
-                        // Create link.
-                        wym._exec(WYMeditor.CREATE_LINK, sStamp);
-
-                        // Set link attributes.
-                        var link = $(`a[href=${sStamp}]`, wym._doc.body);
-                        link.attr(WYMeditor.HREF, sUrl)
-                            .attr(WYMeditor.TITLE, sName)
-                            .attr("id", sId);
-
-                        // If link's text is default (wym-...), change it to the title.
-                        if (link.text().indexOf("wym-") === 0) {
-                            link.text(sName);
-                        }
-                    }
-                    hide_modal();
-                },
-                Cancel: function() {
-                    hide_modal();
-                }
-            },
-            {},
-            set_link_id
-        );
-    }
-
-    // IMAGE DIALOG
-    if (dialogType == WYMeditor.DIALOG_IMAGE) {
-        if (wym._selected_image) {
-            $(`${wym._options.dialogImageSelector} ${wym._options.srcSelector}`).val(
-                $(wym._selected_image).attr(WYMeditor.SRC)
-            );
-            $(`${wym._options.dialogImageSelector} ${wym._options.titleSelector}`).val(
-                $(wym._selected_image).attr(WYMeditor.TITLE)
-            );
-            $(`${wym._options.dialogImageSelector} ${wym._options.altSelector}`).val(
-                $(wym._selected_image).attr(WYMeditor.ALT)
-            );
-        }
-        show_modal(
-            "Image",
-            "<div class='row'>" +
-                "<label>URL</label><br>" +
-                "<input type='text' class='wym_src' value='' size='40' />" +
-                "</div>" +
-                "<div class='row'>" +
-                "<label>Alt text</label><br>" +
-                "<input type='text' class='wym_alt' value='' size='40' />" +
-                "</div>" +
-                "<div class='row'>" +
-                "<label>Title</label><br>" +
-                "<input type='text' class='wym_title' value='' size='40' />" +
-                "</div>",
-            {
-                Insert: function() {
-                    var sUrl = $(wym._options.srcSelector).val();
-                    if (sUrl.length > 0) {
-                        wym._exec(WYMeditor.INSERT_IMAGE, sStamp);
-                        $(`img[src$=${sStamp}]`, wym._doc.body)
-                            .attr(WYMeditor.SRC, sUrl)
-                            .attr(WYMeditor.TITLE, $(wym._options.titleSelector).val())
-                            .attr(WYMeditor.ALT, $(wym._options.altSelector).val());
-                    }
-                    hide_modal();
-                },
-                Cancel: function() {
-                    hide_modal();
-                }
-            }
-        );
-        return;
-    }
-
-    // TABLE DIALOG
-    if (dialogType == WYMeditor.DIALOG_TABLE) {
-        show_modal(
-            "Table",
-            "<div class='row'>" +
-                "<label>Caption</label><br>" +
-                "<input type='text' class='wym_caption' value='' size='40' />" +
-                "</div>" +
-                "<div class='row'>" +
-                "<label>Summary</label><br>" +
-                "<input type='text' class='wym_summary' value='' size='40' />" +
-                "</div>" +
-                "<div class='row'>" +
-                "<label>Number Of Rows<br></label>" +
-                "<input type='text' class='wym_rows' value='3' size='3' />" +
-                "</div>" +
-                "<div class='row'>" +
-                "<label>Number Of Cols<br></label>" +
-                "<input type='text' class='wym_cols' value='2' size='3' />" +
-                "</div>",
-            {
-                Insert: function() {
-                    var iRows = $(wym._options.rowsSelector).val();
-                    var iCols = $(wym._options.colsSelector).val();
-
-                    if (iRows > 0 && iCols > 0) {
-                        var table = wym._doc.createElement(WYMeditor.TABLE);
-                        var newRow = null;
-
-                        var sCaption = $(wym._options.captionSelector).val();
-
-                        //we create the caption
-                        var newCaption = table.createCaption();
-                        newCaption.innerHTML = sCaption;
-
-                        //we create the rows and cells
-                        for (var x = 0; x < iRows; x++) {
-                            newRow = table.insertRow(x);
-                            for (var y = 0; y < iCols; y++) {
-                                newRow.insertCell(y);
-                            }
-                        }
-
-                        //set the summary attr
-                        $(table).attr("summary", $(wym._options.summarySelector).val());
-
-                        //append the table after the selected container
-                        var node = $(wym.findUp(wym.container(), WYMeditor.MAIN_CONTAINERS)).get(0);
-                        if (!node || !node.parentNode) $(wym._doc.body).append(table);
-                        else $(node).after(table);
-                    }
-                    hide_modal();
+export default function pagesEditorOnload() {
+    const pageId = $("#page-editor-content").attr("page_id");
+    axios
+        .get(`${getAppRoot()}api/pages/${pageId}`)
+        .then(response => {
+            const pageEditorInstance = Vue.extend(PageEditor);
+            new pageEditorInstance({
+                propsData: {
+                    pageId: pageId,
+                    content: response.data.content,
+                    title: response.data.title
                 },
-                Cancel: function() {
-                    hide_modal();
-                }
+                el: "#page-editor-content"
+            });
+        })
+        .catch(e => {
+            const response = e.response;
+            if (typeof response.responseJSON !== "undefined") {
+                Toast.error(response.responseJSON.err_msg);
+            } else {
+                Toast.error("An error occurred.");
             }
-        );
-    }
-
-    // INSERT "GALAXY ITEM" LINK DIALOG
-    if (
-        dialogType == CONTROLS.DIALOG_HISTORY_LINK ||
-        dialogType == CONTROLS.DIALOG_DATASET_LINK ||
-        dialogType == CONTROLS.DIALOG_WORKFLOW_LINK ||
-        dialogType == CONTROLS.DIALOG_PAGE_LINK ||
-        dialogType == CONTROLS.DIALOG_VISUALIZATION_LINK
-    ) {
-        // Based on item type, set useful vars.
-        var item_info;
-        switch (dialogType) {
-            case CONTROLS.DIALOG_HISTORY_LINK:
-                item_info = get_item_info(CONTROLS.ITEM_HISTORY);
-                break;
-            case CONTROLS.DIALOG_DATASET_LINK:
-                item_info = get_item_info(CONTROLS.ITEM_DATASET);
-                break;
-            case CONTROLS.DIALOG_WORKFLOW_LINK:
-                item_info = get_item_info(CONTROLS.ITEM_WORKFLOW);
-                break;
-            case CONTROLS.DIALOG_PAGE_LINK:
-                item_info = get_item_info(CONTROLS.ITEM_PAGE);
-                break;
-            case CONTROLS.DIALOG_VISUALIZATION_LINK:
-                item_info = get_item_info(CONTROLS.ITEM_VISUALIZATION);
-                break;
-        }
-
-        var grid = new GridView({
-            url_base: item_info.list_ajax_url,
-            embedded: true
-        });
-        let Galaxy = getGalaxyInstance();
-        Galaxy.modal.show({
-            title: `Insert Link to ${item_info.singular}`,
-            body: $("<div/>")
-                .append(grid.$el)
-                .append(
-                    $("<div/>")
-                        .append('<input id="make-importable" type="checkbox" checked/>')
-                        .append(
-                            `Make the selected ${item_info.plural.toLowerCase()} accessible so that they can viewed by everyone.`
-                        )
-                ),
-            closing_events: true,
-            buttons: {
-                Insert: function() {
-                    // Make selected items accessible (importable) ?
-                    var make_importable = false;
-                    if ($("#make-importable:checked").val() != null) make_importable = true;
-
-                    // Insert links to history for each checked item.
-                    grid.$("input[name=id]:checked").each(function() {
-                        var item_id = $(this).val();
-
-                        // Make item importable?
-                        if (make_importable) make_item_importable(item_info.controller, item_id, item_info.singular);
-
-                        // Insert link(s) to item(s). This is done by getting item info and then manipulating wym.
-                        var url_template = configs.get_name_and_link_url + item_id;
-                        var ajax_url = url_template.replace("ITEM_CONTROLLER", item_info.controller);
-                        $.getJSON(ajax_url, returned_item_info => {
-                            // Get link text.
-                            wym._exec(WYMeditor.CREATE_LINK, sStamp);
-                            var link_text = $(`a[href=${sStamp}]`, wym._doc.body).text();
-
-                            // Insert link: need to do different actions depending on link text.
-                            if (
-                                link_text == "" || // Firefox.
-                                link_text == sStamp // Safari
-                            ) {
-                                // User selected no text; create link from scratch and use default text.
-                                wym.insert(
-                                    `<a href='${returned_item_info.link}'>${item_info.singular} '${
-                                        returned_item_info.name
-                                    }'</a>`
-                                );
-                            } else {
-                                // Link created from selected text; add href and title.
-                                $(`a[href=${sStamp}]`, wym._doc.body)
-                                    .attr(WYMeditor.HREF, returned_item_info.link)
-                                    .attr(WYMeditor.TITLE, item_info.singular + item_id);
-                            }
-                        });
-                    });
-                    Galaxy.modal.hide();
-                },
-                Close: function() {
-                    Galaxy.modal.hide();
-                }
-            }
-        });
-    }
-    // EMBED GALAXY OBJECT DIALOGS
-    if (
-        dialogType == CONTROLS.DIALOG_EMBED_HISTORY ||
-        dialogType == CONTROLS.DIALOG_EMBED_DATASET ||
-        dialogType == CONTROLS.DIALOG_EMBED_WORKFLOW ||
-        dialogType == CONTROLS.DIALOG_EMBED_PAGE ||
-        dialogType == CONTROLS.DIALOG_EMBED_VISUALIZATION
-    ) {
-        // Based on item type, set useful vars.
-        let item_info;
-        switch (dialogType) {
-            case CONTROLS.DIALOG_EMBED_HISTORY:
-                item_info = get_item_info(CONTROLS.ITEM_HISTORY);
-                break;
-            case CONTROLS.DIALOG_EMBED_DATASET:
-                item_info = get_item_info(CONTROLS.ITEM_DATASET);
-                break;
-            case CONTROLS.DIALOG_EMBED_WORKFLOW:
-                item_info = get_item_info(CONTROLS.ITEM_WORKFLOW);
-                break;
-            case CONTROLS.DIALOG_EMBED_PAGE:
-                item_info = get_item_info(CONTROLS.ITEM_PAGE);
-                break;
-            case CONTROLS.DIALOG_EMBED_VISUALIZATION:
-                item_info = get_item_info(CONTROLS.ITEM_VISUALIZATION);
-                break;
-        }
-
-        let grid = new GridView({
-            url_base: item_info.list_ajax_url,
-            embedded: true
         });
-        let Galaxy = getGalaxyInstance();
-        Galaxy.modal.show({
-            title: `Insert Link to ${item_info.singular}`,
-            body: $("<div/>")
-                .append(grid.$el)
-                .append(
-                    $("<div/>")
-                        .append('<input id="make-importable" type="checkbox" checked/>')
-                        .append(
-                            `Make the selected ${item_info.plural.toLowerCase()} accessible so that they can viewed by everyone.`
-                        )
-                ),
-            closing_events: true,
-            buttons: {
-                Embed: function() {
-                    // Make selected items accessible (importable) ?
-                    var make_importable = false;
-                    if ($("#make-importable:checked").val() != null) make_importable = true;
-
-                    grid.$("input[name=id]:checked").each(function() {
-                        var elt = $(this);
-                        // Get item ID and name.
-                        var item_id = elt.val();
-                        // Use ':first' because there are many labels in table; the first one is the item name.
-                        var item_name = elt
-                            .closest("td")
-                            .next("td")
-                            .find("label")
-                            .text();
-
-                        if (make_importable) make_item_importable(item_info.controller, item_id, item_info.singular);
-
-                        // Embedded item HTML; item class is embedded in div container classes; this is necessary because the editor strips
-                        // all non-standard attributes when it returns its content (e.g. it will not return an element attribute of the form
-                        // item_class='History').
-                        var item_elt_id = `${item_info.iclass}-${item_id}`;
-                        var item_embed_html = [
-                            "<div id='",
-                            item_elt_id,
-                            "' class='embedded-item ",
-                            item_info.singular.toLowerCase(),
-                            " placeholder'>",
-                            "<p class='title'>",
-                            "Embedded Galaxy ",
-                            item_info.singular,
-                            " '",
-                            item_name,
-                            "'",
-                            "</p>",
-                            "<p class='content'>",
-                            "[Do not edit this block; Galaxy will fill it in with the annotated ",
-                            item_info.singular.toLowerCase(),
-                            " when it is displayed.]",
-                            "</p>",
-                            "</div>"
-                        ].join("");
-
-                        // Insert embedded item into document.
-                        wym.insert(item_embed_html);
-                    });
-                    Galaxy.modal.hide();
-                },
-                Close: function() {
-                    Galaxy.modal.hide();
-                }
-            }
-        });
-    }
-};
-
-export default function pagesEditorOnload(renderedConfigs = {}) {
-    setPageConfigs(renderedConfigs);
-
-    // Generic error handling
-    $(document).ajaxError((e, x) => {
-        // console.log( e, x );
-        var message = x.responseText || x.statusText || "Could not connect to server";
-        show_modal("Server error", message, { "Ignore error": hide_modal });
-        return false;
-    });
-    // Create editor
-    $("[name=page_content]").wymeditor({
-        skin: "galaxy",
-        basePath: configs.editor_base_path,
-        iframeBasePath: configs.iframe_base_path,
-        // + WYMeditor.HTML
-        boxHtml: `<table class='wym_box' width='100%' height='100%'><tr><td><div class='wym_area_top'>${
-            WYMeditor.TOOLS
-        }</div></td></tr><tr height='100%'><td><div class='wym_area_main' style='height: 100%;'>${
-            // + WYMeditor.HTML
-            WYMeditor.IFRAME
-        }${WYMeditor.STATUS}</div></div></td></tr></table>`,
-        toolsItems: [
-            { name: "Bold", title: "Strong", css: "wym_tools_strong" },
-            { name: "Italic", title: "Emphasis", css: "wym_tools_emphasis" },
-            {
-                name: "Superscript",
-                title: _l("Superscript"),
-                css: "wym_tools_superscript"
-            },
-            {
-                name: "Subscript",
-                title: _l("Subscript"),
-                css: "wym_tools_subscript"
-            },
-            {
-                name: "InsertOrderedList",
-                title: "Ordered_List",
-                css: "wym_tools_ordered_list"
-            },
-            {
-                name: "InsertUnorderedList",
-                title: "Unordered_List",
-                css: "wym_tools_unordered_list"
-            },
-            { name: "Indent", title: "Indent", css: "wym_tools_indent" },
-            { name: "Outdent", title: "Outdent", css: "wym_tools_outdent" },
-            { name: "Undo", title: "Undo", css: "wym_tools_undo" },
-            { name: "Redo", title: "Redo", css: "wym_tools_redo" },
-            { name: "CreateLink", title: "Link", css: "wym_tools_link" },
-            { name: "Unlink", title: "Unlink", css: "wym_tools_unlink" },
-            { name: "InsertImage", title: "Image", css: "wym_tools_image" },
-            { name: "InsertTable", title: "Table", css: "wym_tools_table" }
-        ]
-    });
-    // Get the editor object
-    var editor = $.wymeditors(0);
-    var save = callback => {
-        show_modal("Saving page", "progress");
-
-        // Do save.
-        $.ajax({
-            url: configs.save_url,
-            type: "POST",
-            data: {
-                id: configs.page_id,
-                content: editor.xhtml(),
-                annotations: JSON.stringify({}),
-                // annotations: JSON.stringify(annotations),
-                _: "true"
-            },
-            success: function() {
-                callback();
-            }
-        });
-    };
-    // Save button
-    $("#save-button").click(() => {
-        save(() => {
-            hide_modal();
-        });
-    });
-    // Close button
-    $("#close-button").click(() => {
-        // var new_content = editor.xhtml();
-        // var changed = ( initial_content != new_content );
-        var changed = false;
-        if (changed) {
-            var do_close = () => {
-                window.onbeforeunload = undefined;
-                window.document.location = configs.page_list_url;
-            };
-            show_modal(
-                "Close editor",
-                "There are unsaved changes to your page which will be lost.",
-                {
-                    Cancel: hide_modal,
-                    "Save Changes": function() {
-                        save(do_close);
-                    }
-                },
-                {
-                    "Don't Save": do_close
-                }
-            );
-        } else {
-            window.document.location = configs.page_list_url;
-        }
-    });
-
-    // Initialize galaxy elements.
-    //init_galaxy_elts(editor);
-
-    //
-    // Containers, Galaxy style
-    //
-    var containers_menu = $(
-        "<div class='galaxy-page-editor-button'><a id='insert-galaxy-link' class='action-button popup' href='#'>Paragraph type</a></div>"
-    );
-    $(".wym_area_top").append(containers_menu);
-
-    // Add menu options.
-    var items = {};
-    $.each(editor._options.containersItems, (k, v) => {
-        var tagname = v.name;
-        items[v.title.replace("_", " ")] = () => {
-            editor.container(tagname);
-        };
-    });
-    make_popupmenu(containers_menu, items);
-
-    //
-    // Create 'Insert Link to Galaxy Object' menu.
-    //
-
-    // Add menu button.
-    var insert_link_menu_button = $(
-        "<div><a id='insert-galaxy-link' class='action-button popup' href='#'>Insert Link to Galaxy Object</a></div>"
-    ).addClass("galaxy-page-editor-button");
-    $(".wym_area_top").append(insert_link_menu_button);
-
-    // Add menu options.
-    make_popupmenu(insert_link_menu_button, {
-        "Insert History Link": function() {
-            editor.dialog(CONTROLS.DIALOG_HISTORY_LINK);
-        },
-        "Insert Dataset Link": function() {
-            editor.dialog(CONTROLS.DIALOG_DATASET_LINK);
-        },
-        "Insert Workflow Link": function() {
-            editor.dialog(CONTROLS.DIALOG_WORKFLOW_LINK);
-        },
-        "Insert Page Link": function() {
-            editor.dialog(CONTROLS.DIALOG_PAGE_LINK);
-        },
-        "Insert Visualization Link": function() {
-            editor.dialog(CONTROLS.DIALOG_VISUALIZATION_LINK);
-        }
-    });
-
-    //
-    // Create 'Embed Galaxy Object' menu.
-    //
-
-    // Add menu button.
-    var embed_object_button = $(
-        "<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>"
-    ).addClass("galaxy-page-editor-button");
-    $(".wym_area_top").append(embed_object_button);
-
-    // Add menu options.
-    make_popupmenu(embed_object_button, {
-        "Embed History": function() {
-            editor.dialog(CONTROLS.DIALOG_EMBED_HISTORY);
-        },
-        "Embed Dataset": function() {
-            editor.dialog(CONTROLS.DIALOG_EMBED_DATASET);
-        },
-        "Embed Workflow": function() {
-            editor.dialog(CONTROLS.DIALOG_EMBED_WORKFLOW);
-        },
-        "Embed Visualization": function() {
-            editor.dialog(CONTROLS.DIALOG_EMBED_VISUALIZATION);
-        }
-        //"Embed Page": function() {
-        //    editor.dialog(CONTROLS.DIALOG_EMBED_PAGE);
-        //}
-    });
 }
diff --git a/client/galaxy/scripts/layout/communication-server-view.js b/client/galaxy/scripts/layout/communication-server-view.js
index b54030873a6..1bd1f682300 100644
--- a/client/galaxy/scripts/layout/communication-server-view.js
+++ b/client/galaxy/scripts/layout/communication-server-view.js
@@ -6,38 +6,38 @@ import _l from "utils/localization";
 import Modal from "mvc/ui/ui-modal";
 import { getGalaxyInstance } from "app";
 
-export var CommunicationServerView = Backbone.View.extend({
+export const CommunicationServerView = Backbone.View.extend({
     initialize: function() {
         this.modal = null;
     },
 
     /** makes bootstrap modal and iframe inside it */
     makeModalIframe: function(e) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         // make modal
-        var host = Galaxy.config.communication_server_host;
+        const host = Galaxy.config.communication_server_host;
 
-        var port = Galaxy.config.communication_server_port;
-        var username = _.escape(Galaxy.user.attributes.username);
+        const port = Galaxy.config.communication_server_port;
+        const username = _.escape(Galaxy.user.attributes.username);
 
-        var persistent_communication_rooms = _.escape(Galaxy.config.persistent_communication_rooms);
+        const persistent_communication_rooms = _.escape(Galaxy.config.persistent_communication_rooms);
 
-        var query_string = `?username=${username}&persistent_communication_rooms=${persistent_communication_rooms}`;
+        const query_string = `?username=${username}&persistent_communication_rooms=${persistent_communication_rooms}`;
 
-        var src = `${host}:${port}${query_string}`;
-        var $el_chat_modal_header = null;
-        var $el_chat_modal_body = null;
+        const src = `${host}:${port}${query_string}`;
+        let $el_chat_modal_header = null;
+        let $el_chat_modal_body = null;
 
-        var iframe_template = `<iframe class="h-100 w-100" src="${src}"> </iframe>`;
+        const iframe_template = `<iframe class="h-100 w-100" src="${src}"> </iframe>`;
 
-        var header_template =
+        const header_template =
             '<i class="fa fa-comment" aria-hidden="true" title="Communicate with other users"></i>' +
             '<i class="fa fa-expand expand-compress-modal" aria-hidden="true" title="Maximize"></i>' +
             '<i class="fa fa-times close-modal" aria-hidden="true" title="Close"></i>';
 
-        var frame_height = 350;
-        var frame_width = 600;
-        var class_names = "ui-modal chat-modal";
+        const frame_height = 350;
+        const frame_width = 600;
+        const class_names = "ui-modal chat-modal";
 
         // deletes the chat modal if already present and create one
         if ($(".chat-modal").length > 0) {
@@ -92,14 +92,12 @@ export var CommunicationServerView = Backbone.View.extend({
 
     /**renders the chat icon as a nav item*/
     render: function() {
-        var self = this;
-        var navItem = {};
-        navItem = {
+        const navItem = {
             id: "show-chat-online",
             icon: "fa-comment-o",
             tooltip: _l("Chat online"),
             visible: false,
-            onclick: self.makeModalIframe
+            onclick: this.makeModalIframe
         };
         return navItem;
     }
diff --git a/client/galaxy/scripts/layout/data.js b/client/galaxy/scripts/layout/data.js
index 44f4cad5b6e..3953bda769a 100644
--- a/client/galaxy/scripts/layout/data.js
+++ b/client/galaxy/scripts/layout/data.js
@@ -10,16 +10,16 @@ export default class Data {
      * @param {function} callback - Result function called with selection
      */
     dialog(callback, options = {}) {
-        let galaxy = getGalaxyInstance();
-        let host = `${window.location.protocol}//${window.location.hostname}:${window.location.port}`;
+        const galaxy = getGalaxyInstance();
+        const host = `${window.location.protocol}//${window.location.hostname}:${window.location.port}`;
         Object.assign(options, {
             callback: callback,
             history: galaxy.currHistoryPanel && galaxy.currHistoryPanel.model.id,
             root: galaxy.root,
             host: host
         });
-        var instance = Vue.extend(DataDialog);
-        var vm = document.createElement("div");
+        const instance = Vue.extend(DataDialog);
+        const vm = document.createElement("div");
         $("body").append(vm);
         new instance({
             propsData: options
@@ -30,8 +30,8 @@ export default class Data {
      * Creates a history dataset by submitting an upload request
      */
     create(options) {
-        let Galaxy = getGalaxyInstance();
-        let history_panel = Galaxy.currHistoryPanel;
+        const Galaxy = getGalaxyInstance();
+        const history_panel = Galaxy.currHistoryPanel;
         let history_id = options.history_id;
         if (!history_id && history_panel) {
             history_id = history_panel.model.get("id");
diff --git a/client/galaxy/scripts/layout/masthead.js b/client/galaxy/scripts/layout/masthead.js
index 61b48a899c0..17413de98b4 100644
--- a/client/galaxy/scripts/layout/masthead.js
+++ b/client/galaxy/scripts/layout/masthead.js
@@ -6,11 +6,11 @@ import QuotaMeter from "mvc/user/user-quotameter";
 import { getGalaxyInstance } from "app";
 
 /** Masthead **/
-var View = Backbone.View.extend({
+const View = Backbone.View.extend({
     initialize: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
-        var self = this;
+        const self = this;
         this.options = options;
         this.setElement(this._template());
         this.$navbarBrandLink = this.$(".navbar-brand");
@@ -53,7 +53,7 @@ var View = Backbone.View.extend({
         // loop through beforeunload functions if the user attempts to unload the page
         $(window)
             .on("click", e => {
-                var $download_link = $(e.target).closest("a[download]");
+                const $download_link = $(e.target).closest("a[download]");
                 if ($download_link.length == 1) {
                     if ($("iframe[id=download]").length === 0) {
                         $("body").append(
@@ -67,9 +67,9 @@ var View = Backbone.View.extend({
                 }
             })
             .on("beforeunload", () => {
-                var text = "";
+                let text = "";
                 self.collection.each(model => {
-                    var q = model.get("onbeforeunload") && model.get("onbeforeunload")();
+                    const q = model.get("onbeforeunload") && model.get("onbeforeunload")();
                     if (q) {
                         text += `${q} `;
                     }
diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index 4eb07f03985..1e7c0f76ef3 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -11,9 +11,9 @@ import Webhooks from "mvc/webhooks";
 import Utils from "utils/utils";
 
 function logoutClick() {
-    let galaxy = getGalaxyInstance();
-    let session_csrf_token = galaxy.session_csrf_token;
-    let url = `${galaxy.root}user/logout?session_csrf_token=${session_csrf_token}`;
+    const galaxy = getGalaxyInstance();
+    const session_csrf_token = galaxy.session_csrf_token;
+    const url = `${galaxy.root}user/logout?session_csrf_token=${session_csrf_token}`;
     axios.get(url).then(() => {
         if (galaxy.user) {
             galaxy.user.clearSessionStorage();
@@ -22,7 +22,7 @@ function logoutClick() {
     });
 }
 
-var Collection = Backbone.Collection.extend({
+const Collection = Backbone.Collection.extend({
     model: Backbone.Model.extend({
         defaults: {
             visible: true,
@@ -33,12 +33,12 @@ var Collection = Backbone.Collection.extend({
         options = options || {};
         this.reset();
 
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         //
         // Chat server tab
         //
-        var extendedNavItem = new CommunicationServerView();
+        const extendedNavItem = new CommunicationServerView();
         this.add(extendedNavItem.render());
 
         //
@@ -129,9 +129,9 @@ var Collection = Backbone.Collection.extend({
             callback: function(webhooks) {
                 $(document).ready(() => {
                     webhooks.each(model => {
-                        var webhook = model.toJSON();
+                        const webhook = model.toJSON();
                         if (webhook.activate) {
-                            var obj = {
+                            const obj = {
                                 id: webhook.id,
                                 icon: webhook.config.icon,
                                 url: webhook.config.url,
@@ -141,7 +141,7 @@ var Collection = Backbone.Collection.extend({
                             };
 
                             // Galaxy.page is undefined for data libraries, workflows pages
-                            let Galaxy = getGalaxyInstance();
+                            const Galaxy = getGalaxyInstance();
                             if (Galaxy.page) {
                                 Galaxy.page.masthead.collection.add(obj);
                             } else if (Galaxy.masthead) {
@@ -172,7 +172,7 @@ var Collection = Backbone.Collection.extend({
         //
         // Help tab.
         //
-        var helpTab = {
+        const helpTab = {
             id: "help",
             title: _l("Help"),
             tooltip: _l("Support, contact, and community"),
@@ -232,7 +232,7 @@ var Collection = Backbone.Collection.extend({
         //
         // User tab.
         //
-        var userTab = {};
+        let userTab = {};
         if (!Galaxy.user.id) {
             if (options.allow_user_creation) {
                 userTab = {
@@ -240,7 +240,7 @@ var Collection = Backbone.Collection.extend({
                     title: _l("Login or Register"),
                     cls: "loggedout-only",
                     url: "login",
-                    tooltip: _l("Account registration or login")
+                    tooltip: _l("Log in or register a new account")
                 };
             } else {
                 userTab = {
@@ -248,7 +248,7 @@ var Collection = Backbone.Collection.extend({
                     title: _l("Login"),
                     cls: "loggedout-only",
                     tooltip: _l("Login"),
-                    url: "user/login",
+                    url: "login",
                     target: "galaxy_main",
                     noscratchbook: true
                 };
@@ -279,22 +279,27 @@ var Collection = Backbone.Collection.extend({
                         onclick: logoutClick
                     },
                     {
-                        title: _l("Saved Datasets"),
+                        title: _l("Datasets"),
                         url: "datasets/list",
                         target: "__use_router__"
                     },
                     {
-                        title: _l("Saved Histories"),
+                        title: _l("Histories"),
                         url: "histories/list",
                         target: "__use_router__"
                     },
                     {
-                        title: _l("Saved Pages"),
+                        title: _l("Histories shared with me"),
+                        url: "histories/list_shared",
+                        target: "__use_router__"
+                    },
+                    {
+                        title: _l("Pages"),
                         url: "pages/list",
                         target: "__use_router__"
                     },
                     {
-                        title: _l("Saved Visualizations"),
+                        title: _l("Visualizations"),
                         url: "visualizations/list",
                         target: "__use_router__"
                     }
@@ -307,7 +312,7 @@ var Collection = Backbone.Collection.extend({
 });
 
 /** Masthead tab **/
-var Tab = Backbone.View.extend({
+const Tab = Backbone.View.extend({
     initialize: function(options) {
         this.model = options.model;
         this.setElement(this._template());
@@ -403,7 +408,7 @@ var Tab = Backbone.View.extend({
                 if (options.onclick) {
                     options.onclick();
                 } else {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     if (options.target == "__use_router__" && typeof Galaxy.page != "undefined") {
                         Galaxy.page.router.executeUseRouter(options.url);
                     } else {
@@ -429,7 +434,7 @@ var Tab = Backbone.View.extend({
 
     /** Handle click event */
     _toggleClick: function(e) {
-        var model = this.model;
+        const model = this.model;
         e.preventDefault();
         $(".tooltip").hide();
         model.trigger("dispatch", m => {
@@ -442,7 +447,7 @@ var Tab = Backbone.View.extend({
                 if (model.get("onclick")) {
                     model.get("onclick")();
                 } else {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     if (model.attributes.target == "__use_router__" && typeof Galaxy.page != "undefined") {
                         Galaxy.page.router.executeUseRouter(model.attributes.url);
                     } else {
diff --git a/client/galaxy/scripts/layout/modal.js b/client/galaxy/scripts/layout/modal.js
index b343b092686..d0940b92476 100644
--- a/client/galaxy/scripts/layout/modal.js
+++ b/client/galaxy/scripts/layout/modal.js
@@ -28,7 +28,7 @@ $.extend(Modal.prototype, {
         }
         // Buttons
         this.$footer.hide();
-        var $buttons = this.$footer.find(".buttons").html("");
+        const $buttons = this.$footer.find(".buttons").html("");
         if (options.buttons) {
             $.each(options.buttons, (name, value) => {
                 $buttons
@@ -41,7 +41,7 @@ $.extend(Modal.prototype, {
             });
             this.$footer.show();
         }
-        var $extraButtons = this.$footer.find(".extra_buttons").html("");
+        const $extraButtons = this.$footer.find(".extra_buttons").html("");
         if (options.extra_buttons) {
             $.each(options.extra_buttons, (name, value) => {
                 $extraButtons
@@ -55,7 +55,7 @@ $.extend(Modal.prototype, {
             this.$footer.show();
         }
         // Body
-        var body = options.body;
+        let body = options.body;
         if (body == "progress") {
             body = $(
                 "<div class='progress progress-striped active'><div class='progress-bar' style='width: 100%'></div></div>"
@@ -83,7 +83,7 @@ $.extend(Modal.prototype, {
         }
     },
     hide: function() {
-        var modal = this;
+        const modal = this;
         modal.$dialog.fadeOut(() => {
             modal.$overlay.hide();
             modal.$backdrop.removeClass("in");
@@ -94,7 +94,7 @@ $.extend(Modal.prototype, {
     }
 });
 
-var modal;
+let modal;
 
 // TODO: move into init chain
 $(() => {
@@ -131,9 +131,9 @@ export function show_message(title, body, buttons, extra_buttons, init_fn) {
 }
 
 export function show_in_overlay(options) {
-    var width = options.width || "600";
-    var height = options.height || "400";
-    var scroll = options.scroll || "auto";
+    const width = options.width || "600";
+    const height = options.height || "400";
+    const scroll = options.scroll || "auto";
     $("#overlay-background").bind("click.overlay", () => {
         hide_modal();
         $("#overlay-background").unbind("click.overlay");
diff --git a/client/galaxy/scripts/layout/page.js b/client/galaxy/scripts/layout/page.js
index d7e7b9f2a10..af6b5c2ee99 100644
--- a/client/galaxy/scripts/layout/page.js
+++ b/client/galaxy/scripts/layout/page.js
@@ -9,13 +9,13 @@ import Panel from "layout/panel";
 import Modal from "mvc/ui/ui-modal";
 import Utils from "utils/utils";
 
-var View = Backbone.View.extend({
+const View = Backbone.View.extend({
     el: "body",
     className: "full-content",
     _panelids: ["left", "right"],
 
     initialize: function(options) {
-        var self = this;
+        const self = this;
         this.config = _.defaults(options.config || {}, {
             message_box_visible: false,
             message_box_content: "",
@@ -27,7 +27,7 @@ var View = Backbone.View.extend({
         });
 
         // attach global objects, build mastheads
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.modal = this.modal = new Modal.View();
         Galaxy.router = this.router = options.Router && new options.Router(self, options);
         Galaxy.data = this.data = new Data(this);
@@ -72,11 +72,11 @@ var View = Backbone.View.extend({
         this.panels = {};
         if (!this.config.hide_panels) {
             _.each(this._panelids, panel_id => {
-                var panel_class_name = panel_id.charAt(0).toUpperCase() + panel_id.slice(1);
-                var panel_class = options[panel_class_name];
+                const panel_class_name = panel_id.charAt(0).toUpperCase() + panel_id.slice(1);
+                const panel_class = options[panel_class_name];
                 if (panel_class) {
-                    var panel_instance = new panel_class(self, options);
-                    var panel_el = self.$(`#${panel_id}`);
+                    const panel_instance = new panel_class(self, options);
+                    const panel_el = self.$(`#${panel_id}`);
                     self[panel_instance.toString()] = panel_instance;
                     self.panels[panel_id] = new Panel.SidePanel({
                         id: panel_id,
@@ -116,8 +116,8 @@ var View = Backbone.View.extend({
     /** Render message box */
     renderMessageBox: function() {
         if (this.config.message_box_visible) {
-            var content = this.config.message_box_content || "";
-            var level = this.config.message_box_class || "info";
+            const content = this.config.message_box_content || "";
+            const level = this.config.message_box_class || "info";
             this.$el.addClass("has-message-box");
             this.$messagebox
                 .attr("class", `panel-${level}-message`)
@@ -134,8 +134,8 @@ var View = Backbone.View.extend({
     /** Render inactivity warning */
     renderInactivityBox: function() {
         if (this.config.show_inactivity_warning) {
-            var content = this.config.inactivity_box_content || "";
-            var verificationLink = $("<a/>")
+            const content = this.config.inactivity_box_content || "";
+            const verificationLink = $("<a/>")
                 .attr("href", `${getAppRoot()}user/resend_verification`)
                 .text("Resend verification");
             this.$el.addClass("has-inactivity-box");
@@ -153,9 +153,9 @@ var View = Backbone.View.extend({
 
     /** Render panels */
     renderPanels: function() {
-        var self = this;
+        const self = this;
         _.each(this._panelids, panel_id => {
-            var panel = self.panels[panel_id];
+            const panel = self.panels[panel_id];
             if (panel) {
                 panel.render();
             } else {
@@ -190,11 +190,11 @@ var View = Backbone.View.extend({
 
     /** Check if the communication server is online and show the icon otherwise hide the icon */
     _checkCommunicationServerOnline: function() {
-        let Galaxy = getGalaxyInstance();
-        var host = Galaxy.config.communication_server_host;
-        var port = Galaxy.config.communication_server_port;
-        var preferences = Galaxy.user.attributes.preferences;
-        var $chat_icon_element = $("#show-chat-online");
+        const Galaxy = getGalaxyInstance();
+        const host = Galaxy.config.communication_server_host;
+        const port = Galaxy.config.communication_server_port;
+        const preferences = Galaxy.user.attributes.preferences;
+        const $chat_icon_element = $("#show-chat-online");
         /** Check if the user has deactivated the communication in it's personal settings */
         if (preferences && ["1", "true"].indexOf(preferences.communication_server) != -1) {
             // See if the configured communication server is available
diff --git a/client/galaxy/scripts/layout/panel.js b/client/galaxy/scripts/layout/panel.js
index d277923eb98..78e298c5f4a 100644
--- a/client/galaxy/scripts/layout/panel.js
+++ b/client/galaxy/scripts/layout/panel.js
@@ -3,11 +3,11 @@ import _ from "underscore";
 import Backbone from "backbone";
 import { getGalaxyInstance } from "app";
 
-var MIN_PANEL_WIDTH = 160;
-var MAX_PANEL_WIDTH = 800;
+const MIN_PANEL_WIDTH = 160;
+const MAX_PANEL_WIDTH = 800;
 
 /** View for left/right panels used by Page view */
-var SidePanel = Backbone.View.extend({
+const SidePanel = Backbone.View.extend({
     initialize: function(options) {
         this.view = options.view;
         this.hidden = false;
@@ -24,9 +24,9 @@ var SidePanel = Backbone.View.extend({
     },
 
     render: function() {
-        var self = this;
-        var panel = this.view;
-        var components = this.view.model.attributes || {};
+        const self = this;
+        const panel = this.view;
+        const components = this.view.model.attributes || {};
         this.$el.html(this._templatePanel(this.id));
         _.each(components.buttons, button => {
             self.$(".panel-header-buttons").append(button.$el);
@@ -76,16 +76,16 @@ var SidePanel = Backbone.View.extend({
     },
 
     _mousedownDragHandler: function(ev) {
-        var self = this;
-        var draggingLeft = this.id === "left";
+        const self = this;
+        const draggingLeft = this.id === "left";
         // Save the mouse position and width of the element (panel) when the
         // drag interaction is first started
-        var initialX = ev.pageX;
-        var initialWidth = self.$el.width();
+        const initialX = ev.pageX;
+        const initialWidth = self.$el.width();
 
         function move(e) {
-            var delta = e.pageX - initialX;
-            var newWidth = draggingLeft ? initialWidth + delta : initialWidth - delta;
+            const delta = e.pageX - initialX;
+            let newWidth = draggingLeft ? initialWidth + delta : initialWidth - delta;
             // Limit range
             newWidth = Math.min(MAX_PANEL_WIDTH, Math.max(MIN_PANEL_WIDTH, newWidth));
             self.resize(newWidth);
@@ -113,36 +113,36 @@ var SidePanel = Backbone.View.extend({
     },
 
     show: function() {
-        if (!this.hidden) {
-            return;
+        if (this.hidden && !this.motionQueue) {
+            this.motionQueue = 2;
+            const animation = {};
+            const whichSide = this.id;
+            animation[whichSide] = 0;
+            this.$el
+                .css(whichSide, -this.saved_size)
+                .css("width", this.saved_size)
+                .animate(animation, "fast", () => this.motionQueue--);
+            animation[whichSide] = this.saved_size;
+            this.$center().animate(animation, "fast", () => this.motionQueue--);
+            this.hidden = false;
+            this.$toggleButton().removeClass("hidden");
         }
-        var self = this;
-        var animation = {};
-        var whichSide = this.id;
-        animation[whichSide] = 0;
-        self.$el
-            .css(whichSide, -this.saved_size)
-            .show()
-            .animate(animation, "fast", () => {
-                self.resize(self.saved_size);
-            });
-        self.hidden = false;
-        self.$toggleButton().removeClass("hidden");
         return this;
     },
 
     hide: function() {
-        if (this.hidden) {
-            return;
+        if (!this.hidden && !this.motionQueue) {
+            this.motionQueue = 2;
+            const animation = {};
+            const whichSide = this.id;
+            this.saved_size = this.$el.width();
+            animation[whichSide] = -this.saved_size;
+            this.$el.animate(animation, "fast", () => this.motionQueue--);
+            animation[whichSide] = 0;
+            this.$center().animate(animation, "fast", () => this.motionQueue--);
+            this.hidden = true;
+            this.$toggleButton().addClass("hidden");
         }
-        var animation = {};
-        var whichSide = this.id;
-        this.saved_size = this.$el.width();
-        animation[whichSide] = -this.saved_size;
-        this.$el.animate(animation, "fast");
-        this.$center().css(whichSide, 0);
-        this.hidden = true;
-        this.$toggleButton().addClass("hidden");
         return this;
     },
 
@@ -156,7 +156,7 @@ var SidePanel = Backbone.View.extend({
     //TODO: only used in message.mako?
     /**   */
     handle_minwidth_hint: function(hint) {
-        var space = this.$center().width() - (this.hidden ? this.saved_size : 0);
+        const space = this.$center().width() - (this.hidden ? this.saved_size : 0);
         if (space < hint) {
             if (!this.hidden) {
                 this.toggle();
@@ -189,16 +189,16 @@ var SidePanel = Backbone.View.extend({
 
 // ----------------------------------------------------------------------------
 // TODO: side should be defined by page - not here
-var LeftPanel = SidePanel.extend({
+const LeftPanel = SidePanel.extend({
     id: "left"
 });
 
-var RightPanel = SidePanel.extend({
+const RightPanel = SidePanel.extend({
     id: "right"
 });
 
 /** Center panel with the ability to switch between iframe and view */
-var CenterPanel = Backbone.View.extend({
+const CenterPanel = Backbone.View.extend({
     initialize: function(options) {
         this.setElement($(this.template()));
         this.$frame = this.$(".center-frame");
@@ -208,9 +208,9 @@ var CenterPanel = Backbone.View.extend({
 
     /** Display iframe if its target url changes, hide center panel */
     _iframeChangeHandler: function(ev) {
-        var iframe = ev.currentTarget;
-        var location = iframe.contentWindow && iframe.contentWindow.location;
-        var Galaxy = getGalaxyInstance();
+        const iframe = ev.currentTarget;
+        const location = iframe.contentWindow && iframe.contentWindow.location;
+        const Galaxy = getGalaxyInstance();
         // Adding try/catch to manage a CORS error in toolshed. Accessing
         // location.host is a CORS no-no
         try {
@@ -231,7 +231,7 @@ var CenterPanel = Backbone.View.extend({
 
     /** Display a view in the center panel, hide iframe */
     display: function(view) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         let contentWindow = this.$frame[0].contentWindow || {};
         let message;
         try {
diff --git a/client/galaxy/scripts/layout/router.js b/client/galaxy/scripts/layout/router.js
index dd5f6a6df3d..9132d05f9a6 100644
--- a/client/galaxy/scripts/layout/router.js
+++ b/client/galaxy/scripts/layout/router.js
@@ -5,7 +5,7 @@ import { getGalaxyInstance } from "app";
 import QUERY_STRING from "utils/query-string-parsing";
 import Ui from "mvc/ui/ui-misc";
 
-var Router = Backbone.Router.extend({
+const Router = Backbone.Router.extend({
     // TODO: not many client routes at this point - fill and remove from server.
     // since we're at root here, this may be the last to be routed entirely on the client.
     initialize: function(page, options) {
@@ -14,7 +14,7 @@ var Router = Backbone.Router.extend({
     },
 
     executeUseRouter: function(url) {
-        let prefix = getAppRoot();
+        const prefix = getAppRoot();
         if (url.startsWith(prefix)) {
             url = url.replace(prefix, "/");
         }
@@ -28,9 +28,9 @@ var Router = Backbone.Router.extend({
             .toString(36)
             .substr(2);
         url += url.indexOf("?") == -1 ? "?" : "&";
-        let bustParam = $.param(data, true);
+        const bustParam = $.param(data, true);
         url += bustParam;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.params = data;
         this.navigate(url, { trigger: true });
         window.history.replaceState(window.history.state, "", window.location.pathname.replace(bustParam, ""));
@@ -38,9 +38,9 @@ var Router = Backbone.Router.extend({
 
     /** override to parse query string into obj and send to each route */
     execute: function(callback, args, name) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.debug("router execute:", callback, args, name);
-        var queryObj = QUERY_STRING.parse(args.pop());
+        const queryObj = QUERY_STRING.parse(args.pop());
         args.push(queryObj);
         if (callback) {
             if (this.authenticate(args, name)) {
diff --git a/client/galaxy/scripts/layout/scratchbook.js b/client/galaxy/scripts/layout/scratchbook.js
index e36466546e5..eeb7953ef5d 100644
--- a/client/galaxy/scripts/layout/scratchbook.js
+++ b/client/galaxy/scripts/layout/scratchbook.js
@@ -72,11 +72,11 @@ export default Backbone.View.extend({
 
     /** Add a dataset to the frames */
     addDataset: function(dataset_id) {
-        var self = this;
-        var current_dataset = null;
-        let Galaxy = getGalaxyInstance();
+        const self = this;
+        let current_dataset = null;
+        const Galaxy = getGalaxyInstance();
         if (Galaxy && Galaxy.currHistoryPanel) {
-            var history_id = Galaxy.currHistoryPanel.collection.historyId;
+            const history_id = Galaxy.currHistoryPanel.collection.historyId;
             this.history_cache[history_id] = {
                 name: Galaxy.currHistoryPanel.model.get("name"),
                 dataset_ids: []
@@ -87,20 +87,20 @@ export default Backbone.View.extend({
                 }
             });
         }
-        var _findDataset = (dataset, offset) => {
+        const _findDataset = (dataset, offset) => {
             if (dataset) {
-                var history_details = self.history_cache[dataset.get("history_id")];
+                const history_details = self.history_cache[dataset.get("history_id")];
                 if (history_details && history_details.dataset_ids) {
-                    var dataset_list = history_details.dataset_ids;
-                    var pos = dataset_list.indexOf(dataset.get("id"));
+                    const dataset_list = history_details.dataset_ids;
+                    const pos = dataset_list.indexOf(dataset.get("id"));
                     if (pos !== -1 && pos + offset >= 0 && pos + offset < dataset_list.length) {
                         return dataset_list[pos + offset];
                     }
                 }
             }
         };
-        var _loadDatasetOffset = (dataset, offset, frame) => {
-            var new_dataset_id = _findDataset(dataset, offset);
+        const _loadDatasetOffset = (dataset, offset, frame) => {
+            const new_dataset_id = _findDataset(dataset, offset);
             if (new_dataset_id) {
                 self._loadDataset(new_dataset_id, (new_dataset, config) => {
                     current_dataset = new_dataset;
@@ -145,15 +145,15 @@ export default Backbone.View.extend({
     },
 
     _loadDataset: function(dataset_id, callback) {
-        var self = this;
-        var dataset = new Dataset({ id: dataset_id });
+        const self = this;
+        const dataset = new Dataset({ id: dataset_id });
         $.when(dataset.fetch()).then(() => {
-            var is_tabular = _.find(
+            const is_tabular = _.find(
                 ["tabular", "interval"],
                 data_type => dataset.get("data_type").indexOf(data_type) !== -1
             );
-            var title = dataset.get("name");
-            var history_details = self.history_cache[dataset.get("history_id")];
+            let title = dataset.get("name");
+            const history_details = self.history_cache[dataset.get("history_id")];
             if (history_details) {
                 title = `${history_details.name}: ${title}`;
             }
@@ -180,18 +180,18 @@ export default Backbone.View.extend({
 
     /** Add a trackster visualization to the frames. */
     addTrackster: function(viz_id) {
-        var self = this;
-        var viz = new visualization.Visualization({ id: viz_id });
+        const self = this;
+        const viz = new visualization.Visualization({ id: viz_id });
         $.when(viz.fetch()).then(() => {
-            var ui = new TracksterUI(getAppRoot());
+            const ui = new TracksterUI(getAppRoot());
 
             // Construct frame config based on dataset's type.
-            var frame_config = {
+            const frame_config = {
                 title: viz.get("name"),
                 type: "other",
                 content: function(parent_elt) {
                     // Create view config.
-                    var view_config = {
+                    const view_config = {
                         container: parent_elt,
                         name: viz.get("title"),
                         id: viz.id,
@@ -200,8 +200,8 @@ export default Backbone.View.extend({
                         stand_alone: false
                     };
 
-                    var latest_revision = viz.get("latest_revision");
-                    var drawables = latest_revision.config.view.drawables;
+                    const latest_revision = viz.get("latest_revision");
+                    const drawables = latest_revision.config.view.drawables;
 
                     // Set up datasets in drawables.
                     _.each(drawables, d => {
@@ -230,7 +230,7 @@ export default Backbone.View.extend({
         } else if (options.target == "_top" || options.target == "_parent" || options.target == "_self") {
             window.location = options.url;
         } else if (!this.active || options.noscratchbook) {
-            var $galaxy_main = $(window.parent.document).find("#galaxy_main");
+            const $galaxy_main = $(window.parent.document).find("#galaxy_main");
             if (options.target == "galaxy_main" || options.target == "center") {
                 if ($galaxy_main.length === 0) {
                     window.location = this._build_url(options.url, { use_panels: true });
diff --git a/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js b/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
index d3e483cfead..9b5af96b2ac 100644
--- a/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
+++ b/client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
@@ -28,14 +28,14 @@ var ControlledFetchCollection = Backbone.Collection.extend({
      */
     fetch: function(options) {
         options = this._buildFetchOptions(options);
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.debug("fetch options:", options);
         return Backbone.Collection.prototype.fetch.call(this, options);
     },
 
     /** build ajax data/parameters from options */
     _buildFetchOptions: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         // note: we normally want options passed in to override the defaults built here
         // so most of these fns will generate defaults
@@ -271,7 +271,7 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
 
     /** fetch the first 'page' of data */
     fetchFirst: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.debug("ControlledFetchCollection.fetchFirst:", options);
         options = options ? _.clone(options) : {};
         this.allFetched = false;
@@ -286,7 +286,7 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
 
     /** fetch the next page of data */
     fetchMore: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         Galaxy.debug("ControlledFetchCollection.fetchMore:", options);
         options = _.clone(options || {});
diff --git a/client/galaxy/scripts/mvc/collection/collection-view-edit.js b/client/galaxy/scripts/mvc/collection/collection-view-edit.js
index f90e13f37ef..c77e59cc217 100644
--- a/client/galaxy/scripts/mvc/collection/collection-view-edit.js
+++ b/client/galaxy/scripts/mvc/collection/collection-view-edit.js
@@ -49,7 +49,7 @@ var CollectionViewEdit = _super.extend(
             }
 
             // anon users shouldn't have access to any of the following
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (!Galaxy.user || Galaxy.user.isAnonymous()) {
                 return;
             }
@@ -78,22 +78,22 @@ var CollectionViewEdit = _super.extend(
                     }
                 });
 
-            let el = $where.find(".tags-display")[0];
-            let propsData = {
+            const el = $where.find(".tags-display")[0];
+            const propsData = {
                 model: this.model,
                 disabled: false,
                 context: "collection-view-edit"
             };
 
-            let vm = mountModelTags(propsData, el);
+            const vm = mountModelTags(propsData, el);
 
-            let toggleEditor = () => {
+            const toggleEditor = () => {
                 $(vm.$el).toggleClass("active");
                 this.tagsEditorShown = $(vm.$el).hasClass("active");
             };
 
             if (this.tagsEditorShown) {
-                let editorIsOpen = $(vm.$el).hasClass("active");
+                const editorIsOpen = $(vm.$el).hasClass("active");
                 if (!editorIsOpen) {
                     toggleEditor();
                 }
diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
index ba77f2d039e..3bf74c9a950 100644
--- a/client/galaxy/scripts/mvc/collection/list-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
@@ -851,14 +851,14 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
                     _l("Create a different kind of collection"),
                     ' <span class="caret"></span>',
                     "</button>",
-                    '<ul class="dropdown-menu" role="menu">',
-                    '<li><a href="#">',
+                    '<div class="dropdown-menu" role="menu">',
+                    '<a class="dropdown-item" href="#">',
                     _l("Create a <i>single</i> pair"),
-                    "</a></li>",
-                    '<li><a href="#">',
+                    "</a>",
+                    '<a class="dropdown-item" href="#">',
                     _l("Create a list of <i>unpaired</i> datasets"),
-                    "</a></li>",
-                    "</ul>",
+                    "</a>",
+                    "</div>",
                     "</div>",
                     "</div>",
 
@@ -1011,7 +1011,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
 
 const collectionCreatorModalSetup = function _collectionCreatorModalSetup(options) {
     const deferred = jQuery.Deferred();
-    let Galaxy = getGalaxyInstance();
+    const Galaxy = getGalaxyInstance();
     const modal = Galaxy.modal || new UI_MODAL.View();
 
     const creatorOptions = _.defaults(options || {}, {
diff --git a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
index ff52309e86a..7ff9a260697 100644
--- a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
@@ -1679,14 +1679,14 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     _l("Create a different kind of collection"),
                     ' <span class="caret"></span>',
                     "</button>",
-                    '<ul class="dropdown-menu" role="menu">',
-                    '<li><a href="#">',
+                    '<div class="dropdown-menu" role="menu">',
+                    '<a class="dropdown-item" href="#">',
                     _l("Create a <i>single</i> pair"),
-                    "</a></li>",
-                    '<li><a href="#">',
+                    "</a>",
+                    '<a class="dropdown-item" href="#">',
                     _l("Create a list of <i>unpaired</i> datasets"),
-                    "</a></li>",
-                    "</ul>",
+                    "</a>",
+                    "</div>",
                     "</div>",
                     "</div>",
 
diff --git a/client/galaxy/scripts/mvc/dataset/data.js b/client/galaxy/scripts/mvc/dataset/data.js
index 18b1f3b330b..c054946753d 100644
--- a/client/galaxy/scripts/mvc/dataset/data.js
+++ b/client/galaxy/scripts/mvc/dataset/data.js
@@ -286,7 +286,7 @@ var TabularDatasetChunkedView = Backbone.View.extend({
                         },
                         this
                     );
-                } else {    
+                } else {
                     // Comment line, just return the one cell.
                     row.append(this._renderCell(line, 0, num_columns));
                 }
@@ -405,7 +405,7 @@ var TabularButtonTracksterView = Backbone.View.extend({
     // backbone initialize
     initialize: function(options) {
         // check if environment is available
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         // link galaxy modal or create one
         if (Galaxy && Galaxy.modal) {
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js b/client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
index fca53d24b16..9420974a77d 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
@@ -12,7 +12,7 @@ import Form from "mvc/form/form-view";
 
 var View = Backbone.View.extend({
     initialize: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.setElement("<div/>");
         this.model = new Backbone.Model({
             dataset_id: Galaxy.params.dataset_id
@@ -214,7 +214,7 @@ var View = Backbone.View.extend({
 
     /** reload Galaxy's history after updating dataset's attributes */
     _reloadHistory: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (Galaxy) {
             Galaxy.currHistoryPanel.loadCurrentHistory();
         }
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-error.js b/client/galaxy/scripts/mvc/dataset/dataset-error.js
index 94499260574..efb2af6a857 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-error.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-error.js
@@ -11,7 +11,7 @@ import Form from "mvc/form/form-view";
 /** Dataset edit attributes view */
 var View = Backbone.View.extend({
     initialize: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.setElement("<div/>");
         this.model = new Backbone.Model({
             dataset_id: Galaxy.params.dataset_id
@@ -81,17 +81,15 @@ var View = Backbone.View.extend({
             if (has_empty_inputs) {
                 reportEl.after(`
                     <p>
-                        The tool was executed with one or more empty input datasets, this isn't
-                        always a problem and may not have been but frequently this is a source
-                        of error.
+                        The tool was executed with one or more empty input datasets. This frequently
+                        results in tool errors due to problematic input choices.
                     <p>`);
             }
             if (has_duplicate_inputs) {
                 reportEl.after(`
                     <p>
-                        The tool was executed with one or more duplicate input datasets, this isn't
-                        always a problem and may not have been but frequently this is a source
-                        of error.
+                        The tool was executed with one or more duplicate input datasets. This frequently
+                        results in tool errors due to problematic input choices.
                     <p>`);
             }
         }
@@ -134,7 +132,7 @@ var View = Backbone.View.extend({
         var message = "<h3>Error Details</h3>";
         if (job_messages) {
             message += "<p>Execution resulted in the following messages:</p>";
-            for (let job_message of job_messages) {
+            for (const job_message of job_messages) {
                 message += `<p><pre>${_.escape(job_message["desc"])}</pre></p>`;
             }
         }
@@ -174,7 +172,7 @@ var View = Backbone.View.extend({
 
     /** Convert tab template */
     _getBugFormTemplate: function(dataset, job) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var inputs = [
             {
                 help: _l("Your email address"),
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
index 26928c06936..87417282ce6 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
@@ -63,7 +63,7 @@ var DatasetListItemEdit = _super.extend(
                 faIcon: "fa-pencil",
                 classes: "edit-btn",
                 onclick: function(ev) {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     if (Galaxy.router) {
                         ev.preventDefault();
                         Galaxy.router.push("datasets/edit", {
@@ -164,7 +164,7 @@ var DatasetListItemEdit = _super.extend(
                     });
             };
 
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (Galaxy.user.id === null) {
                 return null;
             }
@@ -226,7 +226,7 @@ var DatasetListItemEdit = _super.extend(
                 classes: "report-error-btn",
                 faIcon: "fa-bug",
                 onclick: function(ev) {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     if (Galaxy.router) {
                         ev.preventDefault();
                         Galaxy.router.push("datasets/error", {
@@ -248,7 +248,7 @@ var DatasetListItemEdit = _super.extend(
                     target: this.linkTarget,
                     faIcon: "fa-refresh",
                     onclick: function(ev) {
-                        let Galaxy = getGalaxyInstance();
+                        const Galaxy = getGalaxyInstance();
                         if (Galaxy.router) {
                             ev.preventDefault();
                             Galaxy.router.push("/", {
@@ -273,15 +273,15 @@ var DatasetListItemEdit = _super.extend(
             }
 
             if (visualizations.length >= 1) {
-                let dsid = this.model.get("id");
-                let url = getAppRoot() + "visualizations?dataset_id=" + dsid;
+                const dsid = this.model.get("id");
+                const url = getAppRoot() + "visualizations?dataset_id=" + dsid;
                 return faIconButton({
                     title: _l("Visualize this data"),
                     href: url,
                     classes: "visualization-link",
                     faIcon: "fa-bar-chart-o",
                     onclick: ev => {
-                        let Galaxy = getGalaxyInstance();
+                        const Galaxy = getGalaxyInstance();
                         if (Galaxy.frame && Galaxy.frame.active) {
                             ev.preventDefault();
                             Galaxy.frame.add({ url: url, title: "Visualization" });
@@ -303,24 +303,24 @@ var DatasetListItemEdit = _super.extend(
                 return;
             }
 
-            let el = $where.find(".tags-display")[0];
+            const el = $where.find(".tags-display")[0];
 
-            let propsData = {
+            const propsData = {
                 model: this.model,
                 disabled: false,
                 context: "dataset-li-edit"
             };
 
-            let vm = mountModelTags(propsData, el);
+            const vm = mountModelTags(propsData, el);
 
             // tag icon button open/closes
-            let activator = faIconButton({
+            const activator = faIconButton({
                 title: _l("Edit dataset tags"),
                 classes: "tag-btn",
                 faIcon: "fa-tags"
             }).appendTo($where.find(".actions .right"));
 
-            let toggleEditor = () => {
+            const toggleEditor = () => {
                 $(vm.$el).toggleClass("active");
                 this.tagsEditorShown = $(vm.$el).hasClass("active");
             };
@@ -328,7 +328,7 @@ var DatasetListItemEdit = _super.extend(
             activator.on("click", toggleEditor);
 
             if (this.tagsEditorShown) {
-                let editorIsOpen = $(vm.$el).hasClass("active");
+                const editorIsOpen = $(vm.$el).hasClass("active");
                 if (!editorIsOpen) {
                     toggleEditor();
                 }
@@ -467,41 +467,8 @@ DatasetListItemEdit.prototype.templates = (() => {
             "dataset"
         )
     });
-
-    var visualizationsTemplate = BASE_MVC.wrapTemplate(
-        [
-            "<% if( visualizations.length === 1 ){ %>",
-            '<a class="visualization-link icon-btn" href="<%- visualizations[0].href %>"',
-            ' target="<%- visualizations[0].target %>" title="',
-            _l("Visualize in"),
-            ' <%- visualizations[0].html %>">',
-            '<span class="fa fa-bar-chart-o"></span>',
-            "</a>",
-
-            "<% } else { %>",
-            '<div class="visualizations-dropdown dropdown icon-btn">',
-            '<a data-toggle="dropdown" title="',
-            _l("Visualize"),
-            '">',
-            '<span class="fa fa-bar-chart-o"></span>',
-            "</a>",
-            '<ul class="dropdown-menu" role="menu">',
-            "<% _.each( visualizations, function( visualization ){ %>",
-            '<li><a class="visualization-link" href="<%- visualization.href %>"',
-            ' target="<%- visualization.target %>">',
-            "<%- visualization.html %>",
-            "</a></li>",
-            "<% }); %>",
-            "</ul>",
-            "</div>",
-            "<% } %>"
-        ],
-        "visualizations"
-    );
-
     return _.extend({}, _super.prototype.templates, {
-        warnings: warnings,
-        visualizations: visualizationsTemplate
+        warnings: warnings
     });
 })();
 
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js
index 99a01609568..17f2701edbd 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -45,15 +45,15 @@ export var DatasetListItemView = _super.extend(
 
         // mount new vue component for tags
         render: function() {
-            let result = _super.prototype.render.apply(this, arguments);
+            const result = _super.prototype.render.apply(this, arguments);
             this._mountVueNametags();
             return result;
         },
 
         _mountVueNametags: function() {
-            let container = this.$(".nametags")[0];
-            let { id, model_class, tags } = this.model.attributes;
-            let storeKey = `${model_class}-${id}`;
+            const container = this.$(".nametags")[0];
+            const { id, model_class, tags } = this.model.attributes;
+            const storeKey = `${model_class}-${id}`;
             mountNametags({ storeKey, tags }, container);
         },
 
@@ -181,7 +181,7 @@ export var DatasetListItemView = _super.extend(
                 // add frame manager option onclick event
                 var self = this;
                 displayBtnData.onclick = ev => {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     if (Galaxy.frame && Galaxy.frame.active) {
                         // Add dataset to frames.
                         Galaxy.frame.addDataset(self.model.get("id"));
@@ -279,7 +279,7 @@ export var DatasetListItemView = _super.extend(
                 target: this.linkTarget,
                 faIcon: "fa-info-circle",
                 onclick: function(ev) {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     if (Galaxy.frame && Galaxy.frame.active) {
                         Galaxy.frame.add({
                             title: _l("Dataset details"),
@@ -323,22 +323,18 @@ export var DatasetListItemView = _super.extend(
             )}">
                         <span class="fa fa-floppy-o"></span>
                     </a>
-                    <ul class="dropdown-menu" role="menu">
-                        <li>
-                            <a href="${urls.download}">
-                                ${_l("Download dataset")}
-                            </a>
-                        </li>
+                    <div class="dropdown-menu" role="menu">
+                        <a class="dropdown-item" href="${urls.download}">
+                            ${_l("Download dataset")}
+                        </a>
                         ${_.map(
                             this.model.get("meta_files"),
                             meta_file =>
-                                `<li>
-                                    <a href="${urls.meta_download + meta_file.file_type}">
-                                        ${_l("Download")} ${meta_file.file_type}
-                                    </a>
-                                </li>`
+                                `<a class="dropdown-item" href="${urls.meta_download + meta_file.file_type}">
+                                    ${_l("Download")} ${meta_file.file_type}
+                                </a>`
                         )}
-                    </ul>
+                    </div>
                 </div>`);
         },
 
diff --git a/client/galaxy/scripts/mvc/embedded-objects.js b/client/galaxy/scripts/mvc/embedded-objects.js
new file mode 100644
index 00000000000..e89bbeb3e5f
--- /dev/null
+++ b/client/galaxy/scripts/mvc/embedded-objects.js
@@ -0,0 +1,79 @@
+import $ from "jquery";
+import { make_popup_menus } from "ui/popupmenu";
+
+export function render_embedded_items() {
+    $(".embedded-item").each(function() {
+        var container = $(this);
+        if (container.hasClass("history")) {
+            return;
+        }
+        //note: we can't do the same override for visualizations
+        // bc builtins (like trackster) need the handlers/ajax below to work.
+        // instead: (for registry visualizations) we'll clear the handlers below
+        //  and add new ones (in embed_in_frame.mako) ...ugh.
+
+        // Show embedded item.
+        var show_embedded_item = function() {
+            var ajax_url = container.find("input[type=hidden]").val();
+
+            // Only get item content if it's not already there.
+            var item_content = $.trim(container.find(".item-content").text());
+            if (!item_content) {
+                $.ajax({
+                    type: "GET",
+                    url: ajax_url,
+                    error: function() {
+                        alert("Getting item content failed.");
+                    },
+                    success: function(item_content) {
+                        container.find(".summary-content").hide("fast");
+                        container.find(".item-content").html(item_content);
+                        container.find(".expanded-content").show("fast");
+                        container.find(".toggle-expand").hide();
+                        container.find(".toggle").show();
+
+                        make_popup_menus();
+                    }
+                });
+            } else {
+                container.find(".summary-content").hide("fast");
+                container.find(".expanded-content").show("fast");
+                container.find(".toggle-expand").hide();
+                container.find(".toggle").show();
+            }
+        };
+
+        // Hide embedded item.
+        var hide_embedded_item = function() {
+            container.find(".expanded-content").hide("fast");
+            container.find(".summary-content").show("fast");
+            container.find(".toggle").hide();
+            container.find(".toggle-expand").show();
+        };
+
+        // Setup toggle expand.
+        var toggle_expand = $(this).find(".toggle-expand");
+        toggle_expand.click(function() {
+            show_embedded_item();
+            return false;
+        });
+
+        // Setup toggle contract.
+        var toggle_contract = $(this).find(".toggle");
+        toggle_contract.click(function() {
+            hide_embedded_item();
+            return false;
+        });
+
+        // Setup toggle embed.
+        var toggle_embed = $(this).find(".toggle-embed");
+        toggle_embed.click(function() {
+            if (container.find(".expanded-content").is(":visible")) {
+                hide_embedded_item();
+            } else {
+                show_embedded_item();
+            }
+            return false;
+        });
+    });
+}
diff --git a/client/galaxy/scripts/mvc/form/form-data.js b/client/galaxy/scripts/mvc/form/form-data.js
index 34206c529b4..ddee9476119 100644
--- a/client/galaxy/scripts/mvc/form/form-data.js
+++ b/client/galaxy/scripts/mvc/form/form-data.js
@@ -214,7 +214,7 @@ export var visitInputs = (inputs, callback, prefix, context) => {
         }
     });
     for (var key in inputs) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var node = inputs[key];
         node.name = node.name || key;
         var name = prefix ? `${prefix}|${node.name}` : node.name;
diff --git a/client/galaxy/scripts/mvc/form/form-parameters.js b/client/galaxy/scripts/mvc/form/form-parameters.js
index 4082e01d419..bae5a5a10be 100644
--- a/client/galaxy/scripts/mvc/form/form-parameters.js
+++ b/client/galaxy/scripts/mvc/form/form-parameters.js
@@ -42,7 +42,7 @@ export default Backbone.Model.extend({
 
     /** Returns an input field for a given field type */
     create: function(input_def) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var fieldClass = this.types[input_def.type];
         var field = typeof this[fieldClass] === "function" ? this[fieldClass].call(this, input_def) : null;
         if (!field) {
@@ -126,7 +126,7 @@ export default Backbone.Model.extend({
     /** Text input field */
     _fieldText: function(input_def) {
         // field replaces e.g. a select field
-        if (input_def.model_class === 'SelectTagParameter' || input_def.options && input_def.data) {
+        if (input_def.model_class === "SelectTagParameter" || (input_def.options && input_def.data)) {
             input_def.area = input_def.multiple;
             if (Utils.isEmpty(input_def.value)) {
                 input_def.value = null;
diff --git a/client/galaxy/scripts/mvc/form/form-repeat.js b/client/galaxy/scripts/mvc/form/form-repeat.js
index 872db3b6795..3adbe7905e4 100644
--- a/client/galaxy/scripts/mvc/form/form-repeat.js
+++ b/client/galaxy/scripts/mvc/form/form-repeat.js
@@ -42,7 +42,7 @@ export var View = Backbone.View.extend({
 
     /** Add new repeat block */
     add: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (!options.id || this.list[options.id]) {
             Galaxy.emit.debug("form-repeat::add()", "Duplicate or invalid repeat block id.");
             return;
@@ -75,7 +75,7 @@ export var View = Backbone.View.extend({
 
     /** Delete repeat block */
     del: function(id) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (!this.list[id]) {
             Galaxy.emit.debug("form-repeat::del()", "Invalid repeat block id.");
             return;
diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js
index 36c17b83281..6d2416fc7a3 100644
--- a/client/galaxy/scripts/mvc/form/form-view.js
+++ b/client/galaxy/scripts/mvc/form/form-view.js
@@ -33,7 +33,7 @@ export default Backbone.View.extend({
             if (field.update) {
                 field.update(node);
                 field.trigger("change");
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 Galaxy.emit.debug("form-view::update()", `Updating input: ${input_id}`);
             }
         });
@@ -157,7 +157,7 @@ export default Backbone.View.extend({
                 message: options.message
             });
         }
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.emit.debug("form-view::initialize()", "Completed");
     }
 });
diff --git a/client/galaxy/scripts/mvc/grid/grid-shared.js b/client/galaxy/scripts/mvc/grid/grid-shared.js
index 307aff1b921..d73f06e2697 100644
--- a/client/galaxy/scripts/mvc/grid/grid-shared.js
+++ b/client/galaxy/scripts/mvc/grid/grid-shared.js
@@ -10,7 +10,7 @@ import LoadingIndicator from "ui/loading-indicator";
 var View = Backbone.View.extend({
     initialize: function(options) {
         var self = this;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         LoadingIndicator.markViewAsLoading(this);
         this.model = new Backbone.Model(options);
         this.item = this.model.get("item");
diff --git a/client/galaxy/scripts/mvc/grid/grid-template.js b/client/galaxy/scripts/mvc/grid/grid-template.js
index 4facf631094..a9975babc93 100644
--- a/client/galaxy/scripts/mvc/grid/grid-template.js
+++ b/client/galaxy/scripts/mvc/grid/grid-template.js
@@ -67,7 +67,7 @@ export default {
                     '<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li>' +
                     '<div popupmenu="popup-global-actions">';
             }
-            for (let action of options.global_actions) {
+            for (const action of options.global_actions) {
                 tmpl += `<li><a class="action-button use-target" target="${action.target}" href="${
                     action.url_args
                 }" onclick="return false;" >${action.label}</a></li>`;
@@ -106,7 +106,7 @@ export default {
         }
 
         // create header elements
-        for (let column of options.columns) {
+        for (const column of options.columns) {
             if (column.visible) {
                 tmpl += `<th id="${column.key}-header">`;
                 if (column.sortable) {
@@ -140,7 +140,7 @@ export default {
         }
 
         // create rows
-        for (let item of options.items) {
+        for (const item of options.items) {
             // Tag current
             tmpl += "<tr ";
             if (options.current_item_id == item.id) {
@@ -156,7 +156,7 @@ export default {
             }
 
             // Data columns
-            for (let column of options.columns) {
+            for (const column of options.columns) {
                 if (column.visible) {
                     // Nowrap
                     var nowrap = "";
@@ -302,7 +302,7 @@ export default {
             `;
 
             // configure buttons for operations
-            for (let operation of options.operations) {
+            for (const operation of options.operations) {
                 if (operation.allow_multiple) {
                     tmpl += `<input type="button" value="${
                         operation.label
@@ -316,7 +316,7 @@ export default {
 
         // count global operations
         var found_global = false;
-        for (let operation of options.operations) {
+        for (const operation of options.operations) {
             if (operation.global_operation) {
                 found_global = true;
                 break;
@@ -326,7 +326,7 @@ export default {
         // add global operations
         if (found_global) {
             tmpl += "<tr>" + '<td colspan="100">';
-            for (let operation of options.operations) {
+            for (const operation of options.operations) {
                 if (operation.global_operation) {
                     tmpl += `<a class="action-button" href="${operation.global_operation}">${operation.label}</a>`;
                 }
@@ -368,7 +368,7 @@ export default {
 
         // identify columns with advanced filtering
         var show_advanced_search_link = false;
-        for (let column of options.columns) {
+        for (const column of options.columns) {
             if (column.filterable == "advanced") {
                 var column_key = column.key;
                 var f_key = filters[column_key];
@@ -392,7 +392,7 @@ export default {
         var tmpl = `<div id="standard-search" style="display: ${standard_search_display};"><table><tr><td style="padding: 0;"><table>`;
 
         // add standard filters
-        for (let column of options.columns) {
+        for (const column of options.columns) {
             if (column.filterable == "standard") {
                 tmpl += this.grid_column_filter(options, column);
             }
@@ -415,7 +415,7 @@ export default {
         tmpl += `<div id="advanced-search" style="display: ${advanced_search_display}; margin-top: 5px;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>`;
 
         // add advanced filters
-        for (let column of options.columns) {
+        for (const column of options.columns) {
             if (column.filterable == "advanced") {
                 tmpl += this.grid_column_filter(options, column);
             }
@@ -448,7 +448,7 @@ export default {
         if (column.is_text) {
             tmpl += `<form class="text-filter-form" column_key="${column_key}" action="${options.url}" method="get" >`;
             // Carry forward filtering criteria with hidden inputs.
-            for (let column of options.columns) {
+            for (const column of options.columns) {
                 var filter_value = filters[column.key];
                 if (filter_value) {
                     if (filter_value != "All") {
@@ -480,7 +480,7 @@ export default {
 
                 // multiple filter values
                 if (type == "array") {
-                    for (let i in column_filter) {
+                    for (const i in column_filter) {
                         // copy filters and remove entry
                         var params = column_filter;
                         params = params.slice(i);
diff --git a/client/galaxy/scripts/mvc/grid/grid-view.js b/client/galaxy/scripts/mvc/grid/grid-view.js
index 45be9958211..dacda894cad 100644
--- a/client/galaxy/scripts/mvc/grid/grid-view.js
+++ b/client/galaxy/scripts/mvc/grid/grid-view.js
@@ -34,7 +34,7 @@ export default Backbone.View.extend({
         store.watch(
             state => state.gridSearch.searchTags,
             newTags => {
-                let tagArray = Array.from(newTags);
+                const tagArray = Array.from(newTags);
                 self.grid.add_filter("tags", tagArray, false);
                 self.openAdvancedSearch();
                 self.render_filter_button("tags", tagArray);
@@ -84,7 +84,7 @@ export default Backbone.View.extend({
     handle_refresh: function(refresh_frames) {
         if (refresh_frames) {
             if ($.inArray("history", refresh_frames) > -1) {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 if (Galaxy && Galaxy.currHistoryPanel) {
                     Galaxy.currHistoryPanel.loadCurrentHistory();
                 }
diff --git a/client/galaxy/scripts/mvc/history/copy-dialog.js b/client/galaxy/scripts/mvc/history/copy-dialog.js
index aeb3b927fac..7a75b6ef641 100644
--- a/client/galaxy/scripts/mvc/history/copy-dialog.js
+++ b/client/galaxy/scripts/mvc/history/copy-dialog.js
@@ -4,6 +4,7 @@ import _l from "utils/localization";
 import _ from "underscore";
 import jQuery from "jquery";
 import { getGalaxyInstance } from "app";
+import { getAppRoot } from "onload/loadConfig";
 
 var $ = jQuery;
 
@@ -35,12 +36,12 @@ var CopyDialog = {
             '<div class="warningmessage">',
             "<%- anonWarning %>",
             _l("You can"),
-            ' <a href="/user/login">',
+            ' <a href="<%= galaxyRoot %>user/login">',
             _l("login here"),
             "</a> ",
             _l("or"),
             " ",
-            ' <a href="/user/create">',
+            ' <a href="<%= galaxyRoot %>user/create">',
             _l("register here"),
             "</a>.",
             "</div>",
@@ -141,12 +142,13 @@ var CopyDialog = {
         }
 
         var originalClosingCallback = options.closing_callback;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         modal.show(
             _.extend(options, {
                 title: this.title({ name: history.get("name") }),
                 body: $(
                     dialog._template({
+                        galaxyRoot: getAppRoot(),
                         name: defaultCopyName,
                         isAnon: Galaxy.user.isAnonymous(),
                         allowAll: allowAll,
@@ -229,7 +231,7 @@ var ImportDialog = _.extend({}, CopyDialog, {
  *     {String} allDatasets default initial checked radio button: 'copy-all' or 'copy-non-deleted',
  */
 var historyCopyDialog = (history, options) => {
-    let Galaxy = getGalaxyInstance();
+    const Galaxy = getGalaxyInstance();
     options = options || {};
     // create our own modal if Galaxy doesn't have one (mako tab without use_panels)
     var modal = Galaxy.modal || new MODAL.View({});
diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js
index 3744648c613..5125126facd 100644
--- a/client/galaxy/scripts/mvc/history/hdca-li.js
+++ b/client/galaxy/scripts/mvc/history/hdca-li.js
@@ -14,7 +14,7 @@ var HDCAListItemView = _super.extend(
         className: `${_super.prototype.className} history-content`,
 
         render: function() {
-            let result = _super.prototype.render.apply(this, arguments);
+            const result = _super.prototype.render.apply(this, arguments);
             this._mountNametags("initialize");
             return result;
         },
@@ -36,10 +36,10 @@ var HDCAListItemView = _super.extend(
         },
 
         _mountNametags(context) {
-            let container = this.$el.find(".nametags")[0];
+            const container = this.$el.find(".nametags")[0];
             if (container) {
-                let { id, model_class, tags } = this.model.attributes;
-                let storeKey = `${model_class}-${id}`;
+                const { id, model_class, tags } = this.model.attributes;
+                const storeKey = `${model_class}-${id}`;
                 mountNametags({ storeKey, tags }, container);
             }
         },
diff --git a/client/galaxy/scripts/mvc/history/history-contents.js b/client/galaxy/scripts/mvc/history/history-contents.js
index 89b9bb67ace..54eb7757e80 100644
--- a/client/galaxy/scripts/mvc/history/history-contents.js
+++ b/client/galaxy/scripts/mvc/history/history-contents.js
@@ -394,7 +394,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     progressivelyFetchDetails: function(options) {
         // TODO: only fetch tags and annotations if specifically requested
         options = options || {};
-        let deferred = jQuery.Deferred();
+        const deferred = jQuery.Deferred();
         this._recursivelyFetch(
             options,
             HDA_MODEL.HistoryDatasetAssociation.prototype.searchAttributes.join(","),
@@ -442,7 +442,8 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
                 data: JSON.stringify({
                     content: id,
                     source: contentType,
-                    type: type
+                    type: type,
+                    copy_elements: true
                 })
             })
             .done(response => {
diff --git a/client/galaxy/scripts/mvc/history/history-list.js b/client/galaxy/scripts/mvc/history/history-list.js
index c5ba80a4867..e1db8645d43 100644
--- a/client/galaxy/scripts/mvc/history/history-list.js
+++ b/client/galaxy/scripts/mvc/history/history-list.js
@@ -32,7 +32,7 @@ var HistoryGridView = GridView.extend({
                     options.success = req => {
                         const contentsStates = req.contents_states;
                         let stateHtml = "";
-                        for (let state of ["ok", "running", "queued", "new", "error"]) {
+                        for (const state of ["ok", "running", "queued", "new", "error"]) {
                             const stateCount = contentsStates[state];
                             if (stateCount) {
                                 stateHtml += `<div class="count-box state-color-${state}" title="Datasets in ${state} state">${stateCount}</div> `;
@@ -67,7 +67,7 @@ var HistoryGridView = GridView.extend({
             })
             .done(() => {
                 historyCopyDialog(history, {}).done(() => {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     if (Galaxy && Galaxy.currHistoryPanel) {
                         Galaxy.currHistoryPanel.loadCurrentHistory();
                     }
@@ -89,7 +89,7 @@ var HistoryGridView = GridView.extend({
 var View = Backbone.View.extend({
     title: _l("Histories"),
     initialize: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         LoadingIndicator.markViewAsLoading(this);
 
         if (options.action_id == "list_published") {
diff --git a/client/galaxy/scripts/mvc/history/history-model.js b/client/galaxy/scripts/mvc/history/history-model.js
index a90de88cab8..bc4f136b46b 100644
--- a/client/galaxy/scripts/mvc/history/history-model.js
+++ b/client/galaxy/scripts/mvc/history/history-model.js
@@ -138,7 +138,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
              *      Note: that this will return false for an anon user even if the history is theirs.
              */
             ownedByCurrUser: function() {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 // no currUser
                 if (!Galaxy || !Galaxy.user) {
                     return false;
diff --git a/client/galaxy/scripts/mvc/history/history-view-edit-current.js b/client/galaxy/scripts/mvc/history/history-view-edit-current.js
index 15b58baf202..ff2f15174d6 100644
--- a/client/galaxy/scripts/mvc/history/history-view-edit-current.js
+++ b/client/galaxy/scripts/mvc/history/history-view-edit-current.js
@@ -117,7 +117,7 @@ var CurrentHistoryView = _super.extend(
 
         /** loads a history & contents w/ details and makes them the current history */
         switchToHistory: function(historyId, attributes) {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (Galaxy.user.isAnonymous()) {
                 this.trigger("error", _l("You must be logged in to switch histories"), _l("Anonymous user"));
                 return $.when();
@@ -129,7 +129,7 @@ var CurrentHistoryView = _super.extend(
 
         /** creates a new history on the server and sets it as the user's current history */
         createNewHistory: function(attributes) {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (Galaxy.user.isAnonymous()) {
                 this.trigger("error", _l("You must be logged in to create histories"), _l("Anonymous user"));
                 return $.when();
@@ -344,7 +344,7 @@ var CurrentHistoryView = _super.extend(
         events: _.extend(_.clone(_super.prototype.events), {
             // the two links in the empty message
             "click .uploader-link": function(ev) {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 Galaxy.upload.show(ev);
             },
             "click .get-data-link": function(ev) {
@@ -384,7 +384,7 @@ var CurrentHistoryView = _super.extend(
                 // when the center panel is given a new view, clear the current indicator
                 "center-panel:load": function(view) {
                     try {
-                        let hdaId = view.model.attributes.dataset_id || null;
+                        const hdaId = view.model.attributes.dataset_id || null;
                         if (hdaId === null) {
                             throw "Invalid id";
                         }
diff --git a/client/galaxy/scripts/mvc/history/history-view-edit.js b/client/galaxy/scripts/mvc/history/history-view-edit.js
index 0f9c17612b9..1531e1f6a94 100644
--- a/client/galaxy/scripts/mvc/history/history-view-edit.js
+++ b/client/galaxy/scripts/mvc/history/history-view-edit.js
@@ -155,18 +155,18 @@ var HistoryViewEdit = _super.extend(
 
         /** render the tags sub-view controller */
         _renderTags: function($where) {
-            let el = $where.find(".controls .tags-display")[0];
+            const el = $where.find(".controls .tags-display")[0];
 
-            let propsData = {
+            const propsData = {
                 model: this.model,
                 disabled: false,
                 context: "history-view-edit"
             };
 
-            let vm = mountModelTags(propsData, el);
+            const vm = mountModelTags(propsData, el);
 
             // tag icon button open/closes
-            let activator = faIconButton({
+            const activator = faIconButton({
                 title: _l("Edit history tags"),
                 classes: "history-tag-btn",
                 faIcon: "fa-tags",
@@ -283,7 +283,7 @@ var HistoryViewEdit = _super.extend(
 
                 var xhr = jQuery.ajax(options);
                 xhr.done((message, status, responseObj) => {
-                    for (let updated of message) {
+                    for (const updated of message) {
                         const typeId = updated.history_content_type + "-" + updated.id;
                         actionModels[typeId].set(updated);
                     }
diff --git a/client/galaxy/scripts/mvc/history/history-view.js b/client/galaxy/scripts/mvc/history/history-view.js
index 67135c2b576..4e96b1ff6f6 100644
--- a/client/galaxy/scripts/mvc/history/history-view.js
+++ b/client/galaxy/scripts/mvc/history/history-view.js
@@ -635,7 +635,7 @@ export function historyEntry(options) {
     $("#switch").click(function() {
         //##HACK:ity hack hack
         //##TODO: remove when out of iframe
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var hview = Galaxy.currHistoryPanel ? Galaxy.currHistoryPanel : null;
         if (hview) {
             hview.switchToHistory("${ history[ 'id' ] }");
@@ -649,12 +649,12 @@ export function historyEntry(options) {
         $("#center").addClass("flex-vertical-container");
     }
 
-    let viewClass = options.userIsOwner ? HistoryViewEdit.HistoryViewEdit : HistoryView.HistoryView;
-    let history = new History(options.historyJSON);
+    const viewClass = options.userIsOwner ? HistoryViewEdit.HistoryViewEdit : HistoryView.HistoryView;
+    const history = new History(options.historyJSON);
 
     // attach the copy dialog to the import button now that we have a history
     $("#import").click(function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         HistoryCopyDialog(history, {
             useImport: true,
             // use default datasets option to match the toggle-deleted button
@@ -668,7 +668,7 @@ export function historyEntry(options) {
         });
     });
 
-    let historyView = new viewClass({
+    const historyView = new viewClass({
         el: $("#history-" + options.historyJSON.id),
         className: viewClass.prototype.className + " wide",
         $scrollContainer: options.hasMasthead
diff --git a/client/galaxy/scripts/mvc/history/multi-panel.js b/client/galaxy/scripts/mvc/history/multi-panel.js
index 7df50251f15..104bcbab12e 100644
--- a/client/galaxy/scripts/mvc/history/multi-panel.js
+++ b/client/galaxy/scripts/mvc/history/multi-panel.js
@@ -218,25 +218,25 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
                     <button type="button" class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">
                         <span class="caret"></span>
                     </button>
-                    <ul class="dropdown-menu" role="menu">
+                    <div class="dropdown-menu" role="menu">
                         <% if( !data.history.deleted ){ %>
-                            <li><a href="javascript:void(0);" class="copy-history">
+                            <a class="dropdown-item" href="javascript:void(0);" class="copy-history">
                                 ${_l("Copy")}
-                            </a></li>
-                            <li><a href="javascript:void(0);" class="delete-history">
+                            </a>
+                            <a class="dropdown-item" href="javascript:void(0);" class="delete-history">
                                 ${_l("Delete")}
-                            </a></li>
+                            </a>
                         <% } else /* if is deleted */ { %>
-                            <li><a href="javascript:void(0);" class="undelete-history">
+                            <a class="dropdown-item" href="javascript:void(0);" class="undelete-history">
                                 ${_l("Undelete")}
-                            </a></li>
+                            </a>
                         <% } %>
                         <% if( data.view.purgeAllowed ){ %>
-                            <li><a href="javascript:void(0);" class="purge-history">
+                            <a class="dropdown-item" href="javascript:void(0);" class="purge-history">
                                 ${_l("Purge")}
-                            </a></li>
+                            </a>
                         <% } %>
-                    </ul>
+                    </div>
                 </div>
             <% } %>
         </div>`,
@@ -473,7 +473,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
 
     /** create a column and its panel and set up any listeners to them */
     createColumn: function createColumn(history, options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         // options passed can be re-used, so extend them before adding the model to prevent pollution for the next
         options = _.extend({}, options, {
             model: history,
@@ -756,7 +756,6 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         "click .order .set-order": "_chooseOrder",
         "click #toggle-deleted": "_clickToggleDeletedDatasets",
         "click #toggle-hidden": "_clickToggleHiddenDatasets"
-        //'dragstart .list-item .title-bar'                       : function( e ){ console.debug( 'ok' ); }
     },
 
     close: function(ev) {
@@ -768,6 +767,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         this.toggleDeletedHistories($(ev.currentTarget).is(":checked"));
         this.toggleOptionsPopover();
     },
+
     /** Include deleted histories in the collection */
     toggleDeletedHistories: function(show) {
         if (show) {
@@ -835,7 +835,19 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     /** Set up any view plugins */
     setUpBehaviors: function() {
         this._moreOptionsPopover();
-
+        const searchHistories = searchFor => {
+            const multipanel = this;
+            this.historySearch = searchFor;
+            this.filters = [
+                function() {
+                    // This is intentionally a function where 'this' gets
+                    // bound, applying the filter to the model of the
+                    // caller.
+                    return this.model.matchesAll(multipanel.historySearch);
+                }
+            ];
+            this.renderColumns(0);
+        };
         // input to search histories
         this.$("#search-histories").searchInput({
             name: "search-histories",
@@ -847,17 +859,11 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
                 this.collection.fetchAll().done(() => {
                     this.$("#search-histories").searchInput("toggle-loading");
                     this.renderInfo("");
+                    searchHistories(searchFor);
                 });
             },
-            onsearch: searchFor => {
-                this.historySearch = searchFor;
-                this.filters = [
-                    () => {
-                        return this.model.matchesAll(this.historySearch);
-                    }
-                ];
-                this.renderColumns(0);
-            },
+
+            onsearch: searchHistories,
             onclear: searchFor => {
                 this.historySearch = null;
                 //TODO: remove specifically not just reset
@@ -1055,36 +1061,40 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     },
 
     optionsPopoverTemplate: _.template(
-        [
-            '<div class="more-options d-flex flex-column">',
-            '<div class="order btn-group mb-2">',
-            '<button type="button" class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">',
-            `${_l("Order histories by")} `,
-            '<span class="current-order"><%- view.orderDescriptions[ view.collection.order ] %></span> ',
-            '<span class="caret"></span>',
-            "</button>",
-            '<ul class="dropdown-menu" role="menu">',
-            "<% _.each( view.orderDescriptions, function( text, order ){ %>",
-            '<li class="dropdown-item"><a href="javascript:void(0);" class="set-order" data-order="<%- order %>">',
-            "<%- text %>",
-            "</a></li>",
-            "<% }); %>",
-            "</ul>",
-            "</div>",
-
-            '<div class="checkbox"><label><input id="include-deleted" type="checkbox"',
-            '<%= view.collection.includeDeleted? " checked" : "" %>>',
-            _l("Include deleted histories"),
-            "</label></div>",
-
-            '<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',
-            _l("Include deleted datasets"),
-            "</label></div>",
-            '<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',
-            _l("Include hidden datasets"),
-            "</label></div>",
-            "</div>"
-        ].join(""),
+        `<div class="more-options d-flex flex-column">
+            <div class="order btn-group mb-2">
+                <button type="button" class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">
+                    ${_l("Order histories by")}
+                    <span class="current-order"><%- view.orderDescriptions[ view.collection.order ] %></span>
+                    <span class="caret"/>
+                </button>
+                <div class="dropdown-menu" role="menu">
+                    <% _.each( view.orderDescriptions, function( text, order ){ %>
+                        <a href="javascript:void(0);" class="dropdown-item set-order" data-order="<%- order %>">
+                            <%- text %>
+                        </a>
+                    <% }); %>
+                </div>
+            </div>
+            <div class="checkbox">
+                <label>
+                    <input id="include-deleted" type="checkbox" <%= view.collection.includeDeleted? " checked" : "" %>>
+                    ${_l("Include deleted histories")}
+                </label>
+            </div>
+            <div class="checkbox">
+                <label>
+                    <input id="toggle-deleted" type="checkbox">
+                    ${_l("Include deleted datasets")}
+                </label>
+            </div>
+            <div class="checkbox">
+                <label>
+                    <input id="toggle-hidden" type="checkbox">
+                    ${_l("Include hidden datasets")}
+                </label>
+            </div>
+        </div>`,
         { variable: "view" }
     )
 });
diff --git a/client/galaxy/scripts/mvc/history/options-menu.js b/client/galaxy/scripts/mvc/history/options-menu.js
index d40885d1d93..411d4a6d2cb 100644
--- a/client/galaxy/scripts/mvc/history/options-menu.js
+++ b/client/galaxy/scripts/mvc/history/options-menu.js
@@ -10,28 +10,14 @@ import Webhooks from "mvc/webhooks";
 // ============================================================================
 var menu = [
     {
-        html: _l("History Lists"),
-        header: true
-    },
-    {
-        html: _l("Saved Histories"),
-        href: "histories/list",
-        target: "_top"
-    },
-    {
-        html: _l("Histories Shared with Me"),
-        href: "histories/list_shared",
-        target: "_top"
-    },
-    {
-        html: _l("Current History"),
+        html: _l("History Actions"),
         header: true,
         anon: true
     },
     {
-        html: _l("Copy History"),
+        html: _l("Copy"),
         func: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             historyCopyDialog(Galaxy.currHistoryPanel.model).done(() => {
                 Galaxy.currHistoryPanel.loadCurrentHistory();
             });
@@ -40,7 +26,7 @@ var menu = [
     {
         html: _l("Share or Publish"),
         func: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
                 Galaxy.router.push(`/histories/sharing?id=${Galaxy.currHistoryPanel.model.id}`);
             }
@@ -50,7 +36,7 @@ var menu = [
         html: _l("Show Structure"),
         anon: true,
         func: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
                 Galaxy.router.push("/histories/show_structure");
             }
@@ -61,39 +47,19 @@ var menu = [
         href: "workflow/build_from_current_history"
     },
     {
-        html: _l("Delete"),
-        anon: true,
+        html: _l("Set Permissions"),
         func: function() {
-            let Galaxy = getGalaxyInstance();
-            if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really delete the current history?"))) {
-                Galaxy.currHistoryPanel.model._delete().done(() => {
-                    Galaxy.currHistoryPanel.loadCurrentHistory();
-                });
+            const Galaxy = getGalaxyInstance();
+            if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
+                Galaxy.router.push(`/histories/permissions?id=${Galaxy.currHistoryPanel.model.id}`);
             }
         }
     },
     {
-        html: _l("Delete Permanently"),
-        purge: true,
+        html: _l("Make Private"),
         anon: true,
         func: function() {
-            let Galaxy = getGalaxyInstance();
-            if (
-                Galaxy &&
-                Galaxy.currHistoryPanel &&
-                confirm(_l("Really delete the current history permanently? This cannot be undone."))
-            ) {
-                Galaxy.currHistoryPanel.model.purge().done(() => {
-                    Galaxy.currHistoryPanel.loadCurrentHistory();
-                });
-            }
-        }
-    },
-    {
-        html: _l("Make Data Private"),
-        anon: true,
-        func: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (
                 Galaxy &&
                 Galaxy.currHistoryPanel &&
@@ -109,6 +75,11 @@ var menu = [
             }
         }
     },
+    {
+        html: _l("Resume Paused Jobs"),
+        href: "history/resume_paused_jobs?current=True",
+        anon: true
+    },
     {
         html: _l("Dataset Actions"),
         header: true,
@@ -118,24 +89,10 @@ var menu = [
         html: _l("Copy Datasets"),
         href: "dataset/copy_datasets"
     },
-    {
-        html: _l("Dataset Security"),
-        func: function() {
-            let Galaxy = getGalaxyInstance();
-            if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
-                Galaxy.router.push(`/histories/permissions?id=${Galaxy.currHistoryPanel.model.id}`);
-            }
-        }
-    },
-    {
-        html: _l("Resume Paused Jobs"),
-        href: "history/resume_paused_jobs?current=True",
-        anon: true
-    },
     {
         html: _l("Collapse Expanded Datasets"),
         func: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel) {
                 Galaxy.currHistoryPanel.collapseAll();
             }
@@ -145,7 +102,7 @@ var menu = [
         html: _l("Unhide Hidden Datasets"),
         anon: true,
         func: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             // TODO: Deprecate this functionality and replace with group dataset selector and action combination
             if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really unhide all hidden datasets?"))) {
                 $.post(`${getAppRoot()}history/adjust_hidden`, { user_action: "unhide" }, () => {
@@ -158,7 +115,7 @@ var menu = [
         html: _l("Delete Hidden Datasets"),
         anon: true,
         func: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             // TODO: Deprecate this functionality and replace with group dataset selector and action combination
             if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really delete all hidden datasets?"))) {
                 $.post(`${getAppRoot()}history/adjust_hidden`, { user_action: "delete" }, () => {
@@ -183,7 +140,7 @@ var menu = [
         html: _l("Export Tool Citations"),
         anon: true,
         func: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
                 Galaxy.router.push(`/histories/citations?id=${Galaxy.currHistoryPanel.model.id}`);
             }
@@ -242,7 +199,7 @@ function buildMenu(isAnon, purgeAllowed, urlRoot) {
         if (menuOption.confirm) {
             menuOption.func = () => {
                 const galaxy_main = window.parent.document.getElementById("galaxy_main");
-                if (confirm(menuOption.confirm) && galaxy_main){
+                if (confirm(menuOption.confirm) && galaxy_main) {
                     galaxy_main.src = menuOption.href;
                 }
             };
diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js
index c357e05e3d0..bd16d475e7f 100644
--- a/client/galaxy/scripts/mvc/library/library-dataset-view.js
+++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js
@@ -67,7 +67,7 @@ var LibraryDatasetView = Backbone.View.extend({
     },
 
     fetchDataset: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         this.model = new mod_library_model.Item({
             id: this.options.id
@@ -184,7 +184,7 @@ var LibraryDatasetView = Backbone.View.extend({
 
     importIntoHistory: function() {
         this.refreshUserHistoriesList(self => {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             var template = self.templateBulkImportInModal();
             self.modal = Galaxy.modal;
             self.modal.show({
@@ -255,7 +255,7 @@ var LibraryDatasetView = Backbone.View.extend({
     },
 
     processImportToHistory: function(history_id) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var historyItem = new mod_library_model.HistoryItem();
         historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
         // set the used history as current so user will see the last one
@@ -285,7 +285,7 @@ var LibraryDatasetView = Backbone.View.extend({
     },
 
     showPermissions: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var template = this.templateDatasetPermissions();
         var self = this;
         this.options = _.extend(this.options, options);
@@ -400,7 +400,7 @@ var LibraryDatasetView = Backbone.View.extend({
     },
 
     detectDatatype: function(options) {
-        let ld = this.model;
+        const ld = this.model;
         ld.set("file_ext", "auto");
         this._submitModification(ld);
     },
@@ -611,516 +611,588 @@ var LibraryDatasetView = Backbone.View.extend({
 
     templateDataset: function() {
         return _.template(
-            [
-                // CONTAINER START
-                '<div class="library_style_container">',
-                '<div class="d-flex mb-2">',
-                '<button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-secondary toolbtn-download-dataset toolbar-item mr-1" type="button">',
-                '<span class="fa fa-download"></span>',
-                "&nbsp;Download",
-                "</button>",
-                '<button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-secondary toolbtn-import-dataset toolbar-item mr-1" type="button">',
-                '<span class="fa fa-book"></span>',
-                "&nbsp;to History",
-                "</button>",
-                '<% if (item.get("can_user_modify")) { %>',
-                '<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-secondary toolbtn_modify_dataset toolbar-item mr-1" type="button">',
-                '<span class="fa fa-pencil"></span>',
-                "&nbsp;Modify",
-                "</button>",
-                '<button data-toggle="tooltip" data-placement="top" title="Attempt to detect the format of dataset" class="btn btn-secondary toolbtn_detect_datatype toolbar-item mr-1" type="button">',
-                '<span class="fa fa-undo"></span>',
-                "&nbsp;Auto-detect datatype",
-                "</button>",
-                "<% } %>",
-                '<% if (item.get("can_user_manage")) { %>',
-                '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">',
-                '<button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-secondary toolbtn_change_permissions toolbar-item mr-1" type="button">',
-                '<span class="fa fa-group"></span>',
-                "&nbsp;Permissions",
-                "</button>",
-                "</a>",
-                "<% } %>",
-                "</div>",
+            `<!-- CONTAINER START -->
+            <div class="library_style_container">
+                <div class="d-flex mb-2">
+                    <button data-toggle="tooltip" data-placement="top" title="Download dataset"
+                        class="btn btn-secondary toolbtn-download-dataset toolbar-item mr-1" type="button">
+                        <span class="fa fa-download"></span>
+                        &nbsp;Download
+                    </button>
+                    <button data-toggle="tooltip" data-placement="top" title="Import dataset into history"
+                        class="btn btn-secondary toolbtn-import-dataset toolbar-item mr-1" type="button">
+                        <span class="fa fa-book"></span>
+                        &nbsp;to History
+                    </button>
+                    <% if (item.get("can_user_modify")) { %>
+                        <button data-toggle="tooltip" data-placement="top" title="Modify library item"
+                            class="btn btn-secondary toolbtn_modify_dataset toolbar-item mr-1" type="button">
+                            <span class="fa fa-pencil"></span>
+                            &nbsp;Modify
+                        </button>
+                        <button data-toggle="tooltip" data-placement="top"
+                            title="Attempt to detect the format of dataset"
+                            class="btn btn-secondary toolbtn_detect_datatype toolbar-item mr-1" type="button">
+                            <span class="fa fa-undo"></span>
+                            &nbsp;Auto-detect datatype
+                        </button>
+                    <% } %>
+                    <% if (item.get("can_user_manage")) { %>
+                        <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">
+                            <button data-toggle="tooltip" data-placement="top" title="Manage permissions"
+                                class="btn btn-secondary toolbtn_change_permissions toolbar-item mr-1"
+                                type="button">
+                                <span class="fa fa-group"></span>
+                                &nbsp;Permissions
+                            </button>
+                        </a>
+                    <% } %>
+                </div>
 
-                // BREADCRUMBS
-                '<ol class="breadcrumb">',
-                '<li class="breadcrumb-item"><a title="Return to the list of libraries" href="#">Libraries</a></li>',
-                '<% _.each(item.get("full_path"), function(path_item) { %>',
-                "<% if (path_item[0] != item.id) { %>",
-                '<li class="breadcrumb-item"><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',
-                "<% } else { %>",
-                '<li class="breadcrumb-item active"><span title="You are here"><%- path_item[1] %></span></li>',
-                "<% } %>",
-                "<% }); %>",
-                "</ol>",
+                <!-- BREADCRUMBS -->
+                <ol class="breadcrumb">
+                    <li class="breadcrumb-item">
+                        <a title="Return to the list of libraries" href="#">Libraries</a>
+                    </li>
+                    <% _.each(item.get("full_path"), function(path_item) { %>
+                        <% if (path_item[0] != item.id) { %>
+                            <li class="breadcrumb-item">
+                                <a title="Return to this folder" href="#/folders/<%- path_item[0] %>">
+                                    <%- path_item[1] %>
+                                </a>
+                            </li>
+                        <% } else { %>
+                            <li class="breadcrumb-item active">
+                                <span title="You are here"><%- path_item[1] %></span>
+                            </li>
+                        <% } %>
+                    <% }); %>
+                </ol>
+                <% if (item.get("is_unrestricted")) { %>
+                    <div>
+                        This dataset is unrestricted so everybody with the link can access it.
+                        Just share <span class="copy-link-to-clipboard"><a href=""a>this page</a></span>.
+                    </div>
+                <% } %>
 
-                '<% if (item.get("is_unrestricted")) { %>',
-                "<div>",
-                'This dataset is unrestricted so everybody with the link can access it. Just share <span class="copy-link-to-clipboard"><a href=""a>this page</a></span>.',
-                "</div>",
-                "<% } %>",
+                <!-- TABLE START -->
+                <div class="dataset_table">
+                    <table class="grid table table-striped table-sm">
+                        <tr>
+                            <th class="dataset-first-column" scope="row" id="id_row"
+                                data-id="<%= _.escape(item.get("ldda_id")) %>">
+                                Name
+                            </th>
+                            <td><%= _.escape(item.get("name")) %></td>
+                        </tr>
+                        <% if (item.get("file_ext")) { %>
+                            <tr>
+                                <th scope="row">Data type</th>
+                                <td><%= _.escape(item.get("file_ext")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("genome_build")) { %>
+                            <tr>
+                                <th scope="row">Genome build</th>
+                                <td><%= _.escape(item.get("genome_build")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("file_size")) { %>
+                            <tr>
+                                <th scope="row">Size</th>
+                                <td><%= _.escape(item.get("file_size")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("date_uploaded")) { %>
+                            <tr>
+                                <th scope="row">Date uploaded (UTC)</th>
+                                <td><%= _.escape(item.get("date_uploaded")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("uploaded_by")) { %>
+                            <tr>
+                                <th scope="row">Uploaded by</th>
+                                <td><%= _.escape(item.get("uploaded_by")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("metadata_data_lines")) { %>
+                            <tr>
+                                <th scope="row">Data Lines</th>
+                                <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("metadata_comment_lines")) { %>
+                            <tr>
+                                <th scope="row">Comment Lines</th>
+                                <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("metadata_columns")) { %>
+                            <tr>
+                                <th scope="row">Number of Columns</th>
+                                <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("metadata_column_types")) { %>
+                            <tr>
+                                <th scope="row">Column Types</th>
+                                <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("message")) { %>
+                            <tr>
+                                <th scope="row">Message</th>
+                                <td scope="row"><%= _.escape(item.get("message")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("misc_blurb")) { %>
+                            <tr>
+                                <th scope="row">Misc. blurb</th>
+                                <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("misc_info")) { %>
+                            <tr>
+                                <th scope="row">Misc. info</th>
+                                <td scope="row"><%= _.escape(item.get("misc_info")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("tags")) { %>
+                            <tr>
+                                <th scope="row">Tags</th>
+                                <td scope="row"><%= _.escape(item.get("tags")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if ( item.get("uuid") !== "ok" ) { %>
+                            <tr>
+                                <th scope="row">UUID</th>
+                                <td scope="row"><%= _.escape(item.get("uuid")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if ( item.get("state") !== "ok" ) { %>
+                            <tr>
+                                <th scope="row">State</th>
+                                <td scope="row"><%= _.escape(item.get("state")) %></td>
+                            </tr>
+                        <% } %>
+                    </table>
+                    <% if (item.get("job_stderr")) { %>
+                        <h4>Job Standard Error</h4>
+                        <pre class="code">
+                            <%= _.escape(item.get("job_stderr")) %>
+                        </pre>
+                    <% } %>
+                    <% if (item.get("job_stdout")) { %>
+                        <h4>Job Standard Output</h4>
+                        <pre class="code">
+                            <%= _.escape(item.get("job_stdout")) %>
+                        </pre>
+                    <% } %>
+                    <div>
+                        <pre class="peek">
+                        </pre>
+                    </div>
+                    <% if (item.get("has_versions")) { %>
+                        <div>
+                            <h3>Expired versions:</h3>
+                            <ul>
+                                <% _.each(item.get("expired_versions"), function(version) { %>
+                                    <li>
+                                        <a title="See details of this version"
+                                            href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>">
+                                            <%- version[1] %>
+                                        </a>
+                                    </li>
+                                <% }) %>
+                            <ul>
+                        </div>
+                    <% } %>
 
-                // TABLE START
-                '<div class="dataset_table">',
-                '<table class="grid table table-striped table-sm">',
-                "<tr>",
-                '<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>',
-                '<td><%= _.escape(item.get("name")) %></td>',
-                "</tr>",
-                '<% if (item.get("file_ext")) { %>',
-                "<tr>",
-                '<th scope="row">Data type</th>',
-                '<td><%= _.escape(item.get("file_ext")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("genome_build")) { %>',
-                "<tr>",
-                '<th scope="row">Genome build</th>',
-                '<td><%= _.escape(item.get("genome_build")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("file_size")) { %>',
-                "<tr>",
-                '<th scope="row">Size</th>',
-                '<td><%= _.escape(item.get("file_size")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("date_uploaded")) { %>',
-                "<tr>",
-                '<th scope="row">Date uploaded (UTC)</th>',
-                '<td><%= _.escape(item.get("date_uploaded")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("uploaded_by")) { %>',
-                "<tr>",
-                '<th scope="row">Uploaded by</th>',
-                '<td><%= _.escape(item.get("uploaded_by")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("metadata_data_lines")) { %>',
-                "<tr>",
-                '<th scope="row">Data Lines</th>',
-                '<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("metadata_comment_lines")) { %>',
-                "<tr>",
-                '<th scope="row">Comment Lines</th>',
-                '<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("metadata_columns")) { %>',
-                "<tr>",
-                '<th scope="row">Number of Columns</th>',
-                '<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("metadata_column_types")) { %>',
-                "<tr>",
-                '<th scope="row">Column Types</th>',
-                '<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("message")) { %>',
-                "<tr>",
-                '<th scope="row">Message</th>',
-                '<td scope="row"><%= _.escape(item.get("message")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("misc_blurb")) { %>',
-                "<tr>",
-                '<th scope="row">Misc. blurb</th>',
-                '<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("misc_info")) { %>',
-                "<tr>",
-                '<th scope="row">Misc. info</th>',
-                '<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("tags")) { %>',
-                "<tr>",
-                '<th scope="row">Tags</th>',
-                '<td scope="row"><%= _.escape(item.get("tags")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if ( item.get("uuid") !== "ok" ) { %>',
-                "<tr>",
-                '<th scope="row">UUID</th>',
-                '<td scope="row"><%= _.escape(item.get("uuid")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if ( item.get("state") !== "ok" ) { %>',
-                "<tr>",
-                '<th scope="row">State</th>',
-                '<td scope="row"><%= _.escape(item.get("state")) %></td>',
-                "</tr>",
-                "<% } %>",
-                "</table>",
+                <!-- TABLE END -->
+                </div>
 
-                '<% if (item.get("job_stderr")) { %>',
-                "<h4>Job Standard Error</h4>",
-                '<pre class="code">',
-                '<%= _.escape(item.get("job_stderr")) %>',
-                "</pre>",
-                "<% } %>",
-
-                '<% if (item.get("job_stdout")) { %>',
-                "<h4>Job Standard Output</h4>",
-                '<pre class="code">',
-                '<%= _.escape(item.get("job_stdout")) %>',
-                "</pre>",
-                "<% } %>",
-
-                "<div>",
-                '<pre class="peek">',
-                "</pre>",
-                "</div>",
-
-                '<% if (item.get("has_versions")) { %>',
-                "<div>",
-                "<h3>Expired versions:</h3>",
-                "<ul>",
-                '<% _.each(item.get("expired_versions"), function(version) { %>',
-                '<li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>',
-                "<% }) %>",
-                "<ul>",
-                "</div>",
-                "<% } %>",
-                // TABLE END
-                "</div>",
-                // CONTAINER END
-                "</div>"
-            ].join("")
+            <!-- CONTAINER END -->
+            </div>`
         );
     },
 
     templateVersion: function() {
         return _.template(
-            [
-                // CONTAINER START
-                '<div class="library_style_container">',
-                '<div class="d-flex mb-2">',
-                '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">',
-                '<button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-secondary toolbar-item mr-1" type="button">',
-                '<span class="fa fa-caret-left fa-lg"></span>',
-                "&nbsp;Latest dataset",
-                "</button>",
-                "<a>",
-                "</div>",
+            `<!-- CONTAINER START -->
+            <div class="library_style_container">
+                <div class="d-flex mb-2">
+                    <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">
+                        <button data-toggle="tooltip" data-placement="top" title="Go to latest dataset"
+                            class="btn btn-secondary toolbar-item mr-1" type="button">
+                            <span class="fa fa-caret-left fa-lg"></span>
+                            &nbsp;Latest dataset
+                        </button>
+                    </a>
+                </div>
 
-                // BREADCRUMBS
-                '<ol class="breadcrumb">',
-                '<li class="breadcrumb-item"><a title="Return to the list of libraries" href="#">Libraries</a></li>',
-                '<% _.each(item.get("full_path"), function(path_item) { %>',
-                "<% if (path_item[0] != item.id) { %>",
-                '<li class="breadcrumb-item"><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',
-                "<% } else { %>",
-                '<li class="breadcrumb-item active"><span title="You are here"><%- path_item[1] %></span></li>',
-                "<% } %>",
-                "<% }); %>",
-                "</ol>",
+                <!-- BREADCRUMBS -->
+                <ol class="breadcrumb">
+                    <li class="breadcrumb-item">
+                        <a title="Return to the list of libraries" href="#">Libraries</a>
+                    </li>
+                    <% _.each(item.get("full_path"), function(path_item) { %>
+                        <% if (path_item[0] != item.id) { %>
+                            <li class="breadcrumb-item">
+                                <a title="Return to this folder" href="#/folders/<%- path_item[0] %>">
+                                    <%- path_item[1] %>
+                                </a>
+                            </li>
+                        <% } else { %>
+                            <li class="breadcrumb-item active">
+                                <span title="You are here">
+                                    <%- path_item[1] %>
+                                </span>
+                            </li>
+                        <% } %>
+                    <% }); %>
+                </ol>
+                <div class="alert alert-warning">
+                    This is an expired version of the library dataset: <%= _.escape(item.get("name")) %>
+                </div>
 
-                '<div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>',
-                // DATASET START
-                '<div class="dataset_table">',
-                '<table class="grid table table-striped table-sm">',
-                "<tr>",
-                '<th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>',
-                '<td><%= _.escape(ldda.get("name")) %></td>',
-                "</tr>",
-                '<% if (ldda.get("file_ext")) { %>',
-                "<tr>",
-                '<th scope="row">Data type</th>',
-                '<td><%= _.escape(ldda.get("file_ext")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("genome_build")) { %>',
-                "<tr>",
-                '<th scope="row">Genome build</th>',
-                '<td><%= _.escape(ldda.get("genome_build")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("file_size")) { %>',
-                "<tr>",
-                '<th scope="row">Size</th>',
-                '<td><%= _.escape(ldda.get("file_size")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("date_uploaded")) { %>',
-                "<tr>",
-                '<th scope="row">Date uploaded (UTC)</th>',
-                '<td><%= _.escape(ldda.get("date_uploaded")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("uploaded_by")) { %>',
-                "<tr>",
-                '<th scope="row">Uploaded by</th>',
-                '<td><%= _.escape(ldda.get("uploaded_by")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("metadata_data_lines")) { %>',
-                "<tr>",
-                '<th scope="row">Data Lines</th>',
-                '<td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("metadata_comment_lines")) { %>',
-                "<tr>",
-                '<th scope="row">Comment Lines</th>',
-                '<td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("metadata_columns")) { %>',
-                "<tr>",
-                '<th scope="row">Number of Columns</th>',
-                '<td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("metadata_column_types")) { %>',
-                "<tr>",
-                '<th scope="row">Column Types</th>',
-                '<td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("message")) { %>',
-                "<tr>",
-                '<th scope="row">Message</th>',
-                '<td scope="row"><%= _.escape(ldda.get("message")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("misc_blurb")) { %>',
-                "<tr>",
-                '<th scope="row">Miscellaneous blurb</th>',
-                '<td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (ldda.get("misc_info")) { %>',
-                "<tr>",
-                '<th scope="row">Miscellaneous information</th>',
-                '<td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if (item.get("tags")) { %>',
-                "<tr>",
-                '<th scope="row">Tags</th>',
-                '<td scope="row"><%= _.escape(item.get("tags")) %></td>',
-                "</tr>",
-                "<% } %>",
-                "</table>",
-                "<div>",
-                '<pre class="peek">',
-                "</pre>",
-                "</div>",
-                // DATASET END
-                "</div>",
-                // CONTAINER END
-                "</div>"
-            ].join("")
+                <!-- DATASET START -->
+                <div class="dataset_table">
+                    <table class="grid table table-striped table-sm">
+                        <tr>
+                            <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>
+                            <td><%= _.escape(ldda.get("name")) %></td>
+                        </tr>
+                        <% if (ldda.get("file_ext")) { %>
+                            <tr>
+                                <th scope="row">Data type</th>
+                                <td><%= _.escape(ldda.get("file_ext")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("genome_build")) { %>
+                            <tr>
+                                <th scope="row">Genome build</th>
+                                <td><%= _.escape(ldda.get("genome_build")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("file_size")) { %>
+                            <tr>
+                                <th scope="row">Size</th>
+                                <td><%= _.escape(ldda.get("file_size")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("date_uploaded")) { %>
+                            <tr>
+                                <th scope="row">Date uploaded (UTC)</th>
+                                <td><%= _.escape(ldda.get("date_uploaded")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("uploaded_by")) { %>
+                            <tr>
+                                <th scope="row">Uploaded by</th>
+                                <td><%= _.escape(ldda.get("uploaded_by")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("metadata_data_lines")) { %>
+                            <tr>
+                                <th scope="row">Data Lines</th>
+                                <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("metadata_comment_lines")) { %>
+                            <tr>
+                                <th scope="row">Comment Lines</th>
+                                <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("metadata_columns")) { %>
+                            <tr>
+                                <th scope="row">Number of Columns</th>
+                                <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("metadata_column_types")) { %>
+                            <tr>
+                                <th scope="row">Column Types</th>
+                                <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("message")) { %>
+                            <tr>
+                                <th scope="row">Message</th>
+                                <td scope="row"><%= _.escape(ldda.get("message")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("misc_blurb")) { %>
+                            <tr>
+                                <th scope="row">Miscellaneous blurb</th>
+                                <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (ldda.get("misc_info")) { %>
+                            <tr>
+                                <th scope="row">Miscellaneous information</th>
+                                <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>
+                            </tr>
+                        <% } %>
+                        <% if (item.get("tags")) { %>
+                            <tr>
+                                <th scope="row">Tags</th>
+                                <td scope="row"><%= _.escape(item.get("tags")) %></td>
+                            </tr>
+                        <% } %>
+                    </table>
+                    <div>
+                        <pre class="peek">
+                        </pre>
+                    </div>
+                <!-- DATASET END -->
+                </div>
+            <!-- CONTAINER END -->
+            </div>`
         );
     },
 
     templateModifyDataset: function() {
         return _.template(
-            [
-                // CONTAINER START
-                '<div class="library_style_container">',
+            `<!-- CONTAINER START -->
+            <div class="library_style_container">
 
-                // BREADCRUMBS
-                '<ol class="breadcrumb">',
-                '<li class="breadcrumb-item"><a title="Return to the list of libraries" href="#">Libraries</a></li>',
-                '<% _.each(item.get("full_path"), function(path_item) { %>',
-                "<% if (path_item[0] != item.id) { %>",
-                '<li class="breadcrumb-item"><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',
-                "<% } else { %>",
-                '<li class="breadcrumb-item active"><span title="You are here"><%- path_item[1] %></span></li>',
-                "<% } %>",
-                "<% }); %>",
-                "</ol>",
+                <!-- BREADCRUMBS -->
+                <ol class="breadcrumb">
+                    <li class="breadcrumb-item">
+                        <a title="Return to the list of libraries" href="#">Libraries</a>
+                    </li>
+                    <% _.each(item.get("full_path"), function(path_item) { %>
+                        <% if (path_item[0] != item.id) { %>
+                            <li class="breadcrumb-item">
+                                <a title="Return to this folder" href="#/folders/<%- path_item[0] %>">
+                                    <%- path_item[1] %>
+                                </a>
+                            </li>
+                        <% } else { %>
+                            <li class="breadcrumb-item active">
+                                <span title="You are here">
+                                    <%- path_item[1] %>
+                                </span>
+                            </li>
+                        <% } %>
+                    <% }); %>
+                </ol>
+                <div class="dataset_table">
+                    <table class="grid table table-striped table-sm">
+                        <tr>
+                            <th class="dataset-first-column" scope="row" id="id_row"
+                                data-id="<%= _.escape(item.get("ldda_id")) %>">
+                                Name
+                            </th>
+                            <td>
+                                <input class="input_dataset_name form-control" type="text"
+                                    placeholder="name" value="<%= _.escape(item.get("name")) %>">
+                            </td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Data type</th>
+                            <td>
+                                <span id="dataset_extension_select" class="dataset-extension-select" />
+                            </td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Genome build</th>
+                            <td>
+                                <span id="dataset_genome_select" class="dataset-genome-select" />
+                            </td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Size</th>
+                            <td><%= _.escape(item.get("file_size")) %></td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Date uploaded (UTC)</th>
+                            <td><%= _.escape(item.get("date_uploaded")) %></td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Uploaded by</th>
+                            <td><%= _.escape(item.get("uploaded_by")) %></td>
+                        </tr>
+                        <tr scope="row">
+                            <th scope="row">Data Lines</th>
+                            <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Comment Lines</th>
+                            <% if (item.get("metadata_comment_lines") === "") { %>
+                                <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>
+                            <% } else { %>
+                                <td scope="row">unknown</td>
+                            <% } %>
+                        </tr>
+                        <tr>
+                            <th scope="row">Number of Columns</th>
+                            <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Column Types</th>
+                            <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Message</th>
+                            <td scope="row"><input class="input_dataset_message form-control" type="text"
+                                placeholder="message" value="<%= _.escape(item.get("message")) %>"></td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Misc. blurb</th>
+                            <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>
+                        </tr>
+                        <tr>
+                            <th scope="row">Misc. information</th>
+                            <td><input class="input_dataset_misc_info form-control" type="text"
+                                placeholder="info" value="<%= _.escape(item.get("misc_info")) %>"></td>
+                        </tr>
 
-                '<div class="dataset_table">',
-                '<table class="grid table table-striped table-sm">',
-                "<tr>",
-                '<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>',
-                '<td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>',
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Data type</th>',
-                "<td>",
-                '<span id="dataset_extension_select" class="dataset-extension-select" />',
-                "</td>",
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Genome build</th>',
-                "<td>",
-                '<span id="dataset_genome_select" class="dataset-genome-select" />',
-                "</td>",
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Size</th>',
-                '<td><%= _.escape(item.get("file_size")) %></td>',
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Date uploaded (UTC)</th>',
-                '<td><%= _.escape(item.get("date_uploaded")) %></td>',
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Uploaded by</th>',
-                '<td><%= _.escape(item.get("uploaded_by")) %></td>',
-                "</tr>",
-                '<tr scope="row">',
-                '<th scope="row">Data Lines</th>',
-                '<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',
-                "</tr>",
-                '<th scope="row">Comment Lines</th>',
-                '<% if (item.get("metadata_comment_lines") === "") { %>',
-                '<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',
-                "<% } else { %>",
-                '<td scope="row">unknown</td>',
-                "<% } %>",
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Number of Columns</th>',
-                '<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Column Types</th>',
-                '<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Message</th>',
-                '<td scope="row"><input class="input_dataset_message form-control" type="text" placeholder="message" value="<%= _.escape(item.get("message")) %>"></td>',
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Misc. blurb</th>',
-                '<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',
-                "</tr>",
-                "<tr>",
-                '<th scope="row">Misc. information</th>',
-                '<td><input class="input_dataset_misc_info form-control" type="text" placeholder="info" value="<%= _.escape(item.get("misc_info")) %>"></td>',
-                "</tr>",
-                //TODO: add functionality to modify tags here
-                '<% if (item.get("tags")) { %>',
-                "<tr>",
-                '<th scope="row">Tags</th>',
-                '<td scope="row"><%= _.escape(item.get("tags")) %></td>',
-                "</tr>",
-                "<% } %>",
-                "</table>",
-                "<div>",
-                '<pre class="peek">',
-                "</pre>",
-                "</div>",
-                "</div>",
+                        <!-- TODO: add functionality to modify tags here -->
+                        <% if (item.get("tags")) { %>
+                            <tr>
+                                <th scope="row">Tags</th>
+                                <td scope="row"><%= _.escape(item.get("tags")) %></td>
+                            </tr>
+                        <% } %>
+                    </table>
+                    <div>
+                        <pre class="peek">
+                        </pre>
+                    </div>
+                </div>
+                <div class="d-flex">
+                    <button data-toggle="tooltip" data-placement="top" title="Cancel modifications"
+                        class="btn btn-secondary toolbtn_cancel_modifications toolbar-item mr-1" type="button">
+                        <span class="fa fa-times"></span>
+                        &nbsp;Cancel
+                    </button>
+                    <button data-toggle="tooltip" data-placement="top" title="Save modifications"
+                        class="btn btn-secondary toolbtn_save_modifications toolbar-item mr-1" type="button">
+                        <span class="fa fa-floppy-o"></span>
+                        &nbsp;Save
+                    </button>
+                </div>
 
-                '<div class="d-flex">',
-                '<button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-secondary toolbtn_cancel_modifications toolbar-item mr-1" type="button">',
-                '<span class="fa fa-times"></span>',
-                "&nbsp;Cancel",
-                "</button>",
-                '<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-secondary toolbtn_save_modifications toolbar-item mr-1" type="button">',
-                '<span class="fa fa-floppy-o"></span>',
-                "&nbsp;Save",
-                "</button>",
-                "</div>",
-
-                // CONTAINER END
-                "</div>"
-            ].join("")
+            <!-- CONTAINER END -->
+            </div>`
         );
     },
 
     templateDatasetPermissions: function() {
         return _.template(
-            [
-                // CONTAINER START
-                '<div class="library_style_container">',
-                '<div class="d-flex mb-2">',
-                '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">',
-                '<button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-secondary toolbar-item mr-1" type="button">',
-                '<span class="fa fa-file-o"></span>',
-                "&nbsp;Dataset Details",
-                "</button>",
-                "<a>",
-                "</div>",
+            `<!-- CONTAINER START -->
+            <div class="library_style_container">
+                <div class="d-flex mb-2">
+                    <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">
+                        <button data-toggle="tooltip" data-placement="top" title="Go back to dataset"
+                            class="btn btn-secondary toolbar-item mr-1" type="button">
+                            <span class="fa fa-file-o"></span>
+                            &nbsp;Dataset Details
+                        </button>
+                    </a>
+                </div>
 
-                // BREADCRUMBS
-                '<ol class="breadcrumb">',
-                '<li class="breadcrumb-item"><a title="Return to the list of libraries" href="#">Libraries</a></li>',
-                '<% _.each(item.get("full_path"), function(path_item) { %>',
-                "<% if (path_item[0] != item.id) { %>",
-                '<li class="breadcrumb-item"><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',
-                "<% } else { %>",
-                '<li class="breadcrumb-item active"><span title="You are here"><%- path_item[1] %></span></li>',
-                "<% } %>",
-                "<% }); %>",
-                "</ol>",
+                <!-- BREADCRUMBS -->
+                <ol class="breadcrumb">
+                    <li class="breadcrumb-item">
+                        <a title="Return to the list of libraries" href="#">Libraries</a>
+                    </li>
+                    <% _.each(item.get("full_path"), function(path_item) { %>
+                        <% if (path_item[0] != item.id) { %>
+                            <li class="breadcrumb-item">
+                                <a title="Return to this folder" href="#/folders/<%- path_item[0] %>">
+                                    <%- path_item[1] %>
+                                </a>
+                            </li>
+                        <% } else { %>
+                            <li class="breadcrumb-item active">
+                                <span title="You are here">
+                                    <%- path_item[1] %>
+                                </span>
+                            </li>
+                        <% } %>
+                    <% }); %>
+                </ol>
 
-                '<h1>Dataset: <%= _.escape(item.get("name")) %></h1>',
-                '<div class="alert alert-warning">',
-                "<% if (is_admin) { %>",
-                "You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.",
-                "<% } else { %>",
-                "You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.",
-                "<% } %>",
-                "</div>",
-                '<div class="dataset_table">',
-                "<h2>Library-related permissions</h2>",
-                "<h4>Roles that can modify the library item</h4>",
-                '<div id="modify_perm" class="modify_perm roles-selection"></div>',
-                '<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>',
-                "<hr/>",
-                "<h2>Dataset-related permissions</h2>",
-                '<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>',
-                '<% if (!item.get("is_unrestricted")) { %>',
-                '<p>You can <span class="remove-restrictions"><a href="">remove all access restrictions</a></span> on this dataset.</p>',
-                "<% } else { %>",
-                '<p>You can <span class="make-private"><a href="">make this dataset private</a></span> to you.</p>',
-                "<% } %>",
-                "<h4>Roles that can access the dataset</h4>",
-                '<div id="access_perm" class="access_perm roles-selection"></div>',
-                '<div class="alert alert-info roles-selection">',
-                "User has to have <strong>all these roles</strong> in order to access this dataset.",
-                " Users without access permission <strong>cannot</strong> have other permissions on this dataset.",
-                " If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.",
-                "</div>",
-                "<h4>Roles that can manage permissions on the dataset</h4>",
-                '<div id="manage_perm" class="manage_perm roles-selection"></div>',
-                '<div class="alert alert-info roles-selection">',
-                "User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will lose the ability manage this dataset unless you are an admin.",
-                "</div>",
-                '<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-secondary toolbtn_save_permissions  type="button">',
-                '<span class="fa fa-floppy-o"></span>',
-                "&nbsp;Save",
-                "</button>",
-                "</div>",
-                // CONTAINER END
-                "</div>"
-            ].join("")
+                <h1>Dataset: <%= _.escape(item.get("name")) %></h1>
+                <div class="alert alert-warning">
+                    <% if (is_admin) { %>
+                        You are logged in as an <strong>administrator</strong> therefore you can manage any dataset
+                        on this Galaxy instance. Please make sure you understand the consequences.
+                    <% } else { %>
+                        You can assign any number of roles to any of the following permission types. However please
+                        read carefully the implications of such actions.
+                    <% } %>
+                </div>
+                <div class="dataset_table">
+                    <h2>Library-related permissions</h2>
+                    <h4>Roles that can modify the library item</h4>
+                    <div id="modify_perm" class="modify_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can modify name, metadata,
+                        and other information about this library item.
+                    </div>
+                    <hr/>
+                    <h2>Dataset-related permissions</h2>
+                    <div class="alert alert-warning">
+                        Changes made below will affect <strong>every</strong> library item that was created from
+                        this dataset and also every history this dataset is part of.
+                    </div>
+                    <% if (!item.get("is_unrestricted")) { %>
+                        <p>
+                            You can <span class="remove-restrictions">
+                            <a href="">remove all access restrictions</a></span> on this dataset.
+                        </p>
+                    <% } else { %>
+                        <p>
+                            You can <span class="make-private">
+                            <a href="">make this dataset private</a></span> to you.</p>
+                    <% } %>
+                    <h4>Roles that can access the dataset</h4>
+                    <div id="access_perm" class="access_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User has to have <strong>all these roles</strong> in order to access this dataset.
+                        Users without access permission <strong>cannot</strong> have other permissions on this dataset.
+                        If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.
+                    </div>
+                    <h4>Roles that can manage permissions on the dataset</h4>
+                    <div id="manage_perm" class="manage_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can manage permissions of this dataset.
+                        If you remove yourself you will lose the ability manage this dataset unless you are an admin.
+                    </div>
+                    <button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page"
+                        class="btn btn-secondary toolbtn_save_permissions type="button">
+                        <span class="fa fa-floppy-o"></span>
+                        &nbsp;Save
+                    </button>
+                </div>
+            <!-- CONTAINER END -->
+            </div>`
         );
     },
 
     templateBulkImportInModal: function() {
         return _.template(
-            [
-                "<div>",
-                '<div class="library-modal-item">',
-                "Select history: ",
-                '<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; " autofocus>',
-                "<% _.each(histories, function(history) { %>",
-                '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
-                "<% }); %>",
-                "</select>",
-                "</div>",
-                '<div class="library-modal-item">',
-                "or create new: ",
-                '<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;">',
-                "</input>",
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div>
+                <div class="library-modal-item">
+                    Select history: 
+                    <select id="dataset_import_single" name="dataset_import_single"
+                        style="width:50%; margin-bottom: 1em;" autofocus>
+                        <% _.each(histories, function(history) { %>
+                            <option value="<%= _.escape(history.get("id")) %>">
+                                <%= _.escape(history.get("name")) %>
+                            </option>
+                        <% }); %>
+                    </select>
+                </div>
+                <div class="library-modal-item">or create new: 
+                    <input type="text" name="history_name" value="" placeholder="name of the new history"
+                        style="width:50%;" />
+                </div>
+            </div>`
         );
     }
 });
diff --git a/client/galaxy/scripts/mvc/library/library-folder-view.js b/client/galaxy/scripts/mvc/library/library-folder-view.js
index c040f323903..d94239dd9a9 100644
--- a/client/galaxy/scripts/mvc/library/library-folder-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folder-view.js
@@ -26,7 +26,7 @@ var FolderView = Backbone.View.extend({
     },
 
     fetchFolder: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         this.model = new mod_library_model.FolderAsModel({
             id: this.options.id
@@ -57,7 +57,7 @@ var FolderView = Backbone.View.extend({
     },
 
     showPermissions: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         $(".tooltip").remove();
 
@@ -202,56 +202,58 @@ var FolderView = Backbone.View.extend({
 
     templateFolderPermissions: function() {
         return _.template(
-            [
-                '<div class="library_style_container">',
-                "<div>",
-                '<a href="#/folders/<%= folder.get("parent_id") %>">',
-                '<button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-secondary primary-button" type="button">',
-                '<span class="fa fa-caret-left fa-lg"/>',
-                "&nbsp;Parent folder",
-                "</button>",
-                "</a>",
-                "</div>",
-                "<h1>",
-                'Folder: <%= _.escape(folder.get("name")) %>',
-                "</h1>",
-                '<div class="alert alert-warning">',
-                "<% if (is_admin) { %>",
-                "You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.",
-                "<% } else { %>",
-                "You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.",
-                "<% }%>",
-                "</div>",
-                '<div class="dataset_table">',
-                "<h2>Folder permissions</h2>",
-                "<h4>",
-                "Roles that can manage permissions on this folder",
-                "</h4>",
-                '<div id="manage_perm" class="manage_perm roles-selection"/>',
-                '<div class="alert alert-info roles-selection">',
-                "User with <strong>any</strong> of these roles can manage permissions on this folder.",
-                "</div>",
-                "<h4>",
-                "Roles that can add items to this folder",
-                "</h4>",
-                '<div id="add_perm" class="add_perm roles-selection"/>',
-                '<div class="alert alert-info roles-selection">',
-                "User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).",
-                "</div>",
-                "<h4>",
-                "Roles that can modify this folder",
-                "</h4>",
-                '<div id="modify_perm" class="modify_perm roles-selection"/>',
-                '<div class="alert alert-info roles-selection">',
-                "User with <strong>any</strong> of these roles can modify this folder (name, etc.).",
-                "</div>",
-                '<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-secondary toolbtn_save_permissions primary-button" type="button">',
-                '<span class="fa fa-floppy-o"/>',
-                "&nbsp;Save",
-                "</button>",
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div class="library_style_container">
+                <div>
+                    <a href="#/folders/<%= folder.get("parent_id") %>">
+                        <button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder"
+                            class="btn btn-secondary primary-button" type="button">
+                            <span class="fa fa-caret-left fa-lg"/>
+                            &nbsp;Parent folder
+                        </button>
+                    </a>
+                </div>
+                <h1>
+                    Folder: <%= _.escape(folder.get("name")) %>
+                </h1>
+                <div class="alert alert-warning">
+                    <% if (is_admin) { %>
+                        You are logged in as an <strong>administrator</strong> therefore you can manage any
+                        folder on this Galaxy instance. Please make sure you understand the consequences.
+                    <% } else { %>
+                        You can assign any number of roles to any of the following permission types.
+                        However please read carefully the implications of such actions.
+                    <% }%>
+                </div>
+                <div class="dataset_table">
+                    <h2>Folder permissions</h2>
+                    <h4>
+                        Roles that can manage permissions on this folder
+                    </h4>
+                    <div id="manage_perm" class="manage_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can manage permissions on this folder.
+                    </div>
+                    <h4>
+                        Roles that can add items to this folder
+                    </h4>
+                    <div id="add_perm" class="add_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).
+                    </div>
+                    <h4>
+                        Roles that can modify this folder
+                    </h4>
+                    <div id="modify_perm" class="modify_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can modify this folder (name, etc.).
+                    </div>
+                    <button data-toggle="tooltip" data-placement="top" title="Save modifications"
+                        class="btn btn-secondary toolbtn_save_permissions primary-button" type="button">
+                        <span class="fa fa-floppy-o"/>
+                        &nbsp;Save
+                    </button>
+                </div>
+            </div>`
         );
     }
 });
diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
index 07e04e66958..55d210fb633 100644
--- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
@@ -77,7 +77,7 @@ var FolderListView = Backbone.View.extend({
                 self.render();
             },
             error: function(model, response) {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(`${response.responseJSON.err_msg} Click this to go back.`, "", {
                         onclick: function() {
@@ -141,7 +141,7 @@ var FolderListView = Backbone.View.extend({
     },
 
     paginate: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
 
         if (this.options.show_page === null || this.options.show_page < 1) {
@@ -181,7 +181,7 @@ var FolderListView = Backbone.View.extend({
      *  be added to the view's collection.
      */
     addAll: function(models) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         _.each(models, model => {
             Galaxy.libraries.folderListView.collection.add(model, {
                 current_sort_order: false
@@ -198,7 +198,7 @@ var FolderListView = Backbone.View.extend({
      * and that event will be bound on all subviews.
      */
     postRender: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var fetched_metadata = this.folderContainer.attributes.metadata;
         fetched_metadata.contains_file_or_folder =
             typeof this.collection.findWhere({ type: "file" }) !== "undefined" ||
@@ -329,29 +329,11 @@ var FolderListView = Backbone.View.extend({
     },
 
     makeDarkRow: function($row) {
-        $row.removeClass("light").addClass("dark");
-        $row.find("a")
-            .removeClass("light")
-            .addClass("dark");
-        $row.find(".fa-file-o")
-            .removeClass("fa-file-o")
-            .addClass("fa-file");
-        $row.find(".fa-folder-o")
-            .removeClass("fa-folder-o")
-            .addClass("fa-folder");
+        $row.addClass("table-primary");
     },
 
     makeWhiteRow: function($row) {
-        $row.removeClass("dark").addClass("light");
-        $row.find("a")
-            .removeClass("dark")
-            .addClass("light");
-        $row.find(".fa-file")
-            .removeClass("fa-file")
-            .addClass("fa-file-o");
-        $row.find(".fa-folder")
-            .removeClass("fa-folder")
-            .addClass("fa-folder-o");
+        $row.removeClass("table-primary");
     },
 
     renderSortIcon: function() {
@@ -365,54 +347,186 @@ var FolderListView = Backbone.View.extend({
         }
     },
 
+    /**
+     * Create the new folder inline
+     */
+    createFolderInline: function() {
+        if (this.$el.find("tr.new-row").length) {
+            this.$el.find("tr.new-row textarea")[0].focus();
+        } else {
+            const template = this.templateNewFolder();
+            this.$el.find("#first_folder_item").after(template);
+
+            this.$el.find("tr.new-row textarea")[0].focus();
+
+            this.$el.find("tr.new-row .save_folder_btn").click(() => {
+                this.createNewFolder(
+                    this.$el.find("tr.new-row textarea")[0].value,
+                    this.$el.find("tr.new-row textarea")[1].value
+                );
+            });
+
+            this.$el.find("tr.new-row .cancel_folder_btn").click(() => {
+                this.$el.find("tr.new-row").remove();
+            });
+        }
+    },
+
+    /**
+     * Create the new library using the API asynchronously.
+     */
+    createNewFolder: function(name, description) {
+        const Galaxy = getGalaxyInstance();
+        const folderDetails = {
+            name,
+            description
+        };
+        if (folderDetails.name !== "") {
+            var folder = new mod_library_model.FolderAsModel();
+            var url_items = Backbone.history.fragment.split("/");
+            var current_folder_id;
+            if (url_items.indexOf("page") > -1) {
+                current_folder_id = url_items[url_items.length - 3];
+            } else {
+                current_folder_id = url_items[url_items.length - 1];
+            }
+            folder.url = folder.urlRoot + current_folder_id;
+
+            folder.save(folderDetails, {
+                success: folder => {
+                    Toast.success("Folder created.");
+                    folder.set({ type: "folder" });
+                    this.$el.find("tr.new-row").remove();
+                    Galaxy.libraries.folderListView.collection.add(folder);
+
+                    $(`tr[data-id="${folder.attributes.id}"`)
+                        .addClass("table-success")
+                        .on("mouseover click", function() {
+                            $(this).removeClass("table-success");
+                        });
+                },
+                error: (model, response) => {
+                    Galaxy.modal.hide();
+                    if (typeof response.responseJSON !== "undefined") {
+                        Toast.error(response.responseJSON.err_msg);
+                    } else {
+                        Toast.error("An error occurred.");
+                    }
+                }
+            });
+        } else {
+            Toast.error("Folder's name is missing.");
+        }
+        return false;
+    },
+
+    templateNewFolder: function() {
+        return _.template(
+            `<tr class="new-row">
+                <td class="mid">
+                    <span title="Folder" class="fa fa-folder-o"></span>
+                </td>
+                <td></td>
+                <td>
+                    <textarea name="input_folder_name" rows="4" class="form-control input_folder_name" placeholder="name" ></textarea>
+                </td>
+                <td>
+                    <textarea rows="4" class="form-control input_folder_description" placeholder="description" ></textarea>
+                </td>
+                <td>folder</td>
+                <td></td>
+                <td></td>
+                <td></td>
+                <td class="right-center">
+                    <button data-toggle="tooltip" data-placement="left" title="Save changes"
+                        class="btn btn-secondary btn-sm save_folder_btn" type="button">
+                        <span class="fa fa-floppy-o"></span> Save
+                    </button>
+                    <button data-toggle="tooltip" data-placement="left" title="Discard changes"
+                        class="btn btn-secondary btn-sm cancel_folder_btn" type="button">
+                        <span class="fa fa-times"></span> Cancel
+                    </button>
+                </td>
+            </tr>`
+        );
+    },
+
     templateFolder: function() {
         return _.template(
-            [
-                '<ol class="breadcrumb">',
-                '<li class="breadcrumb-item"><a title="Return to the list of libraries" href="#">Libraries</a></li>',
-                "<% _.each(path, function(path_item) { %>",
-                "<% if (path_item[0] != id) { %>",
-                '<li class="breadcrumb-item"><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',
-                "<% } else { %>",
-                '<li class="breadcrumb-item active"><span title="You are in this folder"><%- path_item[1] %></span></li>',
-                "<% } %>",
-                "<% }); %>",
-                "</ol>",
+            `<ol class="breadcrumb">
+                <li class="breadcrumb-item">
+                    <a title="Return to the list of libraries" href="#">Libraries</a>
+                </li>
+                <% _.each(path, function(path_item) { %>
+                    <% if (path_item[0] != id) { %>
+                        <li class="breadcrumb-item">
+                            <a title="Return to this folder" href="#/folders/<%- path_item[0] %>">
+                                <%- path_item[1] %>
+                            </a>
+                        </li> 
+                    <% } else { %>
+                        <li class="breadcrumb-item active">
+                            <span title="You are in this folder">
+                                <%- path_item[1] %>
+                            </span>
+                        </li>
+                    <% } %>
+                <% }); %>
+            </ol>
 
-                // FOLDER CONTENT
-                '<table data-library-id="<%- parent_library_id  %>" class="grid table table-sm">',
-                "<thead>",
-                '<th class="button_heading"></th>',
-                '<th class="mid" style="width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>',
-                '<th><a class="sort-folder-name" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="sort-icon-name fa fa-sort-alpha-<%- order %>"></span></th>',
-                '<th style="width:20%;"><a class="sort-folder-description" title="Click to reverse order" href="#">description</a> <span title="Sorted alphabetically" class="sort-icon-description fa"></span></th>',
-                '<th style="width:5%;"><a class="sort-folder-file_ext" title="Click to reverse order" href="#">data type</a> <span title="Sorted alphabetically" class="sort-icon-file_ext fa"></span></th>',
-                '<th style="width:10%;">size</th>',
-                '<th style="width:160px;">time updated (UTC)</th>',
-                '<th style="width:5%;"><a class="sort-folder-state" title="Click to reverse order" href="#">state</a> <span title="Sorted alphabetically" class="sort-icon-state fa"></span></th>',
-                '<th style="width:150px;"></th> ',
-                "</thead>",
-                '<tbody id="folder_list_body">',
-                '<tr id="first_folder_item">',
-                "<td>",
-                '<a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-secondary btn-sm">..<a>',
-                "</td>",
-                "<td></td>",
-                "<td></td>",
-                "<td></td>",
-                "<td></td>",
-                "<td></td>",
-                "<td></td>",
-                "<td></td>",
-                "<td></td>",
-                "</tr>",
-                "</tbody>",
-                "</table>",
-                '<div class="empty-folder-message" style="display:none;">',
-                "This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up",
-                ' please consult the <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>.',
-                "</div>"
-            ].join("")
+            <!-- FOLDER CONTENT -->
+            <table data-library-id="<%- parent_library_id  %>" class="grid table table-hover table-sm">
+                <thead>
+                    <th class="button_heading"></th>
+                    <th class="mid" style="width: 20px;"
+                        title="Check to select all datasets">
+                        <input id="select-all-checkboxes" style="margin: 0;" type="checkbox">
+                    </th>
+                    <th>
+                        <a class="sort-folder-name" title="Click to reverse order" href="#">Name</a>
+                        <span title="Sorted alphabetically"
+                            class="sort-icon-name fa fa-sort-alpha-<%- order %>"></span>
+                    </th>
+                    <th style="width:20%;">
+                        <a class="sort-folder-description" title="Click to reverse order" href="#">Description</a>
+                        <span title="Sorted alphabetically" class="sort-icon-description fa"></span>
+                    </th>
+                    <th style="width:5%;">
+                        <a class="sort-folder-file_ext" title="Click to reverse order" href="#">Data Type</a>
+                        <span title="Sorted alphabetically" class="sort-icon-file_ext fa"></span>
+                    </th>
+                    <th style="width:10%;">Size</th>
+                    <th style="width:160px;">Time Updated (UTC)</th>
+                    <th style="width:5%;">
+                        <a class="sort-folder-state" title="Click to reverse order" href="#">State</a>
+                        <span title="Sorted alphabetically" class="sort-icon-state fa"></span>
+                    </th>
+                    <th style="width:160px;"></th> 
+                </thead>
+                <tbody id="folder_list_body">
+                    <tr id="first_folder_item">
+                        <td>
+                            <a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>"
+                                title="Go to parent folder" class="btn_open_folder btn btn-secondary btn-sm">..<a>
+                        </td>
+                        <td></td>
+                        <td></td>
+                        <td></td>
+                        <td></td>
+                        <td></td>
+                        <td></td>
+                        <td></td>
+                        <td></td>
+                    </tr>
+                </tbody>
+            </table>
+            <div class="empty-folder-message" style="display:none;">
+                This folder is either empty or you do not have proper access permissions to see the contents.
+                If you expected something to show up please consult the
+                <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">
+                    library security wikipage
+                </a>.
+            </div>`
         );
     }
 });
diff --git a/client/galaxy/scripts/mvc/library/library-folderrow-view.js b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
index 2493f11402e..21eefe51224 100644
--- a/client/galaxy/scripts/mvc/library/library-folderrow-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
@@ -36,7 +36,7 @@ var FolderRowView = Backbone.View.extend({
         this.options = _.extend(this.options, options);
         var folder_item = this.options.model;
         var template = null;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         if (folder_item.get("type") === "folder" || folder_item.get("model_class") === "LibraryFolder") {
             this.options.type = "folder";
@@ -105,14 +105,14 @@ var FolderRowView = Backbone.View.extend({
 
     /* Show the page with dataset details. */
     showDatasetDetails: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({ id: this.id });
     },
 
     /* Undelete the dataset on server and render the row again. */
     undeleteDataset: function(event) {
         $(".tooltip").hide();
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var that = this;
         var dataset_id = $(event.target)
             .closest("tr")
@@ -144,7 +144,7 @@ var FolderRowView = Backbone.View.extend({
 
     /* Undelete the folder on server and render the row again. */
     undeleteFolder: function(event) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         $(".tooltip").hide();
         var folder_id = $(event.target)
             .closest("tr")
@@ -182,7 +182,7 @@ var FolderRowView = Backbone.View.extend({
     },
 
     saveModifications: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var folder = Galaxy.libraries.folderListView.collection.get(this.$el.data("id"));
         var is_changed = false;
         var new_name = this.$el.find(".input_folder_name").val();
@@ -241,169 +241,205 @@ var FolderRowView = Backbone.View.extend({
 
     templateRowFolder: function() {
         return _.template(
-            [
-                '<tr class="folder_row light library-row" data-id="<%- content_item.id %>">',
-                '<td class="mid">',
-                '<span title="Folder" class="fa fa-folder-o"/>',
-                "</td>",
-                '<td class="mid"><input style="margin: 0;" type="checkbox"></td>',
-                "<% if(!edit_mode) { %>",
-                "<td>",
-                '<a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>',
-                "</td>",
-                "<td>",
-                '<%- content_item.get("description") %>',
-                "</td>",
-                "<% } else if(edit_mode){ %>",
-                '<td><textarea rows="4" class="form-control input_folder_name" placeholder="name" ><%- content_item.get("name") %></textarea></td>',
-                '<td><textarea rows="4" class="form-control input_folder_description" placeholder="description" ><%- content_item.get("description") %></textarea></td>',
-                "<% } %>",
-                "<td>folder</td>",
-                "<td></td>",
-                "<td>",
-                '<%= _.escape(content_item.get("update_time")) %>',
-                "</td>",
-                "<td></td>",
-                "<td>",
-                "<% if(edit_mode) { %>", // start edit mode
-                '<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-sm save_folder_btn" type="button" style="<% if(button_config.save_folder_btn === false) { print("display:none;") } %>">',
-                '<span class="fa fa-floppy-o"/> Save',
-                "</button>",
-                '<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-sm cancel_folder_btn" type="button" style="<% if(button_config.cancel_folder_btn === false) { print("display:none;") } %>">',
-                '<span class="fa fa-times"/> Cancel',
-                "</button>",
-                "<% } else if (!edit_mode){%>", // start no edit mode
-                '<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- content_item.get("name") %>\'" class="primary-button btn-sm edit_folder_btn" type="button" style="<% if(button_config.edit_folder_btn === false) { print("display:none;") } %>">',
-                '<span class="fa fa-pencil"/> Edit',
-                "</button>",
-                '<a href="#/folders/<%- content_item.id %>/permissions">',
-                '<button data-toggle="tooltip" data-placement="top" class="primary-button btn-sm permission_folder_btn" title="Permissions of \'<%- content_item.get("name") %>\'" style="<% if(button_config.permission_folder_btn === false) { print("display:none;") } %>">',
-                '<span class="fa fa-group"/> Manage',
-                "</button>",
-                "</a>",
-                "<% } %>", //end no edit mode
-                "</td>",
-                "</tr>"
-            ].join("")
+            `<tr class="folder_row library-row" data-id="<%- content_item.id %>">
+                <td class="mid">
+                    <span title="Folder" class="fa fa-folder-o"></span>
+                </td>
+                <td class="mid"><input style="margin: 0;" type="checkbox"></td>
+                <% if(!edit_mode) { %>
+                    <td>
+                        <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>
+                    </td>
+                    <% if( content_item.get("description") ) { %>
+                        <% if( content_item.get("description").length> 80 ) { %>
+                            <td data-toggle="tooltip" data-placement="auto"
+                                title='<%= _.escape(content_item.get("description")) %>'>
+                                <%= _.escape(content_item.get("description")).substring(0, 80) + "..." %>
+                            </td>
+                        <% } else { %>
+                            <td><%= _.escape(content_item.get("description"))%></td>
+                        <% } %>
+                    <% } else { %>
+                        <td></td>
+                    <% } %>
+                <% } else if(edit_mode){ %>
+                    <td>
+                        <textarea rows="4" class="form-control input_folder_name" placeholder="name" ><%- content_item.get("name") %></textarea>
+                    </td>
+                    <td>
+                        <textarea rows="4" class="form-control input_folder_description" placeholder="description" ><%- content_item.get("description") %></textarea>
+                    </td>
+                <% } %>
+                <td>folder</td>
+                <td></td>
+                <td>
+                    <%= _.escape(content_item.get("update_time")) %>
+                </td>
+                <td></td>
+                <td class="right-center">
+                    <% if(edit_mode) { %> <!-- start edit mode -->
+                        <button data-toggle="tooltip" data-placement="top" title="Save changes"
+                            class="primary-button btn-sm save_folder_btn" type="button"
+                            style="<% if(button_config.save_folder_btn === false) { print("display:none;") } %>">
+                            <span class="fa fa-floppy-o"></span> Save
+                        </button>
+                        <button data-toggle="tooltip" data-placement="top" title="Discard changes"
+                            class="primary-button btn-sm cancel_folder_btn" type="button"
+                            style="<% if(button_config.cancel_folder_btn === false) { print("display:none;") } %>">
+                            <span class="fa fa-times"></span> Cancel
+                        </button>
+                    <% } else if (!edit_mode){%> <!-- start no edit mode -->
+                        <button data-toggle="tooltip" data-placement="top"
+                            title="Modify '<%- content_item.get("name") %>'"
+                            class="primary-button btn-sm edit_folder_btn" type="button"
+                            style="<% if(button_config.edit_folder_btn === false) { print("display:none;") } %>">
+                            <span class="fa fa-pencil"></span> Edit
+                        </button>
+                        <a href="#/folders/<%- content_item.id %>/permissions">
+                            <button data-toggle="tooltip" data-placement="top"
+                                class="primary-button btn-sm permission_folder_btn"
+                                title="Permissions of '<%- content_item.get("name") %>'"
+                                    style="<% if(button_config.permission_folder_btn === false) { print("display:none;") } %>">
+                                <span class="fa fa-group"></span> Manage
+                            </button>
+                        </a>
+                    <% } %> <!-- end no edit mode -->
+               </td>
+            </tr>`
         );
     },
 
     templateRowFile: function() {
         return _.template(
-            [
-                '<tr class="dataset_row light library-row" data-id="<%- content_item.id %>">',
-                '<td class="mid">',
-                '<span title="Dataset" class="fa fa-file-o"/>',
-                "</td>",
-                '<td class="mid">',
-                '<input style="margin: 0;" type="checkbox">',
-                "</td>",
-                "<td>",
-                '<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset">',
-                '<%- content_item.get("name") %>',
-                "<a>",
-                "</td>",
-                '<td><%- content_item.get("message") %></td>',
-                '<td><%= _.escape(content_item.get("file_ext")) %></td>',
-                '<td><%= _.escape(content_item.get("file_size")) %></td>',
-                '<td><%= _.escape(content_item.get("update_time")) %></td>',
-                "<td>",
-                '<% if ( content_item.get("state") !== "ok" ) { %>',
-                '<%= _.escape(content_item.get("state")) %>',
-                "<% } %>",
-                "</td>",
-                "<td>",
-                '<% if (content_item.get("is_unrestricted")) { %>',
-                '<span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe"/>',
-                "<% } %>",
-                '<% if (content_item.get("is_private")) { %>',
-                '<span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key"/>',
-                "<% } %>",
-                '<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>',
-                '<span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield"/>',
-                "<% } %>",
-                '<% if (content_item.get("can_manage")) { %>',
-                '<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions">',
-                '<button data-toggle="tooltip" data-placement="top" class="primary-button btn-sm permissions-dataset-btn" title="Permissions of \'<%- content_item.get("name") %>\'">',
-                '<span class="fa fa-group"/> Manage',
-                "</button>",
-                "</a>",
-                "<% } %>",
-                "</td>",
-                "</tr>"
-            ].join("")
+            `<tr class="dataset_row library-row" data-id="<%- content_item.id %>">
+                <td class="mid">
+                    <span title="Dataset" class="fa fa-file-o"></span>
+                </td>
+                <td class="mid">
+                    <input style="margin: 0;" type="checkbox">
+                </td>
+                <td>
+                    <a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>"
+                        class="library-dataset">
+                        <%- content_item.get("name") %>
+                    <a>
+                </td>
+                <td><%- content_item.get("message") %></td>
+                <td><%= _.escape(content_item.get("file_ext")) %></td>
+                <td><%= _.escape(content_item.get("file_size")) %></td>
+                <td><%= _.escape(content_item.get("update_time")) %></td>
+                <td>
+                    <% if ( content_item.get("state") !== "ok" ) { %>
+                        <%= _.escape(content_item.get("state")) %>
+                    <% } %>
+                </td>
+                <td class="right-center">
+                    <% if (content_item.get("is_unrestricted")) { %>
+                        <span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset"
+                            class="fa fa-globe"></span>
+                    <% } %>
+                    <% if (content_item.get("is_private")) { %>
+                        <span data-toggle="tooltip" data-placement="top" title="Private dataset"
+                            class="fa fa-key"></span>
+                    <% } %>
+                    <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>
+                        <span data-toggle="tooltip" data-placement="top" title="Restricted dataset"
+                            class="fa fa-shield"></span>
+                    <% } %>
+                    <% if (content_item.get("can_manage")) { %>
+                        <a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions">
+                            <button data-toggle="tooltip" data-placement="top"
+                                class="primary-button btn-sm permissions-dataset-btn"
+                                title="Permissions of '<%- content_item.get("name") %>'">
+                                <span class="fa fa-group"></span> Manage
+                            </button>
+                        </a>
+                    <% } %>
+                </td>
+            </tr>`
         );
     },
 
     templateRowDeletedFile: function() {
         return _.template(
-            [
-                '<tr class="active deleted_dataset library-row" data-id="<%- content_item.id %>">',
-                '<td class="mid">',
-                '<span title="Dataset" class="fa fa-file-o"/>',
-                "</td>",
-                "<td></td>",
-                '<td style="color:grey;">',
-                '<%- content_item.get("name") %>',
-                "</td>",
-                "<td>",
-                '<%- content_item.get("message") %>',
-                "</td>",
-                "<td>",
-                '<%= _.escape(content_item.get("file_ext")) %>',
-                "</td>",
-                "<td>",
-                '<%= _.escape(content_item.get("file_size")) %>',
-                "</td>",
-                "<td>",
-                '<%= _.escape(content_item.get("update_time")) %>',
-                "</td>",
-                "<td>",
-                '<% if ( content_item.get("state") !== "ok" ) { %>',
-                '<%= _.escape(content_item.get("state")) %>',
-                "<% } %>",
-                "</td>",
-                "<td>",
-                '<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban"/>',
-                '<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- content_item.get("name") %>\'" class="primary-button btn-sm undelete_dataset_btn" type="button" style="margin-left:1em;">',
-                '<span class="fa fa-unlock"/> Undelete',
-                "</button>",
-                "</td>",
-                "</tr>"
-            ].join("")
+            `<tr class="active deleted_dataset library-row" data-id="<%- content_item.id %>">
+                <td class="mid">
+                    <span title="Dataset" class="fa fa-file-o"></span>
+                </td>
+                <td></td>
+                <td style="color:grey;">
+                    <%- content_item.get("name") %>
+                </td>
+                <td>
+                    <%- content_item.get("message") %>
+                </td>
+                <td>
+                    <%= _.escape(content_item.get("file_ext")) %>
+                </td>
+                <td>
+                    <%= _.escape(content_item.get("file_size")) %>
+                </td>
+                <td>
+                    <%= _.escape(content_item.get("update_time")) %>
+                </td>
+                <td>
+                    <% if ( content_item.get("state") !== "ok" ) { %>
+                        <%= _.escape(content_item.get("state")) %>
+                    <% } %>
+                </td>
+                <td class="right-center">
+                    <span data-toggle="tooltip" data-placement="top"
+                        title="Marked deleted" class="fa fa-ban"></span>
+                    <button data-toggle="tooltip" data-placement="top"
+                        title="Undelete '<%- content_item.get("name") %>'"
+                        class="primary-button btn-sm undelete_dataset_btn" type="button" style="margin-left:1em;">
+                        <span class="fa fa-unlock"></span> Undelete
+                    </button>
+                </td>
+            </tr>`
         );
     },
 
     templateRowDeletedFolder: function() {
         return _.template(
-            [
-                '<tr class="active deleted_folder light library-row" data-id="<%- content_item.id %>">',
-                '<td class="mid">',
-                '<span title="Folder" class="fa fa-folder-o"/>',
-                "</td>",
-                "<td></td>",
-                '<td style="color:grey;">',
-                '<%- content_item.get("name") %>',
-                "</td>",
-                "<td>",
-                '<%- content_item.get("description") %>',
-                "</td>",
-                "<td>",
-                "folder",
-                "</td>",
-                "<td></td>",
-                "<td>",
-                '<%= _.escape(content_item.get("update_time")) %>',
-                "</td>",
-                "<td></td>",
-                "<td>",
-                '<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban"/>',
-                '<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- content_item.get("name") %>\'" class="primary-button btn-sm undelete_folder_btn" type="button" style="margin-left:1em;">',
-                '<span class="fa fa-unlock"/> Undelete',
-                "</button>",
-                "</td>",
-                "</tr>"
-            ].join("")
+            `<tr class="active deleted_folder library-row" data-id="<%- content_item.id %>">
+                <td class="mid">
+                    <span title="Folder" class="fa fa-folder-o"></span>
+                </td>
+                <td></td>
+                <td style="color:grey;">
+                    <%- content_item.get("name") %>
+                </td>
+                <% if( content_item.get("description") ) { %>
+                    <% if( content_item.get("description").length> 80 ) { %>
+                        <td data-toggle="tooltip" data-placement="bottom"
+                            title='<%= _.escape(content_item.get("description")) %>'>
+                            <%= _.escape(content_item.get("description")).substring(0, 80) + "..." %>
+                        </td>
+                    <% } else { %>
+                        <td><%= _.escape(content_item.get("description"))%></td>
+                    <% } %>
+                <% } else { %>
+                    <td></td>
+                <% } %>
+                <td>
+                    folder
+                </td>
+                <td></td>
+                <td>
+                    <%= _.escape(content_item.get("update_time")) %>
+                </td>
+                <td></td>
+                <td class="right-center">
+                    <span data-toggle="tooltip" data-placement="top"
+                        title="Marked deleted" class="fa fa-ban"></span>
+                    <button data-toggle="tooltip" data-placement="top"
+                        title="Undelete '<%- content_item.get("name") %>'"
+                        class="primary-button btn-sm undelete_folder_btn" type="button" style="margin-left:1em;">
+                        <span class="fa fa-unlock"></span> Undelete
+                    </button>
+                </td>
+            </tr>`
         );
     }
 });
diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
index 5af390bd69c..b3d5ec39d6d 100644
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -18,12 +18,13 @@ var FolderToolbarView = Backbone.View.extend({
     el: "#center",
 
     events: {
-        "click .toolbtn-create-folder": "createFolderFromModal",
+        "click .toolbtn-create-folder": "createFolderInline",
         "click .toolbtn-bulk-import": "importToHistoryModal",
         "click .include-deleted-datasets-chk": "checkIncludeDeleted",
         "click .toolbtn-bulk-delete": "deleteSelectedItems",
         "click .toolbtn-show-locinfo": "showLocInfo",
-        "click .page-size-prompt": "showPageSizePrompt",
+        "keydown .page_size": "changePageSize",
+        "blur .page_size": "changePageSize",
         "click .toolbtn-collection-import": "showCollectionSelect"
     },
 
@@ -78,14 +79,15 @@ var FolderToolbarView = Backbone.View.extend({
 
     render: function(options) {
         this.options = _.extend(this.options, options);
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var toolbar_template = this.templateToolBar();
         var template_defaults = {
             id: this.options.id,
             is_admin: false,
             is_anonym: true,
             multiple_add_dataset_options: false,
-            Galaxy: Galaxy
+            Galaxy: Galaxy,
+            folder_page_size: Galaxy.libraries.preferences.get("folder_page_size")
         };
         if (Galaxy.user) {
             template_defaults.is_admin = Galaxy.user.isAdmin();
@@ -107,10 +109,11 @@ var FolderToolbarView = Backbone.View.extend({
      */
     renderPaginator: function(options) {
         this.options = _.extend(this.options, options);
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var paginator_template = this.templatePaginator();
+        var paginator_text_template = this.templatePaginatorText();
         $("body")
-            .find(".folder-paginator")
+            .find(".folder-paginator > .paginator")
             .html(
                 paginator_template({
                     id: this.options.id,
@@ -121,11 +124,23 @@ var FolderToolbarView = Backbone.View.extend({
                     folder_page_size: Galaxy.libraries.preferences.get("folder_page_size")
                 })
             );
+        $("body")
+            .find(".folder-paginator > .paginator-text")
+            .html(
+                paginator_text_template({
+                    id: this.options.id,
+                    show_page: parseInt(this.options.show_page),
+                    page_count: parseInt(this.options.page_count),
+                    total_items_count: this.options.total_items_count,
+                    items_shown: this.options.items_shown,
+                    folder_page_size: Galaxy.libraries.preferences.get("folder_page_size")
+                })
+            );
     },
 
     configureElements: function(options) {
         this.options = _.extend(this.options, options);
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         if (this.options.can_add_library_item === true) {
             $(".add-library-items").show();
@@ -152,77 +167,14 @@ var FolderToolbarView = Backbone.View.extend({
         this.$el.find('[data-toggle="tooltip"]').tooltip({ trigger: "hover" });
     },
 
-    createFolderFromModal: function(event) {
-        event.preventDefault();
-        event.stopPropagation();
-        let Galaxy = getGalaxyInstance();
-        var template = this.templateNewFolderInModal();
-        this.modal = Galaxy.modal;
-        this.modal.show({
-            closing_events: true,
-            title: _l("Create New Folder"),
-            body: template(),
-            buttons: {
-                Create: () => {
-                    this.createNewFolderEvent();
-                },
-                Close: () => {
-                    Galaxy.modal.hide();
-                }
-            }
-        });
-    },
-
-    createNewFolderEvent: function() {
-        let Galaxy = getGalaxyInstance();
-        var folderDetails = this.serializeNewFolder();
-        if (this.validateNewFolder(folderDetails)) {
-            var folder = new mod_library_model.FolderAsModel();
-            var url_items = Backbone.history.fragment.split("/");
-            var current_folder_id;
-            if (url_items.indexOf("page") > -1) {
-                current_folder_id = url_items[url_items.length - 3];
-            } else {
-                current_folder_id = url_items[url_items.length - 1];
-            }
-            folder.url = folder.urlRoot + current_folder_id;
-
-            folder.save(folderDetails, {
-                success: function(folder) {
-                    Galaxy.modal.hide();
-                    Toast.success("Folder created.");
-                    folder.set({ type: "folder" });
-                    Galaxy.libraries.folderListView.collection.add(folder);
-                },
-                error: function(model, response) {
-                    Galaxy.modal.hide();
-                    if (typeof response.responseJSON !== "undefined") {
-                        Toast.error(response.responseJSON.err_msg);
-                    } else {
-                        Toast.error("An error occurred.");
-                    }
-                }
-            });
-        } else {
-            Toast.error("Folder's name is missing.");
-        }
-        return false;
-    },
-
-    serializeNewFolder: function() {
-        return {
-            name: $("input[name='Name']").val(),
-            description: $("input[name='Description']").val()
-        };
-    },
-
-    validateNewFolder: function(folderDetails) {
-        return folderDetails.name !== "";
+    createFolderInline: function() {
+        const Galaxy = getGalaxyInstance();
+        Galaxy.libraries.folderListView.createFolderInline();
     },
 
     importToHistoryModal: function(e) {
         e.preventDefault();
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var $checkedValues = this.findCheckedRows();
         var template = this.templateImportIntoHistoryModal();
         if ($checkedValues.length === 0) {
@@ -296,8 +248,8 @@ var FolderToolbarView = Backbone.View.extend({
         var items_to_import = [];
         // prepare the dataset objects to be imported
         for (let i = checked_items.dataset_ids.length - 1; i >= 0; i--) {
-            let library_dataset_id = checked_items.dataset_ids[i];
-            let historyItem = new mod_library_model.HistoryItem();
+            const library_dataset_id = checked_items.dataset_ids[i];
+            const historyItem = new mod_library_model.HistoryItem();
             historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
             historyItem.content = library_dataset_id;
             historyItem.source = "library";
@@ -305,8 +257,8 @@ var FolderToolbarView = Backbone.View.extend({
         }
         // prepare the folder objects to be imported
         for (let i = checked_items.folder_ids.length - 1; i >= 0; i--) {
-            let library_folder_id = checked_items.folder_ids[i];
-            let historyItem = new mod_library_model.HistoryItem();
+            const library_folder_id = checked_items.folder_ids[i];
+            const historyItem = new mod_library_model.HistoryItem();
             historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
             historyItem.content = library_folder_id;
             historyItem.source = "library_folder";
@@ -373,7 +325,7 @@ var FolderToolbarView = Backbone.View.extend({
     },
 
     addFilesFromHistoryModal: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.histories = new mod_library_model.GalaxyHistories();
         this.histories
             .fetch()
@@ -416,7 +368,7 @@ var FolderToolbarView = Backbone.View.extend({
      * Create modal for importing from Galaxy path.
      */
     importFilesFromPathModal: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal;
         var template_modal = this.templateImportPathModal();
         this.modal.show({
@@ -450,7 +402,7 @@ var FolderToolbarView = Backbone.View.extend({
             url: `${getAppRoot()}api/datatypes?extension_only=False`,
             success: datatypes => {
                 this.list_extensions = [];
-                for (let key in datatypes) {
+                for (const key in datatypes) {
                     this.list_extensions.push({
                         id: datatypes[key].extension,
                         text: datatypes[key].extension,
@@ -467,7 +419,7 @@ var FolderToolbarView = Backbone.View.extend({
             url: `${getAppRoot()}api/genomes`,
             success: genomes => {
                 this.list_genomes = [];
-                for (let key in genomes) {
+                for (const key in genomes) {
                     this.list_genomes.push({
                         id: genomes[key][1],
                         text: genomes[key][0]
@@ -480,7 +432,7 @@ var FolderToolbarView = Backbone.View.extend({
     },
 
     renderSelectBoxes: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         // This won't work properly unlesss we already have the data fetched.
         // See this.fetchExtAndGenomes()
         this.select_genome = new mod_select.View({
@@ -503,7 +455,7 @@ var FolderToolbarView = Backbone.View.extend({
      */
     importFilesFromGalaxyFolderModal: function(options) {
         var template_modal = this.templateBrowserModal();
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal;
         this.modal.show({
             closing_events: true,
@@ -650,7 +602,7 @@ var FolderToolbarView = Backbone.View.extend({
      * @param {int} length The number of items in the chain call.
      */
     initChainCallControl: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var template;
         switch (options.action) {
             case "adding_datasets":
@@ -719,7 +671,7 @@ var FolderToolbarView = Backbone.View.extend({
                 action: "adding_datasets"
             });
             if (selection_type === "folder") {
-                let full_source = `${options.source}_folder`;
+                const full_source = `${options.source}_folder`;
                 this.chainCallImportingFolders({
                     paths: paths,
                     preserve_dirs: preserve_dirs,
@@ -732,7 +684,7 @@ var FolderToolbarView = Backbone.View.extend({
                     tag_using_filenames: tag_using_filenames
                 });
             } else if (selection_type === "file") {
-                let full_source = `${options.source}_file`;
+                const full_source = `${options.source}_file`;
                 this.chainCallImportingUserdirFiles({
                     paths: paths,
                     file_type: file_type,
@@ -754,18 +706,31 @@ var FolderToolbarView = Backbone.View.extend({
         history_contents.fetch({
             success: history_contents => {
                 var history_contents_template = this.templateHistoryContents();
-                this.histories.get(history_id).set({ contents: history_contents });
-                this.modal.$el.find(".library_selected_history_content").html(
-                    history_contents_template({
-                        history_contents: history_contents.models.reverse()
-                    })
-                );
-                this.modal.$el.find(".history-import-select-all").bind("click", () => {
-                    $(".library_selected_history_content [type=checkbox]").prop("checked", true);
-                });
-                this.modal.$el.find(".history-import-unselect-all").bind("click", () => {
-                    $(".library_selected_history_content [type=checkbox]").prop("checked", false);
-                });
+
+                if (history_contents.length > 0) {
+                    this.histories.get(history_id).set({ contents: history_contents });
+                    this.modal.$el.find(".library_selected_history_content").html(
+                        history_contents_template({
+                            history_contents: history_contents.models.reverse()
+                        })
+                    );
+                    this.modal.$el.find(".history-import-select-all").bind("click", () => {
+                        $(".library_selected_history_content [type=checkbox]").prop("checked", true);
+                    });
+                    this.modal.$el.find(".history-import-unselect-all").bind("click", () => {
+                        $(".library_selected_history_content [type=checkbox]").prop("checked", false);
+                    });
+
+                    this.modal.$el.find(".history-import-toggle-all").bind("click", e => {
+                        this.selectAll(e);
+                    });
+
+                    this.modal.$el.find(".dataset_row").bind("click", e => {
+                        this.selectClickedRow(e);
+                    });
+                } else {
+                    this.modal.$el.find(".library_selected_history_content").html(`<p>Selected history is empty.</p>`);
+                }
             },
             error: (model, response) => {
                 if (typeof response.responseJSON !== "undefined") {
@@ -791,11 +756,11 @@ var FolderToolbarView = Backbone.View.extend({
             this.modal.disableButton("Add");
             checked_hdas.each(function() {
                 var hid = $(this)
-                    .closest("li")
+                    .closest("tr")
                     .data("id");
                 if (hid) {
                     var item_type = $(this)
-                        .closest("li")
+                        .closest("tr")
                         .data("name");
                     history_item_ids.push(hid);
                     history_item_types.push(item_type);
@@ -820,6 +785,67 @@ var FolderToolbarView = Backbone.View.extend({
         }
     },
 
+    /**
+     * User clicked the checkbox in the table heading
+     * @param  {context} event
+     */
+    selectAll: function(event) {
+        var selected = event.target.checked;
+        var self = this;
+        // Iterate each checkbox
+        $(":checkbox", "#dataset_list tbody").each(function() {
+            this.checked = selected;
+            var $row = $(this).closest("tr");
+            // Change color of selected/unselected
+            if (selected) {
+                self.makeDarkRow($row);
+            } else {
+                self.makeWhiteRow($row);
+            }
+        });
+    },
+
+    /**
+     * Check checkbox if user clicks on the whole row or
+     *  on the checkbox itself
+     */
+    selectClickedRow: function(event) {
+        var checkbox = "";
+        var $row;
+        var source;
+        $row = $(event.target).closest("tr");
+        if (event.target.localName === "input") {
+            checkbox = event.target;
+            source = "input";
+        } else if (event.target.localName === "td") {
+            checkbox = $row.find(":checkbox")[0];
+            source = "td";
+        }
+        if (checkbox.checked) {
+            if (source === "td") {
+                checkbox.checked = "";
+                this.makeWhiteRow($row);
+            } else if (source === "input") {
+                this.makeDarkRow($row);
+            }
+        } else {
+            if (source === "td") {
+                checkbox.checked = "selected";
+                this.makeDarkRow($row);
+            } else if (source === "input") {
+                this.makeWhiteRow($row);
+            }
+        }
+    },
+
+    makeDarkRow: function($row) {
+        $row.addClass("table-primary");
+    },
+
+    makeWhiteRow: function($row) {
+        $row.removeClass("table-primary");
+    },
+
     /**
      * Take array of empty history items and make request for each of them
      * to create it on server. Update progress in between calls.
@@ -827,7 +853,7 @@ var FolderToolbarView = Backbone.View.extend({
      * @param  {str} history_name     name of the history to import to
      */
     chainCallImportingIntoHistory: function(history_item_set, history_name) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var popped_item = history_item_set.pop();
         if (typeof popped_item == "undefined") {
             if (this.options.chain_call_control.failed_number === 0) {
@@ -878,8 +904,8 @@ var FolderToolbarView = Backbone.View.extend({
      * @param  {boolean} tag_using_filenames    add tags to datasets using names of files
      */
     chainCallImportingUserdirFiles: function(options) {
-        let Galaxy = getGalaxyInstance();
-        let popped_item = options.paths.pop();
+        const Galaxy = getGalaxyInstance();
+        const popped_item = options.paths.pop();
         if (typeof popped_item === "undefined") {
             if (this.options.chain_call_control.failed_number === 0) {
                 Toast.success("Selected files imported into the current folder");
@@ -889,8 +915,8 @@ var FolderToolbarView = Backbone.View.extend({
             }
             return true;
         }
-        let post_url = `${getAppRoot()}api/libraries/datasets`;
-        let post_data = {
+        const post_url = `${getAppRoot()}api/libraries/datasets`;
+        const post_data = {
             encoded_folder_id: this.id,
             source: options.source,
             path: popped_item,
@@ -901,7 +927,7 @@ var FolderToolbarView = Backbone.View.extend({
             dbkey: options.dbkey,
             tag_using_filenames: options.tag_using_filenames
         };
-        let promise = $.when($.post(post_url, post_data));
+        const promise = $.when($.post(post_url, post_data));
         promise
             .done(response => {
                 this.updateProgress();
@@ -927,9 +953,9 @@ var FolderToolbarView = Backbone.View.extend({
      * @param  {boolean} tag_using_filenames    add tags to datasets using names of files
      */
     chainCallImportingFolders: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         // TODO need to check which paths to call
-        let popped_item = options.paths.pop();
+        const popped_item = options.paths.pop();
         if (typeof popped_item == "undefined") {
             if (this.options.chain_call_control.failed_number === 0) {
                 Toast.success("Selected folders and their contents imported into the current folder.");
@@ -940,8 +966,8 @@ var FolderToolbarView = Backbone.View.extend({
             }
             return true;
         }
-        let post_url = `${getAppRoot()}api/libraries/datasets`;
-        let post_data = {
+        const post_url = `${getAppRoot()}api/libraries/datasets`;
+        const post_data = {
             encoded_folder_id: this.id,
             source: options.source,
             path: popped_item,
@@ -953,7 +979,7 @@ var FolderToolbarView = Backbone.View.extend({
             dbkey: options.dbkey,
             tag_using_filenames: options.tag_using_filenames
         };
-        let promise = $.when($.post(post_url, post_data));
+        const promise = $.when($.post(post_url, post_data));
         promise
             .done(response => {
                 this.updateProgress();
@@ -972,7 +998,7 @@ var FolderToolbarView = Backbone.View.extend({
      * @param  {array} hdas_set array of empty hda objects
      */
     chainCallAddingHdas: function(hdas_set) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.added_hdas = new mod_library_model.Folder();
         var popped_item = hdas_set.pop();
         if (typeof popped_item == "undefined") {
@@ -1011,7 +1037,7 @@ var FolderToolbarView = Backbone.View.extend({
      * @param  {array} lddas_set array of lddas to delete
      */
     chainCallDeletingItems: function(items_to_delete) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.deleted_items = new mod_library_model.Folder();
         var item_to_delete = items_to_delete.pop();
         if (typeof item_to_delete === "undefined") {
@@ -1060,7 +1086,7 @@ var FolderToolbarView = Backbone.View.extend({
      * Handles the click on 'show deleted' checkbox
      */
     checkIncludeDeleted: function(event) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (event.target.checked) {
             Galaxy.libraries.folderListView.fetchFolder({
                 include_deleted: true
@@ -1076,7 +1102,7 @@ var FolderToolbarView = Backbone.View.extend({
      * Delete the selected items. Atomic. One by one.
      */
     deleteSelectedItems: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var dataset_ids = [];
         var folder_ids = [];
         var $checkedValues = this.findCheckedRows();
@@ -1138,7 +1164,7 @@ var FolderToolbarView = Backbone.View.extend({
     },
 
     showLocInfo: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var library = null;
         if (Galaxy.libraries.libraryListView !== null) {
             library = Galaxy.libraries.libraryListView.collection.get(this.options.parent_library_id);
@@ -1163,7 +1189,7 @@ var FolderToolbarView = Backbone.View.extend({
     },
 
     showLocInfoModal: function(library) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var template = this.templateLocInfoInModal();
         this.modal = Galaxy.modal;
         this.modal.show({
@@ -1179,7 +1205,7 @@ var FolderToolbarView = Backbone.View.extend({
     },
 
     showImportModal: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         switch (options.source) {
             case "history":
                 this.addFilesFromHistoryModal();
@@ -1205,18 +1231,14 @@ var FolderToolbarView = Backbone.View.extend({
     },
 
     /**
-     * Show user the prompt to change the number of items shown on page.
+     * Change the number of libs shown on page.
      */
-    showPageSizePrompt: function(e) {
-        e.preventDefault();
-        let Galaxy = getGalaxyInstance();
-        var folder_page_size = prompt(
-            "How many items per page do you want to see?",
-            Galaxy.libraries.preferences.get("folder_page_size")
-        );
-        if (folder_page_size != null && folder_page_size == parseInt(folder_page_size)) {
+    changePageSize: function(e) {
+        if (e.type === "focusout" || (e.type === "keydown" && e.keyCode === 13)) {
+            e.preventDefault();
+            const Galaxy = getGalaxyInstance();
             Galaxy.libraries.preferences.set({
-                folder_page_size: parseInt(folder_page_size)
+                folder_page_size: parseInt(e.target.value)
             });
             Galaxy.libraries.folderListView.render({
                 id: this.options.id,
@@ -1248,67 +1270,38 @@ var FolderToolbarView = Backbone.View.extend({
 
     showCollectionSelect: function(e) {
         e.preventDefault();
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var checked_items = this.findCheckedItems();
         var template = this.templateCollectionSelectModal();
-        this.modal = Galaxy.modal;
-        this.modal.show({
-            closing_events: true,
-            title: "Create History Collection from Datasets",
-            body: template({ selected_datasets: checked_items.dataset_ids.length }),
-            buttons: {
-                Continue: () => {
-                    this.showCollectionBuilder(checked_items.dataset_ids);
-                },
-                Close: () => {
-                    Galaxy.modal.hide();
-                }
-            }
-        });
-        this.prepareCollectionTypeSelect();
-        this.prepareHistoryTypeSelect();
-    },
 
-    prepareCollectionTypeSelect: function() {
-        this.collectionType = "list";
-        this.select_collection_type = new mod_select.View({
-            css: "library-collection-type-select",
-            container: this.modal.$el.find(".library-collection-type-select"),
-            data: [
-                { id: "list", text: "List" },
-                { id: "paired", text: "Paired" },
-                { id: "list:paired", text: "List of Pairs" },
-                { id: "rules", text: "From Rules" }
-            ],
-            value: "list",
-            onchange: collectionType => {
-                this.updateCollectionType(collectionType);
-            }
-        });
-    },
-
-    prepareHistoryTypeSelect: function() {
         var promise = this.fetchUserHistories();
-        promise.done(() => {
-            var history_options = [];
-            for (let i = this.histories.length - 1; i >= 0; i--) {
-                history_options.unshift({
-                    id: this.histories.models[i].id,
-                    text: this.histories.models[i].get("name")
+        promise
+            .done(() => {
+                this.modal = Galaxy.modal;
+                this.modal.show({
+                    closing_events: true,
+                    title: "Create History Collection from Datasets",
+                    body: template({
+                        selected_datasets: checked_items.dataset_ids.length,
+                        histories: this.histories.models
+                    }),
+                    buttons: {
+                        Continue: () => {
+                            this.showCollectionBuilder(checked_items.dataset_ids);
+                        },
+                        Close: () => {
+                            Galaxy.modal.hide();
+                        }
+                    }
                 });
-            }
-            this.select_collection_history = new mod_select.View({
-                css: "library-collection-history-select",
-                container: this.modal.$el.find(".library-collection-history-select"),
-                data: history_options,
-                value: history_options[0].id
+            })
+            .fail((model, response) => {
+                if (typeof response.responseJSON !== "undefined") {
+                    Toast.error(response.responseJSON.err_msg);
+                } else {
+                    Toast.error("An error occurred.");
+                }
             });
-        });
-    },
-
-    /** Update collection type */
-    updateCollectionType: function(collectionType) {
-        this.collectionType = collectionType;
     },
 
     /**
@@ -1317,13 +1310,13 @@ var FolderToolbarView = Backbone.View.extend({
      * The code below overwrites the id with ldda_id for this reason.
      */
     showCollectionBuilder: function(checked_items) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         let collection_elements = [];
-        let elements_source = this.modal.$('input[type="radio"]:checked').val();
+        const elements_source = this.modal.$('input[type="radio"]:checked').val();
         if (elements_source === "selection") {
             for (let i = checked_items.length - 1; i >= 0; i--) {
-                let collection_item = {};
-                let dataset = Galaxy.libraries.folderListView.folder_container.get("folder").get(checked_items[i]);
+                const collection_item = {};
+                const dataset = Galaxy.libraries.folderListView.folder_container.get("folder").get(checked_items[i]);
                 collection_item.id = dataset.get("ldda_id");
                 collection_item.name = dataset.get("name");
                 collection_item.deleted = dataset.get("deleted");
@@ -1331,13 +1324,13 @@ var FolderToolbarView = Backbone.View.extend({
                 collection_elements.push(collection_item);
             }
         } else if (elements_source === "folder") {
-            let all_datasets = Galaxy.libraries.folderListView.folder_container.get("folder").where({ type: "file" });
+            const all_datasets = Galaxy.libraries.folderListView.folder_container.get("folder").where({ type: "file" });
             collection_elements = new Backbone.Collection(all_datasets).toJSON();
             for (var i = collection_elements.length - 1; i >= 0; i--) {
                 collection_elements[i].id = collection_elements[i].ldda_id;
             }
         }
-        let new_history_name = this.modal.$("input[name=history_name]").val();
+        const new_history_name = this.modal.$("input[name=history_name]").val();
         if (new_history_name !== "") {
             this.createNewHistory(new_history_name)
                 .done(new_history => {
@@ -1348,16 +1341,18 @@ var FolderToolbarView = Backbone.View.extend({
                     Toast.error("An error occurred.");
                 });
         } else {
-            let selected_history_id = this.select_collection_history.value();
-            let selected_history_name = this.select_collection_history.text();
+            this.select_collection_history = this.modal.$el.find("#library-collection-history-select");
+            const selected_history_id = this.select_collection_history.val();
+            const selected_history_name = this.select_collection_history.find("option:selected").text();
             this.collectionImport(collection_elements, selected_history_id, selected_history_name);
         }
     },
 
     collectionImport: function(collection_elements, history_id, history_name) {
-        let modal_title = `Creating Collection in ${history_name}`;
+        const modal_title = `Creating Collection in ${history_name}`;
         let creator_class;
         let creationFn;
+        this.collectionType = this.modal.$el.find("#library-collection-type-select").val();
         if (this.collectionType === "list") {
             creator_class = LIST_CREATOR.ListCollectionCreator;
             creationFn = (elements, name, hideSourceItems) => {
@@ -1388,7 +1383,7 @@ var FolderToolbarView = Backbone.View.extend({
                 creator_class
             );
         } else if (this.collectionType === "list:paired") {
-            let elements = collection_elements.map(element => ({
+            const elements = collection_elements.map(element => ({
                 id: element.id,
                 name: element.name,
                 src: "ldda"
@@ -1410,7 +1405,7 @@ var FolderToolbarView = Backbone.View.extend({
     },
 
     createHDCA: function(elementIdentifiers, collectionType, name, hideSourceItems, history_id, options) {
-        let hdca = new HDCA_MODEL.HistoryDatasetCollection({
+        const hdca = new HDCA_MODEL.HistoryDatasetCollection({
             history_content_type: "dataset_collection",
             collection_type: collectionType,
             history_id: history_id,
@@ -1428,55 +1423,66 @@ var FolderToolbarView = Backbone.View.extend({
                     <a class="mr-1 btn btn-secondary" href="list" data-toggle="tooltip" title="Go to first page">
                         <span class="fa fa-home"/>
                     </a>
-                    <a class="mr-1 btn btn-secondary" data-toggle="tooltip" title="See this screen annotated" href="https://galaxyproject.org/data-libraries/screen/folder-contents/" target="_blank">
-                        <span class="fa fa-question"/>
-                    </a>
                     <div>
                         <form class="form-inline">
-                            <div class="form-check logged-dataset-manipulation mr-1" style="display:none;">
-                                <input class="form-check-input include-deleted-datasets-chk" id="include_deleted_datasets_chk" type="checkbox">
-                                <label class="form-check-label" for="include_deleted_datasets_chk">include deleted</label>
-                            </div>
-                            <button style="display:none;" title="Create new folder" class="btn btn-secondary toolbtn-create-folder add-library-items add-library-items-folder mr-1" type="button">
-                            <span class="fa fa-folder"/> Create Folder</button>
+                            <button style="display:none;" title="Create new folder"
+                                class="btn btn-secondary toolbtn-create-folder add-library-items add-library-items-folder mr-1"
+                                type="button">
+                                <span class="fa fa-plus"></span> Folder
+                            </button>
                             <% if(multiple_add_dataset_options) { %>
-                                <div title="Add datasets to current folder" class="dropdown add-library-items add-library-items-datasets mr-1" style="display:none;">
-                                <button type="button" class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">
-                                    <span class="fa fa-file"/> Add Datasets <span class="caret"/>
-                                </button>
+                                <div title="Add datasets to current folder"
+                                    class="dropdown add-library-items add-library-items-datasets mr-1" style="display:none;">
+                                    <button type="button" class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">
+                                        <span class="fa fa-plus"></span> Datasets <span class="caret"/>
+                                    </button>
                                 <div class="dropdown-menu">
                                     <a class="dropdown-item" href="#folders/<%= id %>/import/history"> from History</a>
                                     <% if(Galaxy.config.user_library_import_dir !== null) { %>
-                                        <a class="dropdown-item" href="#folders/<%= id %>/import/userdir"> from User Directory</a>
+                                        <a class="dropdown-item" href="#folders/<%= id %>/import/userdir">
+                                            from User Directory
+                                        </a>
                                     <% } %>
                                     <% if(Galaxy.config.library_import_dir !== null || Galaxy.config.allow_library_path_paste) { %>
                                         <h5 class="dropdown-header">Admins only</h5>
                                         <% if(Galaxy.config.library_import_dir !== null) { %>
-                                            <a class="dropdown-item" href="#folders/<%= id %>/import/importdir">from Import Directory</a>
+                                            <a class="dropdown-item" href="#folders/<%= id %>/import/importdir">
+                                                from Import Directory
+                                            </a>
                                         <% } %>
                                         <% if(Galaxy.config.allow_library_path_paste) { %>
-                                            <a class="dropdown-item" href="#folders/<%= id %>/import/path">from Path</a>
+                                            <a class="dropdown-item" href="#folders/<%= id %>/import/path">
+                                                from Path
+                                            </a>
                                         <% } %>
                                     <% } %>
                                 </div>
                             </div>
                             <% } else { %>
-                                <a title="Add Datasets to Current Folder" style="display:none;" class="btn btn-secondary add-library-items add-library-items-datasets mr-1" href="#folders/<%= id %>/import/history" role="button">
-                                    <span class="fa fa-file"/> Add Datasets
+                                <a title="Add Datasets to Current Folder" style="display:none;"
+                                    class="btn btn-secondary add-library-items add-library-items-datasets mr-1"
+                                    href="#folders/<%= id %>/import/history" role="button">
+                                    <span class="fa fa-plus"></span> Datasets
                                 </a>
                             <% } %>
                             <div class="dropdown mr-1">
-                                <button type="button" class="primary-button dropdown-toggle add-to-history" data-toggle="dropdown">
-                                    <span class="fa fa-book"></span> Export to History <span class="caret"/>
+                                <button type="button" class="primary-button dropdown-toggle add-to-history"
+                                    data-toggle="dropdown">
+                                    <span class="fa fa-book"></span> Export to History <span class="caret"></span>
                                 </button>
                                 <div class="dropdown-menu" role="menu">
-                                    <a href="#" class="toolbtn-bulk-import add-to-history-datasets dropdown-item">as Datasets</a>
-                                    <a href="#" class="toolbtn-collection-import add-to-history-collection dropdown-item">as a Collection</a>
+                                    <a href="#" class="toolbtn-bulk-import add-to-history-datasets dropdown-item">
+                                        as Datasets
+                                    </a>
+                                    <a href="#" class="toolbtn-collection-import add-to-history-collection dropdown-item">
+                                        as a Collection
+                                    </a>
                                 </div>
                             </div>
-                            <div title="Download items as archive" class="dropdown dataset-manipulation mr-1" style="display:none; ">
+                            <div title="Download items as archive"
+                                class="dropdown dataset-manipulation mr-1" style="display:none; ">
                                 <button type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">
-                                    <span class="fa fa-save"/> Download <span class="caret"/>
+                                    <span class="fa fa-save"></span> Download <span class="caret"></span>
                                 </button>
                                 <div class="dropdown-menu" role="menu">
                                     <a class="dropdown-item" href="#/folders/<%= id %>/download/tgz">.tar.gz</a>
@@ -1484,423 +1490,493 @@ var FolderToolbarView = Backbone.View.extend({
                                     <a class="dropdown-item" href="#/folders/<%= id %>/download/zip">.zip</a>
                                 </div>
                             </div>
-                            <button data-toggle="tooltip" title="Mark items deleted" class="primary-button toolbtn-bulk-delete logged-dataset-manipulation mr-1" style="display:none;" type="button">
-                                <span class="fa fa-trash"/> Delete
+                            <button data-toggle="tooltip" title="Mark items deleted"
+                                class="primary-button toolbtn-bulk-delete logged-dataset-manipulation mr-1"
+                                style="display:none;" type="button">
+                                <span class="fa fa-trash"></span> Delete
                             </button>
                             <span class="mr-1" data-toggle="tooltip" title="Show location details">
                                 <button data-id="<%- id %>" class="primary-button toolbtn-show-locinfo" type="button">
-                                    <span class="fa fa-info-circle"/>&nbsp;Details
+                                    <span class="fa fa-info-circle"></span>&nbsp;Details
                                 </button>
                             </span>
+                            <div class="form-check logged-dataset-manipulation mr-1" style="display:none;">
+                                <input class="form-check-input include-deleted-datasets-chk"
+                                    id="include_deleted_datasets_chk" type="checkbox" />
+                                <label class="form-check-label" for="include_deleted_datasets_chk">
+                                    include deleted
+                                </label>
+                            </div>
                         </form>
                     </div>
                 </div>
                 <div id="folder_items_element" />
-                <div class="d-flex justify-content-center align-items-center folder-paginator mt-2 mb-2" />
+
+                <div class="d-flex justify-content-center align-items-center folder-paginator mt-2 mb-2">
+                    <ul class="pagination paginator mr-1" />
+                    <input style="width: initial;" min="0" max="999" class="page_size form-control" type="number" value="<%- folder_page_size %>" />
+                    <span class="text-muted ml-1 paginator-text" />
+                </div>
             </div>`
         );
     },
 
     templateLocInfoInModal: function() {
         return _.template(
-            [
-                "<div>",
-                '<table class="grid table table-sm">',
-                "<thead>",
-                '<th style="width: 25%;">library</th>',
-                "<th></th>",
-                "</thead>",
-                "<tbody>",
-                "<tr>",
-                "<td>name</td>",
-                '<td><%- library.get("name") %></td>',
-                "</tr>",
-                '<% if(library.get("description") !== "") { %>',
-                "<tr>",
-                "<td>description</td>",
-                '<td><%- library.get("description") %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if(library.get("synopsis") !== "") { %>',
-                "<tr>",
-                "<td>synopsis</td>",
-                '<td><%- library.get("synopsis") %></td>',
-                "</tr>",
-                "<% } %>",
-                '<% if(library.get("create_time_pretty") !== "") { %>',
-                "<tr>",
-                "<td>created</td>",
-                '<td><span title="<%- library.get("create_time") %>"><%- library.get("create_time_pretty") %></span></td>',
-                "</tr>",
-                "<% } %>",
-                "<tr>",
-                "<td>id</td>",
-                '<td><%- library.get("id") %></td>',
-                "</tr>",
-                "</tbody>",
-                "</table>",
-                '<table class="grid table table-sm">',
-                "<thead>",
-                '<th style="width: 25%;">folder</th>',
-                "<th></th>",
-                "</thead>",
-                "<tbody>",
-                "<tr>",
-                "<td>name</td>",
-                "<td><%- options.folder_name %></td>",
-                "</tr>",
-                '<% if(options.folder_description !== "") { %>',
-                "<tr>",
-                "<td>description</td>",
-                "<td><%- options.folder_description %></td>",
-                "</tr>",
-                "<% } %>",
-                "<tr>",
-                "<td>id</td>",
-                "<td><%- options.id %></td>",
-                "</tr>",
-                "</tbody>",
-                "</table>",
-                "</div>"
-            ].join("")
-        );
-    },
-
-    templateNewFolderInModal: function() {
-        return _.template(
-            [
-                '<div id="new_folder_modal">',
-                "<form>",
-                '<input type="text" name="Name" value="" placeholder="Name" autofocus>',
-                '<input type="text" name="Description" value="" placeholder="Description">',
-                "</form>",
-                "</div>"
-            ].join("")
+            `<div>
+                <table class="grid table table-sm">
+                    <thead>
+                        <th style="width: 25%;">Library</th>
+                        <th></th>
+                    </thead>
+                    <tbody>
+                        <tr>
+                            <td>name</td>
+                            <td><%- library.get("name") %></td>
+                        </tr>
+                        <% if(library.get("description") !== "") { %>
+                            <tr>
+                                <td>description</td>
+                                <td><%- library.get("description") %></td>
+                            </tr>
+                        <% } %>
+                        <% if(library.get("synopsis") !== "") { %>
+                            <tr>
+                                <td>synopsis</td>
+                                <td><%- library.get("synopsis") %></td>
+                            </tr>
+                        <% } %>
+                        <% if(library.get("create_time_pretty") !== "") { %>
+                            <tr>
+                                <td>created</td>
+                                <td>
+                                    <span title="<%- library.get("create_time") %>">
+                                        <%- library.get("create_time_pretty") %>
+                                    </span>
+                                </td>
+                            </tr>
+                        <% } %>
+                        <tr>
+                            <td>id</td>
+                            <td><%- library.get("id") %></td>
+                        </tr>
+                    </tbody>
+                </table>
+                <table class="grid table table-sm">
+                    <thead>
+                        <th style="width: 25%;">Folder</th>
+                        <th></th>
+                    </thead>
+                    <tbody>
+                        <tr>
+                            <td>name</td>
+                            <td><%- options.folder_name %></td>
+                        </tr>
+                        <% if(options.folder_description !== "") { %>
+                            <tr>
+                                <td>description</td>
+                                <td><%- options.folder_description %></td>
+                            </tr>
+                        <% } %>
+                        <tr>
+                            <td>id</td>
+                            <td><%- options.id %></td>
+                        </tr>
+                    </tbody>
+                </table>
+            </div>`
         );
     },
 
     templateImportIntoHistoryModal: function() {
         return _.template(
-            [
-                "<div>",
-                '<div class="library-modal-item">',
-                "Select history: ",
-                '<select name="import_to_history" style="width:50%; margin-bottom: 1em; " autofocus>',
-                "<% _.each(histories, function(history) { %>",
-                '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
-                "<% }); %>",
-                "</select>",
-                "</div>",
-                '<div class="library-modal-item">',
-                "or create new: ",
-                '<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;" />',
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div>
+                <div class="library-modal-item">
+                    Select history:
+                    <select name="import_to_history" style="width:50%; margin-bottom: 1em; " autofocus>
+                        <% _.each(histories, function(history) { %>
+                            <option value="<%= _.escape(history.get("id")) %>">
+                                <%= _.escape(history.get("name")) %>
+                            </option>
+                        <% }); %>
+                    </select>
+                </div>
+                <div class="library-modal-item">
+                    or create new:
+                    <input type="text" name="history_name" value=""
+                        placeholder="name of the new history" style="width:50%;" />
+                </div>
+            </div>`
         );
     },
 
     templateImportIntoHistoryProgressBar: function() {
         return _.template(
-            [
-                '<div class="import_text">',
-                "Importing selected items to history <b><%= _.escape(history_name) %></b>",
-                "</div>",
-                '<div class="progress">',
-                '<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">',
-                '<span class="completion_span">0% Complete</span>',
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div class="import_text">
+                Importing selected items to history <b><%= _.escape(history_name) %></b>
+            </div>
+            <div class="progress">
+                <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0"
+                    aria-valuemax="100" style="width: 00%;">
+                    <span class="completion_span">0% Complete</span>
+                </div>
+            </div>`
         );
     },
 
     templateAddingDatasetsProgressBar: function() {
         return _.template(
-            [
-                '<div class="import_text">',
-                "Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>",
-                "</div>",
-                '<div class="progress">',
-                '<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">',
-                '<span class="completion_span">0% Complete</span>',
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div class="import_text">
+                Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>
+            </div>
+            <div class="progress">
+                <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0"
+                    aria-valuemax="100" style="width: 00%;">
+                    <span class="completion_span">0% Complete</span>
+                </div>
+            </div>`
         );
     },
 
     templateDeletingItemsProgressBar: function() {
         return _.template(
-            [
-                '<div class="import_text">',
-                "</div>",
-                '<div class="progress">',
-                '<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">',
-                '<span class="completion_span">0% Complete</span>',
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div class="import_text">
+            </div>
+            <div class="progress">
+                <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0"
+                    aria-valuemax="100" style="width: 00%;">
+                    <span class="completion_span">0% Complete</span>
+                </div>
+            </div>`
         );
     },
 
     templateBrowserModal: function() {
         return _.template(
-            [
-                '<div id="file_browser_modal">',
-                '<div style="margin-bottom:1em;">',
-                '<label title="Switch to selecting files" class="radio-inline import-type-switch">',
-                '<input type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Choose Files',
-                "</label>",
-                '<label title="Switch to selecting folders" class="radio-inline import-type-switch">',
-                '<input type="radio" name="jstree-radio" value="jstree-disable-files"> Choose Folders',
-                "</label>",
-                "</div>",
-                '<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder ignoring their folder structure.</div>',
-                '<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>',
-                '<div style="margin-bottom:1em;">',
-                '<label class="checkbox-inline jstree-preserve-structure" style="display:none;">',
-                '<input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">',
-                "Preserve directory structure",
-                "</label>",
-                '<label class="checkbox-inline">',
-                '<input class="link-checkbox" type="checkbox" value="link_files">',
-                "Link files instead of copying",
-                "</label>",
-                '<label class="checkbox-inline">',
-                '<input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">',
-                "Convert line endings to POSIX",
-                "</label>",
-                '<label class="checkbox-inline">',
-                '<input class="spacetab-checkbox" type="checkbox" value="space_to_tab">',
-                "Convert spaces to tabs",
-                "</label>",
-                "</div>",
-                '<button title="Select all files" type="button" class="button primary-button libimport-select-all">',
-                "Select all",
-                "</button>",
-                '<button title="Select no files" type="button" class="button primary-button libimport-select-none">',
-                "Unselect all",
-                "</button>",
-                "<hr />",
-                // append jstree object here
-                '<div id="jstree_browser">',
-                "</div>",
-                "<hr />",
-                "<p>You can set extension type and genome for all imported datasets at once:</p>",
-                "<div>",
-                'Type: <span id="library_extension_select" class="library-extension-select" />',
-                'Genome: <span id="library_genome_select" class="library-genome-select" />',
-                "</div>",
-                "<br>",
-                "<div>",
-                '<label class="checkbox-inline tag-files">',
-                "Tag datasets based on file names",
-                '<input class="tag-files" type="checkbox" value="tag_using_filenames">',
-                "</label>",
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div id="file_browser_modal">
+                    <div style="margin-bottom:1em;">
+                        <label title="Switch to selecting files" class="radio-inline import-type-switch">
+                            <input type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked">
+                            Choose Files
+                        </label>
+                        <label title="Switch to selecting folders" class="radio-inline import-type-switch">
+                            <input type="radio" name="jstree-radio" value="jstree-disable-files">
+                            Choose Folders
+                        </label>
+                    </div>
+                    <div class="alert alert-info jstree-files-message">
+                        All files you select will be imported into the current folder ignoring their folder structure.
+                    </div>
+                    <div class="alert alert-info jstree-folders-message" style="display:none;">
+                        All files within the selected folders and their subfolders will be imported into the current folder.
+                    </div>
+                    <div style="margin-bottom:1em;">
+                        <label class="checkbox-inline jstree-preserve-structure" style="display:none;">
+                            <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">
+                                Preserve directory structure
+                            </label>
+                        <label class="checkbox-inline">
+                            <input class="link-checkbox" type="checkbox" value="link_files">
+                                Link files instead of copying
+                        </label>
+                        <label class="checkbox-inline">
+                            <input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">
+                                Convert line endings to POSIX
+                        </label>
+                        <label class="checkbox-inline">
+                            <input class="spacetab-checkbox" type="checkbox" value="space_to_tab">
+                                Convert spaces to tabs
+                        </label>
+                    </div>
+                    <button title="Select all files" type="button" class="button primary-button libimport-select-all">
+                        Select all
+                    </button>
+                    <button title="Select no files" type="button" class="button primary-button libimport-select-none">
+                        Unselect all
+                    </button>
+                    <hr /> <!-- append jstree object here -->
+                    <div id="jstree_browser">
+                    </div>
+                    <hr />
+                    <p>You can set extension type and genome for all imported datasets at once:</p>
+                    <div>
+                        Type: <span id="library_extension_select" class="library-extension-select" />
+                        Genome: <span id="library_genome_select" class="library-genome-select" />
+                    </div>
+                    <br />
+                    <div>
+                        <label class="checkbox-inline tag-files">
+                            Tag datasets based on file names
+                            <input class="tag-files" type="checkbox" value="tag_using_filenames">
+                        </label>
+                    </div>
+                </div>`
         );
     },
 
     templateImportPathModal: function() {
         return _.template(
-            [
-                '<div id="file_browser_modal">',
-                '<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>',
-                '<div style="margin-bottom: 0.5em;">',
-                '<label class="checkbox-inline">',
-                '<input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">',
-                "Preserve directory structure",
-                "</label>",
-                '<label class="checkbox-inline">',
-                '<input class="link-checkbox" type="checkbox" value="link_files">',
-                "Link files instead of copying",
-                "</label>",
-                "<br>",
-                '<label class="checkbox-inline">',
-                '<input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">',
-                "Convert line endings to POSIX",
-                "</label>",
-                '<label class="checkbox-inline">',
-                '<input class="spacetab-checkbox" type="checkbox" value="space_to_tab">',
-                "Convert spaces to tabs",
-                "</label>",
-                "</div>",
-                '<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline" autofocus></textarea>',
-                "<hr />",
-                "<p>You can set extension type and genome for all imported datasets at once:</p>",
-                "<div>",
-                'Type: <span id="library_extension_select" class="library-extension-select" />',
-                'Genome: <span id="library_genome_select" class="library-genome-select" />',
-                "</div>",
-                "<div>",
-                '<label class="checkbox-inline tag-files">',
-                "Tag datasets based on file names",
-                '<input class="tag-files" type="checkbox" value="tag_using_filenames">',
-                "</label>",
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div id="file_browser_modal">
+                <div class="alert alert-info jstree-folders-message">
+                    All files within the given folders and their subfolders will be imported into the current folder.
+                </div>
+                <div style="margin-bottom: 0.5em;">
+                    <label class="checkbox-inline">
+                        <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">
+                        Preserve directory structure
+                    </label>
+                    <label class="checkbox-inline">
+                        <input class="link-checkbox" type="checkbox" value="link_files">
+                        Link files instead of copying
+                    </label>
+                    <br>
+                    <label class="checkbox-inline">
+                        <input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">
+                        Convert line endings to POSIX
+                    </label>
+                    <label class="checkbox-inline">
+                        <input class="spacetab-checkbox" type="checkbox" value="space_to_tab">
+                        Convert spaces to tabs
+                    </label>
+                </div>
+                <textarea id="import_paths" class="form-control" rows="5"
+                    placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline" autofocus>
+                </textarea>
+                <hr />
+                <p>You can set extension type and genome for all imported datasets at once:</p>
+                <div>
+                    Type: <span id="library_extension_select" class="library-extension-select"></span>
+                    Genome: <span id="library_genome_select" class="library-genome-select"></span>
+                </div>
+                <div>
+                    <label class="checkbox-inline tag-files">
+                        Tag datasets based on file names
+                        <input class="tag-files" type="checkbox" value="tag_using_filenames">
+                    </label>
+                </div>
+            </div>`
         );
     },
 
     templateAddFilesFromHistory: function() {
         return _.template(
-            [
-                '<div id="add_files_modal">',
-                "<div>",
-                "1.&nbsp;Select history:&nbsp;",
-                '<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ',
-                "<% _.each(histories, function(history) { %>", //history select box
-                '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
-                "<% }); %>",
-                "</select>",
-                "</div>",
-                "<br/>",
-                '<div class="library_selected_history_content">',
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div id="add_files_modal">
+                <div class="form-group">
+                    <label>1. Select history:</label>
+                    <select id="dataset_add_bulk" name="dataset_add_bulk" class="form-control">
+                        <% _.each(histories, function(history) { %> <!-- history select box -->
+                            <option value="<%= _.escape(history.get("id")) %>">
+                                <%= _.escape(history.get("name")) %>
+                            </option>
+                        <% }); %>
+                    </select>
+                </div>
+                <div class="library_selected_history_content">
+                </div>
+            </div>`
         );
     },
 
     templateHistoryContents: function() {
         return _.template(
-            [
-                "<p>2.&nbsp;Choose the datasets to import:</p>",
-                "<div>",
-                '<button title="Select all datasets" type="button" class="button primary-button history-import-select-all">',
-                "Select all",
-                "</button>",
-                '<button title="Select all datasets" type="button" class="button primary-button history-import-unselect-all">',
-                "Unselect all",
-                "</button>",
-                "</div>",
-                "<br>",
-                "<ul>",
-                "<% _.each(history_contents, function(history_item) { %>",
-                '<% if (history_item.get("deleted") != true ) { %>',
-                '<% var item_name = history_item.get("name") %>',
-                '<% if (history_item.get("type") === "collection") { %>',
-                '<% var collection_type = history_item.get("collection_type") %>',
-                '<% if (collection_type === "list") { %>',
-                '<li data-id="<%= _.escape(history_item.get("id")) %>" data-name="<%= _.escape(history_item.get("type")) %>">',
-                "<label>",
-                '<label title="<%= _.escape(item_name) %>">',
-                '<input style="margin: 0;" type="checkbox"> <%= _.escape(history_item.get("hid")) %>: ',
-                '<%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %> (Dataset Collection)',
-                "</label>",
-                "</li>",
-                "<% } else { %>",
-                '<li><input style="margin: 0;" type="checkbox" onclick="return false;" disabled="disabled">',
-                '<span title="You can convert this collection into a collection of type list using the Collection Tools">',
-                '<%= _.escape(history_item.get("hid")) %>: ',
-                '<%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %> (Dataset Collection of type <%= _.escape(collection_type) %> not supported.)',
-                "</span>",
-                "</li>",
-                "<% } %>",
-                '<% } else if (history_item.get("visible") === true && history_item.get("state") === "ok") { %>',
-                '<li data-id="<%= _.escape(history_item.get("id")) %>" data-name="<%= _.escape(history_item.get("type")) %>">',
-                '<label title="<%= _.escape(item_name) %>">',
-                '<input style="margin: 0;" type="checkbox"> <%= _.escape(history_item.get("hid")) %>: ',
-                '<%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %>',
-                "</label>",
-                "</li>",
-                "<% } %>",
-                "<% } %>",
-                "<% }); %>",
-                "</ul>"
-            ].join("")
+            `<div class="form-group">
+                <label>2. Choose the datasets to import:</label>
+                <div class="library_style_container" style="width: 100%;" id="dataset_list">
+                    <table class="grid table table-hover table-sm">
+                        <thead>
+                            <tr>
+                                <th style="width: 30px;" class="mid" title="Check to select all datasets">
+                                    <input class="history-import-toggle-all" style="margin: 0;" type="checkbox" />
+                                </th>
+                                <th style="width: 30px;"></th>
+                                <th>Name</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            <% _.each(history_contents, function(history_item) { %>
+                                <% if (history_item.get("deleted") != true ) { %>
+                                    <% var item_name = history_item.get("name") %>
+                                    <% if (history_item.get("type") === "collection") { %>
+                                        <% var collection_type = history_item.get("collection_type") %>
+                                        <% if (collection_type === "list") { %>
+                                            <tr class="dataset_row" data-id="<%= _.escape(history_item.get("id")) %>"
+                                                data-name="<%= _.escape(history_item.get("type")) %>">
+                                                <td><input style="margin: 0;" type="checkbox"></td>
+                                                <td><%= _.escape(history_item.get("hid")) %></td>
+                                                <td>
+                                                    <%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %>
+                                                    (Dataset Collection)
+                                                </td>
+                                            </tr>
+                                        <% } else { %>
+                                            <tr class="dataset_row" title="You can convert this collection into a collection of type list using the Collection Tools">
+                                                <td><input style="margin: 0;" type="checkbox" onclick="return false;" disabled="disabled" /></td>
+                                                <td><%= _.escape(history_item.get("hid")) %></td>
+                                                <td>
+                                                    <%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %>
+                                                    (Dataset Collection of type <%= _.escape(collection_type) %> not supported.)
+                                                </td>
+                                            </tr>
+                                        <% } %>
+                                    <% } else if (history_item.get("visible") === true && history_item.get("state") === "ok") { %>
+                                        <tr class="dataset_row" data-id="<%= _.escape(history_item.get("id")) %>"
+                                            data-name="<%= _.escape(history_item.get("type")) %>">
+                                            <td><input style="margin: 0;" type="checkbox"></td>
+                                            <td><%= _.escape(history_item.get("hid")) %></td>
+                                            <td>
+                                                <%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %>
+                                            </td>
+                                        </tr>
+                                    <% } %>
+                                <% } %>
+                            <% }); %>
+                        </tbody>
+                    </table>
+                </div>
+            </div>`
         );
     },
 
     templatePaginator: function() {
         return _.template(
-            [
-                '<ul class="pagination mr-1">',
-                "<% if ( ( show_page - 1 ) > 0 ) { %>",
-                "<% if ( ( show_page - 1 ) > page_count ) { %>", // we are on higher page than total page count
-                '<li class="page-item"><a class="page-link" href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>',
-                '<li class="page-item disabled"><a class="page-link" href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',
-                "<% } else { %>",
-                '<li class="page-item"><a class="page-link" href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>',
-                '<li class="page-item"><a class="page-link" href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>',
-                "<% } %>",
-                "<% } else { %>", // we are on the first page
-                '<li class="page-item disabled"><a class="page-link" href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>',
-                '<li class="page-item disabled"><a class="page-link" href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',
-                "<% } %>",
-                '<li class="page-item active">',
-                '<a class="page-link" href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>',
-                "</li>",
-                "<% if ( ( show_page ) < page_count ) { %>",
-                '<li class="page-item"><a class="page-link" href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>',
-                '<li class="page-item"><a class="page-link" href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',
-                "<% } else { %>",
-                '<li class="page-item disabled"><a class="page-link" href="#folders/<%= id %>/page/<% print( show_page  ) %>"><% print( show_page + 1 ) %></a></li>',
-                '<li class="page-item disabled"><a class="page-link" href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',
-                "<% } %>",
-                "</ul>",
-                '<span class="mr-1">',
-                ' <%- items_shown %> items shown <a href="" data-toggle="tooltip" data-placement="top" title="currently <%- folder_page_size %> per page" class="page-size-prompt">(change)</a>',
-                "</span>",
-                '<span class="mr-1">',
-                " <%- total_items_count %> total",
-                "</span>"
-            ].join("")
+            `
+                <% if ( ( show_page - 1 ) > 0 ) { %>
+                    <% if ( ( show_page - 1 ) > page_count ) { %> <!-- we are on higher page than total page count -->
+                        <li class="page-item">
+                            <a class="page-link" href="#folders/<%= id %>/page/1">
+                                <span class="fa fa-angle-double-left"></span>
+                            </a>
+                        </li>
+                        <li class="page-item disabled">
+                            <a class="page-link" href="#folders/<%= id %>/page/<% print( show_page ) %>">
+                                <% print( show_page - 1 ) %>
+                            </a>
+                        </li>
+                    <% } else { %>
+                        <li class="page-item">
+                            <a class="page-link" href="#folders/<%= id %>/page/1">
+                                <span class="fa fa-angle-double-left"></span>
+                            </a>
+                        </li>
+                        <li class="page-item">
+                            <a class="page-link" href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>">
+                                <% print( show_page - 1 ) %>
+                            </a>
+                        </li>
+                    <% } %>
+                <% } else { %> <!-- we are on the first page -->
+                    <li class="page-item disabled">
+                        <a class="page-link" href="#folders/<%= id %>/page/1">
+                            <span class="fa fa-angle-double-left"></span>
+                        </a>
+                    </li>
+                    <li class="page-item disabled">
+                        <a class="page-link" href="#folders/<%= id %>/page/<% print( show_page ) %>">
+                            <% print( show_page - 1 ) %>
+                        </a>
+                    </li>
+                <% } %>
+                <li class="page-item active">
+                    <a class="page-link" href="#folders/<%= id %>/page/<% print( show_page ) %>">
+                        <% print( show_page ) %>
+                    </a>
+                </li>
+                <% if ( ( show_page ) < page_count ) { %>
+                    <li class="page-item">
+                        <a class="page-link" href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>">
+                            <% print( show_page + 1 ) %>
+                        </a>
+                    </li>
+                    <li class="page-item">
+                        <a class="page-link" href="#folders/<%= id %>/page/<% print( page_count ) %>">
+                            <span class="fa fa-angle-double-right"></span>
+                        </a>
+                    </li>
+                <% } else { %>
+                    <li class="page-item disabled">
+                        <a class="page-link" href="#folders/<%= id %>/page/<% print( show_page  ) %>">
+                            <% print( show_page + 1 ) %>
+                        </a>
+                    </li>
+                    <li class="page-item disabled">
+                        <a class="page-link" href="#folders/<%= id %>/page/<% print( page_count ) %>">
+                            <span class="fa fa-angle-double-right"></span>
+                        </a>
+                    </li>
+                <% } %>
+            `
         );
     },
 
+    templatePaginatorText: function() {
+        return _.template(`per page,
+            <%- total_items_count %> total`);
+    },
+
     templateCollectionSelectModal: function() {
         return _.template(
-            [
-                "<div>",
-                // elements selection
-                '<div class="library-modal-item">',
-                "<h4>Which datasets?</h4>",
-                '<form class="form-inline">',
-                '<label class="radio-inline">',
-                '<input type="radio" name="radio_elements" id="selection_radio" value="selection" <% if (!selected_datasets) { %> disabled <% } else { %> checked <% } %> > current selection',
-                "<% if (selected_datasets) { %>",
-                " (<%- selected_datasets %>)",
-                "<% } %>",
-                "</label>",
-                '<label class="radio-inline">',
-                '<input type="radio" name="radio_elements" id="folder_radio" value="folder" <% if (!selected_datasets) { %> checked <% } %> > all datasets in current folder',
-                "</label>",
-                "</form>",
-                "</div>",
-                // type selection
-                '<div class="library-modal-item">',
-                "<h4>Collection type</h4>",
-                '<span class="library-collection-type-select"/>',
-                "<h5>Which type to choose?</h5>",
-                "<ul>",
-                "<li>",
-                "List: Generic collection which groups any number of datasets into a set; similar to file system folder.",
-                "</li>",
-                "<li>",
-                "Paired: Simple collection containing exactly two sequence datasets; one reverse and the other forward.",
-                "</li>",
-                "<li>",
-                "List of Pairs: Advanced collection containing any number of Pairs; imagine as Pair-type collections inside of a List-type collection.",
-                "</li>",
-                "<li>",
-                "From Rules: Use Galaxy's rule builder to describe collections. This is more of an advanced feature that allows building any number of collections or any type.",
-                "</li>",
-                "</ul>",
-                "</div>",
-                // history selection/creation
-                '<div class="library-modal-item">',
-                "<h4>Select history</h4>",
-                '<span class="library-collection-history-select"/>',
-                " or create new: ",
-                '<input type="text" name="history_name" value="" placeholder="name of the new history" />',
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div> <!-- elements selection -->
+                <div class="library-modal-item">
+                    <h4>Which datasets?</h4>
+                    <form class="form-inline">
+                        <div class="form-check form-check-inline">
+                            <input class="form-check-input" type="radio" name="radio_elements" id="selection_radio" value="selection"
+                                <% if (!selected_datasets) { %> disabled <% } else { %> checked <% } %> />
+                            <label class="form-check-label" for="selection_radio">
+                                current selection
+                                <% if (selected_datasets) { %>
+                                    (<%- selected_datasets %>)
+                                <% } %>
+                            </label>
+                        </div>
+                        <div class="form-check form-check-inline">
+                            <input class="form-check-input" type="radio" name="radio_elements" id="folder_radio" value="folder" <% if (!selected_datasets) { %> checked <% } %> >
+                            <label class="form-check-label" for="folder_radio">all datasets in current folder</label>
+                        </div>
+                    </form>
+                </div>
+                <!-- type selection -->
+                <div class="library-modal-item">
+                    <h4>Collection type</h4>
+                    <div class="form-group">
+                        <select id="library-collection-type-select" name="library-collection-type-select" class="form-control">
+                            <option value="list">List</option>
+                            <option value="paired">Paired</option>
+                            <option value="list:paired">List of Pairs</option>
+                            <option value="rules">From Rules</option>
+                        </select>
+                    </div>
+                    <h5>Which type to choose?</h5>
+                    <dl class="row">
+                        <dt class="col-sm-3">List</dt>
+                        <dd class="col-sm-9">Generic collection which groups any number of datasets into a set; similar to file system folder.</dd>
+
+                        <dt class="col-sm-3">Paired</dt>
+                        <dd class="col-sm-9">Simple collection containing exactly two sequence datasets; one reverse and the other forward.</dd>
+
+                        <dt class="col-sm-3">List of Pairs</dt>
+                        <dd class="col-sm-9">Advanced collection containing any number of Pairs; imagine as Pair-type collections inside of a List-type collection.</dd>
+
+                        <dt class="col-sm-3">From Rules</dt>
+                        <dd class="col-sm-9">Use Galaxy's rule builder to describe collections. This is more of an advanced feature that allows building any number of collections or any type.</dd>
+                    </dl>
+                </div>
+                <!-- history selection/creation -->
+                <div class="library-modal-item">
+                    <h4>Select history</h4>
+                    <div class="form-group">
+                        <select id="library-collection-history-select" name="library-collection-history-select" class="form-control">
+                            <% _.each(histories, function(history) { %> <!-- history select box -->
+                                <option value="<%= _.escape(history.get("id")) %>">
+                                    <%= _.escape(history.get("name")) %>
+                                </option>
+                            <% }); %>
+                        </select>
+                        <label>or create new:</label>
+                        <input class="form-control" type="text" name="history_name" value="" placeholder="name of the new history" />
+                    </div>
+                </div>
+            </div>`
         );
     }
 });
diff --git a/client/galaxy/scripts/mvc/library/library-library-view.js b/client/galaxy/scripts/mvc/library/library-library-view.js
index f86aff62a0b..af02f41dc1a 100644
--- a/client/galaxy/scripts/mvc/library/library-library-view.js
+++ b/client/galaxy/scripts/mvc/library/library-library-view.js
@@ -38,7 +38,7 @@ var LibraryView = Backbone.View.extend({
                 }
             },
             error: function(model, response) {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 if (typeof response.responseJSON !== "undefined") {
                     Toast.error(`${response.responseJSON.err_msg} Click this to go back.`, "", {
                         onclick: function() {
@@ -68,7 +68,7 @@ var LibraryView = Backbone.View.extend({
             }
         }
         var is_admin = false;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (Galaxy.user) {
             is_admin = Galaxy.user.isAdmin();
         }
@@ -245,55 +245,58 @@ var LibraryView = Backbone.View.extend({
 
     templateLibraryPermissions: function() {
         return _.template(
-            [
-                '<div class="library_style_container">',
-                "<div>",
-                '<a href="#">',
-                '<button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-secondary primary-button" type="button">',
-                '<span class="fa fa-list"/>',
-                "&nbsp;Libraries",
-                "</button>",
-                "</a>",
-                "</div>",
-                "<h1>",
-                'Library: <%= _.escape(library.get("name")) %>',
-                "</h1>",
-                '<div class="alert alert-warning">',
-                "<% if (is_admin) { %>",
-                "You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.",
-                "<% } else { %>",
-                "You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.",
-                "<% }%>",
-                "</div>",
-                '<div class="dataset_table">',
-                "<h2>Library permissions</h2>",
-                "<h4>Roles that can access the library</h4>",
-                '<div id="access_perm" class="access_perm roles-selection"/>',
-                '<div class="alert alert-info roles-selection">',
-                "User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.",
-                "</div>",
-                "<h4>Roles that can manage permissions on this library</h4>",
-                '<div id="manage_perm" class="manage_perm roles-selection"/>',
-                '<div class="alert alert-info roles-selection">',
-                "User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).",
-                "</div>",
-                "<h4>Roles that can add items to this library</h4>",
-                '<div id="add_perm" class="add_perm roles-selection"/>',
-                '<div class="alert alert-info roles-selection">',
-                "User with <strong>any</strong> of these roles can add items to this library (folders and datasets).",
-                "</div>",
-                "<h4>Roles that can modify this library</h4>",
-                '<div id="modify_perm" class="modify_perm roles-selection"/>',
-                '<div class="alert alert-info roles-selection">',
-                "User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).",
-                "</div>",
-                '<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-secondary toolbtn_save_permissions primary-button" type="button">',
-                '<span class="fa fa-floppy-o"/>',
-                "&nbsp;Save",
-                "</button>",
-                "</div>",
-                "</div>"
-            ].join("")
+            `<div class="library_style_container">
+                <div>
+                    <a href="#">
+                        <button data-toggle="tooltip" data-placement="top"
+                            title="Go back to the list of Libraries" class="btn btn-secondary primary-button" type="button">
+                            <span class="fa fa-list"></span>&nbsp;Libraries
+                        </button>
+                    </a>
+                </div>
+                <h1>
+                    Library: <%= _.escape(library.get("name")) %>
+                </h1>
+                <div class="alert alert-warning">
+                    <% if (is_admin) { %>
+                        You are logged in as an <strong>administrator</strong> therefore you can manage any library
+                        on this Galaxy instance. Please make sure you understand the consequences.
+                    <% } else { %>
+                        You can assign any number of roles to any of the following permission types.
+                        However please read carefully the implications of such actions.
+                    <% }%>
+                </div>
+                <div class="dataset_table">
+                    <h2>Library permissions</h2>
+                    <h4>Roles that can access the library</h4>
+                    <div id="access_perm" class="access_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can access this library.
+                        If there are no access roles set on the library it is considered <strong>unrestricted</strong>.
+                    </div>
+                    <h4>Roles that can manage permissions on this library</h4>
+                    <div id="manage_perm" class="manage_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can manage permissions on this library
+                        (includes giving access).
+                    </div>
+                    <h4>Roles that can add items to this library</h4>
+                    <div id="add_perm" class="add_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can add items to this library (folders and datasets).
+                    </div>
+                    <h4>Roles that can modify this library</h4>
+                    <div id="modify_perm" class="modify_perm roles-selection"></div>
+                    <div class="alert alert-info roles-selection">
+                        User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).
+                    </div>
+                    <button data-toggle="tooltip" data-placement="top"
+                        title="Save modifications made on this page"
+                        class="btn btn-secondary toolbtn_save_permissions primary-button" type="button">
+                        <span class="fa fa-floppy-o"></span>&nbsp;Save
+                    </button>
+                </div>
+            </div>`
         );
     }
 });
diff --git a/client/galaxy/scripts/mvc/library/library-librarylist-view.js b/client/galaxy/scripts/mvc/library/library-librarylist-view.js
index 7e36cf370b1..52d43570a95 100644
--- a/client/galaxy/scripts/mvc/library/library-librarylist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-librarylist-view.js
@@ -51,7 +51,7 @@ var LibraryListView = Backbone.View.extend({
      * or render an empty list in case no data is given.
      */
     render: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         this.setElement("#libraries_element");
         var template = this.templateLibraryList();
@@ -182,7 +182,7 @@ var LibraryListView = Backbone.View.extend({
      * @return {[type]} [description]
      */
     sort_clicked: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (Galaxy.libraries.preferences.get("sort_order") === "asc") {
             Galaxy.libraries.preferences.set({ sort_order: "desc" });
         } else {
@@ -196,7 +196,7 @@ var LibraryListView = Backbone.View.extend({
      * Currently supports only sorting by name.
      */
     sortLibraries: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (Galaxy.libraries.preferences.get("sort_by") === "name") {
             if (Galaxy.libraries.preferences.get("sort_order") === "asc") {
                 this.collection.sortLibraries("name", "asc");
@@ -224,45 +224,140 @@ var LibraryListView = Backbone.View.extend({
         }
     },
 
+    /**
+     * Create the new library inline
+     */
+    createLibraryInline: function() {
+        if (this.$el.find("tr.new-row").length) {
+            this.$el.find("tr.new-row textarea")[0].focus();
+        } else {
+            const template = this.templateNewRow();
+            this.$el
+                .find("#library_list_body")
+                .closest("table")
+                .show();
+            this.$el.find("#library_list_body").prepend(template);
+
+            this.$el.find("tr.new-row textarea")[0].focus();
+
+            this.$el.find("tr.new-row .save_library_btn").click(() => {
+                this.createNewLibrary(
+                    this.$el.find("tr.new-row textarea")[0].value,
+                    this.$el.find("tr.new-row textarea")[1].value,
+                    this.$el.find("tr.new-row textarea")[2].value
+                );
+            });
+
+            this.$el.find("tr.new-row .cancel_library_btn").click(() => {
+                this.$el.find("tr.new-row").remove();
+            });
+        }
+    },
+
+    /**
+     * Create the new library using the API asynchronously.
+     */
+    createNewLibrary: function(name, description, synopsis) {
+        const Galaxy = getGalaxyInstance();
+        const libraryDetails = {
+            name,
+            description,
+            synopsis
+        };
+        if (libraryDetails.name !== "") {
+            var library = new mod_library_model.Library();
+            library.save(libraryDetails, {
+                success: library => {
+                    Galaxy.libraries.libraryListView.collection.add(library);
+                    this.$el.find("tr.new-row").remove();
+                    Galaxy.libraries.libraryListView.render();
+
+                    $(`tr[data-id="${library.attributes.id}"`)
+                        .addClass("table-success")
+                        .on("mouseover click", function() {
+                            $(this).removeClass("table-success");
+                        });
+
+                    Toast.success("Library created.");
+                },
+                error: (model, response) => {
+                    if (typeof response.responseJSON !== "undefined") {
+                        Toast.error(response.responseJSON.err_msg);
+                    } else {
+                        Toast.error("An error occurred.");
+                    }
+                }
+            });
+        } else {
+            Toast.error("Library's name is missing.");
+        }
+        return false;
+    },
+
     // MMMMMMMMMMMMMMMMMM
     // === TEMPLATES ====
     // MMMMMMMMMMMMMMMMMM
 
+    templateNewRow: function() {
+        return _.template(
+            `<tr class="new-row">
+                    <td>
+                        <textarea name="input_library_name" rows="4" class="form-control input_library_name" placeholder="name" ></textarea>
+                    </td>
+                    <td>
+                        <textarea rows="4" class="form-control input_library_description" placeholder="description"></textarea>
+                    </td>
+                    <td>
+                        <textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis"></textarea>
+                    </td>
+                    <td class="right-center">
+                        <button data-toggle="tooltip" data-placement="left" title="Save changes"
+                            class="btn btn-secondary btn-sm save_library_btn" type="button">
+                            <span class="fa fa-floppy-o"></span> Save
+                        </button>
+                        <button data-toggle="tooltip" data-placement="left" title="Discard changes"
+                            class="btn btn-secondary btn-sm cancel_library_btn" type="button">
+                            <span class="fa fa-times"></span> Cancel
+                        </button>
+                    </td>     
+            </tr>`
+        );
+    },
+
     templateLibraryList: function() {
         return _.template(
-            [
-                '<div class="library_container table-responsive">',
-                "<% if(length === 0) { %>",
-                "<% if(search_term.length > 0) { %>",
-                "<div>",
-                "There are no libraries matching your search. Try different keyword.",
-                "</div>",
-                "<% } else{ %>",
-                "<div>",
-                "There are no libraries visible to you here. If you expected some to show up please consult the",
-                ' <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>.',
-                "</div>",
-                "<% }%>",
-                "<% } else{ %>",
-                '<table class="grid table table-sm">',
-                "<thead>",
-                '<th style="width:30%;">',
-                '<a class="sort-libraries-link" title="Click to reverse order" href="#">',
-                "name",
-                "</a>",
-                '<span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"/>',
-                "</th>",
-                '<th style="width:22%;">description</th>',
-                '<th style="width:22%;">synopsis</th> ',
-                '<th style="width:26%;"></th>',
-                "</thead>",
-                '<tbody id="library_list_body">',
-                // library item views will attach here
-                "</tbody>",
-                "</table>",
-                "<% }%>",
-                "</div>"
-            ].join("")
+            `<div class="library_container table-responsive">
+                <table class="grid table table-sm"
+                    <% if(length === 0) { %> style="display:none;" <% }%> >
+                    <thead>
+                        <th style="width:30%;">
+                            <a class="sort-libraries-link" title="Click to reverse order" href="#">
+                                Name
+                            </a>
+                            <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span>
+                        </th>
+                        <th style="width:22%;">Description</th>
+                        <th style="width:22%;">Synopsis</th> 
+                        <th style="width:26%;"></th>
+                    </thead>
+                    <tbody id="library_list_body">
+                    <!-- library item views will attach here -->
+                   </tbody>
+                </table>
+                    
+                <% if(length === 0) { %>
+                    <% if(search_term.length > 0) { %>
+                        <div>
+                            There are no libraries matching your search. Try different keyword.
+                        </div>
+                    <% } else{ %>
+                        <div>
+                            There are no libraries visible to you here. If you expected some to show up please consult the
+                            <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>.
+                        </div>
+                    <% }%>
+                <% }%>
+            </div>`
         );
     }
 });
diff --git a/client/galaxy/scripts/mvc/library/library-libraryrow-view.js b/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
index 15315685052..d7e7482f4d2 100644
--- a/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
+++ b/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
@@ -32,7 +32,7 @@ var LibraryRowView = Backbone.View.extend({
 
     render: function(library) {
         if (typeof library === "undefined") {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
             console.log(library);
         }
@@ -122,7 +122,7 @@ var LibraryRowView = Backbone.View.extend({
     },
 
     save_library_modification: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
         var is_changed = false;
 
@@ -174,7 +174,7 @@ var LibraryRowView = Backbone.View.extend({
     },
 
     delete_library: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
         var row_view = this;
         // mark the library deleted
@@ -204,7 +204,7 @@ var LibraryRowView = Backbone.View.extend({
     },
 
     undelete_library: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
         var row_view = this;
 
@@ -232,52 +232,96 @@ var LibraryRowView = Backbone.View.extend({
 
     templateRow: function() {
         return _.template(
-            [
-                '<tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">',
-                "<% if(!edit_mode) { %>",
-                '<% if(library.get("deleted")) { %>',
-                '<td style="color:grey;"><%- library.get("name") %></td>',
-                "<% } else { %>",
-                '<td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>',
-                "<% } %>",
-                '<% if(library.get("description")) { %>',
-                '<% if( (library.get("description")).length> 80 ) { %>',
-                '<td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>',
-                "<% } else { %>",
-                '<td><%= _.escape(library.get("description"))%></td>',
-                "<% } %>",
-                "<% } else { %>",
-                "<td></td>",
-                "<% } %>",
-                '<% if(library.get("synopsis")) { %>',
-                '<% if( (library.get("synopsis")).length> 120 ) { %>',
-                '<td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>',
-                "<% } else { %>",
-                '<td><%= _.escape(library.get("synopsis"))%></td>',
-                "<% } %>",
-                "<% } else { %>",
-                "<td></td>",
-                "<% } %>",
-                "<% } else if(edit_mode){ %>",
-                '<td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>',
-                '<td><textarea rows="4" class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>',
-                '<td><textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>',
-                "<% } %>",
-                '<td class="right-center">',
-                '<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>',
-                '<span data-toggle="tooltip" data-placement="left" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg"> </span>',
-                "<% }%>",
-                '<button data-toggle="tooltip" data-placement="left" title="Modify \'<%- library.get("name") %>\'" class="btn btn-sm edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span> Edit</button>',
-                '<a data-toggle="tooltip" data-placement="left" title="Permissions of \'<%- library.get("name") %>\'" href="#library/<%- library.get("id") %>/permissions"><button class="btn btn-sm permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span> Manage</button></a>',
-                '<button data-toggle="tooltip" data-placement="left" title="Save changes" class="btn btn-sm save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"></span> Save</button>',
-                '<button data-toggle="tooltip" data-placement="left" title="Discard changes" class="btn btn-sm cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"></span> Cancel</button>',
-                '<button data-toggle="tooltip" data-placement="left" title="Delete \'<%- library.get("name") %>\'" class="btn btn-sm delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"></span> Delete</button>',
-                // For deleted libraries
-                '<span data-toggle="tooltip" data-placement="left" title="Marked deleted" style="color:grey; <% if(button_config.undelete_library_btn === false) { print("display:none;") } %>" class="fa fa-ban fa-lg"></span>',
-                '<button data-toggle="tooltip" data-placement="left" title="Undelete \'<%- library.get("name") %>\' " class="btn btn-sm undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"></span> Undelete</button>',
-                "</td>",
-                "</tr>"
-            ].join("")
+            `<tr class="<% if(library.get("deleted") === true) { print("active") } %>"
+                style="display:none;" data-id="<%- library.get("id") %>">
+                <% if(!edit_mode) { %>
+                    <% if(library.get("deleted")) { %>
+                        <td style="color:grey;"><%- library.get("name") %></td>
+                    <% } else { %>
+                        <td>
+                            <a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a>
+                        </td>
+                    <% } %>
+                    <% if(library.get("description")) { %>
+                        <% if( (library.get("description")).length> 80 ) { %>
+                            <td data-toggle="tooltip" data-placement="bottom"
+                                title="<%= _.escape(library.get("description")) %>">
+                                <%= _.escape(library.get("description")).substring(0, 80) + "..." %>
+                            </td>
+                        <% } else { %>
+                            <td><%= _.escape(library.get("description"))%></td>
+                        <% } %>
+                    <% } else { %>
+                        <td></td>
+                    <% } %>
+                    <% if(library.get("synopsis")) { %>
+                        <% if( (library.get("synopsis")).length> 120 ) { %>
+                            <td data-toggle="tooltip" data-placement="bottom"
+                                title="<%= _.escape(library.get("synopsis")) %>">
+                                <%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %>
+                            </td>
+                        <% } else { %>
+                            <td><%= _.escape(library.get("synopsis"))%></td>
+                        <% } %>
+                    <% } else { %>
+                        <td></td>
+                    <% } %>
+                <% } else if(edit_mode){ %>
+                    <td>
+                        <textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea>
+                    </td>
+                    <td>
+                        <textarea rows="4" class="form-control input_library_description" placeholder="description"><%- library.get("description") %></textarea>
+                    </td>
+                    <td>
+                        <textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis"><%- library.get("synopsis") %></textarea>
+                    </td>
+                <% } %>
+                <td class="right-center">
+                    <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>
+                        <span data-toggle="tooltip" data-placement="left" title="Unrestricted library"
+                            class="fa fa-globe fa-lg"></span>
+                    <% }%>
+                    <button data-toggle="tooltip" data-placement="left" title="Modify '<%- library.get("name") %>'"
+                        class="btn btn-secondary btn-sm edit_library_btn" type="button"
+                        style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>">
+                        <span class="fa fa-pencil"></span> Edit
+                    </button>
+                    <a data-toggle="tooltip" data-placement="left"
+                        title="Permissions of '<%- library.get("name") %>'"
+                        href="#library/<%- library.get("id") %>/permissions">
+                        <button class="btn btn-secondary btn-sm permission_library_btn" type="button"
+                            style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>">
+                            <span class="fa fa-group"></span> Manage
+                        </button>
+                    </a>
+                    <button data-toggle="tooltip" data-placement="left" title="Save changes"
+                        class="btn btn-secondary btn-sm save_library_btn" type="button"
+                        style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>">
+                        <span class="fa fa-floppy-o"></span> Save
+                    </button>
+                    <button data-toggle="tooltip" data-placement="left" title="Discard changes"
+                        class="btn btn-secondary btn-sm cancel_library_btn" type="button"
+                        style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>">
+                        <span class="fa fa-times"></span> Cancel
+                    </button>
+                    <button data-toggle="tooltip" data-placement="left" title="Delete '<%- library.get("name") %>'"
+                        class="btn btn-secondary btn-sm delete_library_btn" type="button"
+                        style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>">
+                        <span class="fa fa-trash-o"></span> Delete
+                    </button>
+                    <!-- For deleted libraries -->
+                    <span data-toggle="tooltip" data-placement="left" title="Marked deleted"
+                        style="color:grey; <% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"
+                        class="fa fa-ban fa-lg">
+                    </span>
+                    <button data-toggle="tooltip" data-placement="left" title="Undelete '<%- library.get("name") %>' "
+                        class="btn btn-secondary btn-sm undelete_library_btn" type="button"
+                        style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>">
+                        <span class="fa fa-unlock"></span> Undelete
+                    </button>
+                </td>
+            </tr>`
         );
     }
 });
diff --git a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
index 543f52e3254..92141dbd3e7 100644
--- a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
@@ -1,9 +1,6 @@
 import _ from "underscore";
 import $ from "jquery";
 import Backbone from "backbone";
-import _l from "utils/localization";
-import { Toast } from "ui/toast";
-import mod_library_model from "mvc/library/library-model";
 import { getGalaxyInstance } from "app";
 
 /**
@@ -18,10 +15,11 @@ var LibraryToolbarView = Backbone.View.extend({
     },
 
     events: {
-        "click #create_new_library_btn": "createLibraryFromModal",
+        "click #create_new_library_btn": "createLibraryInline",
         "click #include_deleted_chk": "includeDeletedChecked",
         "click #exclude_restricted_chk": "excludeRestrictedChecked",
-        "click .page_size_prompt": "showPageSizePrompt",
+        "keydown .page_size": "changePageSize",
+        "blur .page_size": "changePageSize",
         "keyup .library-search-input": "searchLibraries"
     },
 
@@ -31,7 +29,7 @@ var LibraryToolbarView = Backbone.View.extend({
     },
 
     render: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var toolbar_template = this.templateToolBar();
         var is_admin = false;
         var is_anonym = true;
@@ -39,7 +37,13 @@ var LibraryToolbarView = Backbone.View.extend({
             is_admin = Galaxy.user.isAdmin();
             is_anonym = Galaxy.user.isAnonymous();
         }
-        this.$el.html(toolbar_template({ admin_user: is_admin, anon_user: is_anonym }));
+        this.$el.html(
+            toolbar_template({
+                admin_user: is_admin,
+                anon_user: is_anonym,
+                library_page_size: Galaxy.libraries.preferences.get("library_page_size")
+            })
+        );
         if (is_admin) {
             this.$el.find("#include_deleted_chk")[0].checked = Galaxy.libraries.preferences.get("with_deleted");
             this.$el.find("#exclude_restricted_chk")[0].checked = Galaxy.libraries.preferences.get(
@@ -52,10 +56,11 @@ var LibraryToolbarView = Backbone.View.extend({
      * Renders the element that shows pages into its div within the toolbar.
      */
     renderPaginator: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.options = _.extend(this.options, options);
         var paginator_template = this.templatePaginator();
-        this.$el.find(".library-paginator").html(
+        var paginator_text_template = this.templatePaginatorText();
+        this.$el.find(".library-paginator > .paginator").html(
             paginator_template({
                 show_page: parseInt(this.options.show_page),
                 page_count: parseInt(this.options.page_count),
@@ -64,114 +69,44 @@ var LibraryToolbarView = Backbone.View.extend({
                 library_page_size: Galaxy.libraries.preferences.get("library_page_size")
             })
         );
+        this.$el.find(".library-paginator > .paginator-text").html(
+            paginator_text_template({
+                show_page: parseInt(this.options.show_page),
+                page_count: parseInt(this.options.page_count),
+                total_libraries_count: this.options.total_libraries_count,
+                libraries_shown: this.options.libraries_shown,
+                library_page_size: Galaxy.libraries.preferences.get("library_page_size")
+            })
+        );
     },
 
     /**
-     * User clicked on 'New library' button. Show modal to
-     * satisfy the wish.
+     * Crreate the new library inline
      */
-    createLibraryFromModal: function(event) {
-        event.preventDefault();
-        event.stopPropagation();
-        let Galaxy = getGalaxyInstance();
-        var self = this;
-        this.modal = Galaxy.modal;
-        this.modal.show({
-            closing_events: true,
-            title: _l("Create New Library"),
-            body: this.templateNewLibraryInModal(),
-            buttons: {
-                Create: function() {
-                    self.createNewLibrary();
-                },
-                Close: function() {
-                    self.modal.hide();
-                }
-            }
-        });
+    createLibraryInline: function() {
+        const Galaxy = getGalaxyInstance();
+        Galaxy.libraries.libraryListView.createLibraryInline();
     },
 
     /**
-     * Create the new library using the API asynchronously.
+     * Change the number of libs shown on page.
      */
-    createNewLibrary: function() {
-        let Galaxy = getGalaxyInstance();
-        var libraryDetails = this.serializeNewLibrary();
-        if (this.validateNewLibrary(libraryDetails)) {
-            var library = new mod_library_model.Library();
-            var self = this;
-            library.save(libraryDetails, {
-                success: function(library) {
-                    Galaxy.libraries.libraryListView.collection.add(library);
-                    self.modal.hide();
-                    self.clearLibraryModal();
-                    Galaxy.libraries.libraryListView.render();
-                    Toast.success("Library created.");
-                },
-                error: function(model, response) {
-                    if (typeof response.responseJSON !== "undefined") {
-                        Toast.error(response.responseJSON.err_msg);
-                    } else {
-                        Toast.error("An error occurred.");
-                    }
-                }
-            });
-        } else {
-            Toast.error("Library's name is missing.");
-        }
-        return false;
-    },
-
-    /**
-     * Show user the propmpt to change the number of libs shown on page.
-     */
-    showPageSizePrompt: function(e) {
-        e.preventDefault();
-        let Galaxy = getGalaxyInstance();
-        var library_page_size = prompt(
-            "How many libraries per page do you want to see?",
-            Galaxy.libraries.preferences.get("library_page_size")
-        );
-        if (library_page_size != null && library_page_size == parseInt(library_page_size)) {
+    changePageSize: function(e) {
+        if (e.type === "focusout" || (e.type === "keydown" && e.keyCode === 13)) {
+            e.preventDefault();
+            const Galaxy = getGalaxyInstance();
             Galaxy.libraries.preferences.set({
-                library_page_size: parseInt(library_page_size)
+                library_page_size: parseInt(e.target.value)
             });
             Galaxy.libraries.libraryListView.render({ show_page: 1 });
         }
     },
 
-    /**
-     * Clear the library modal once it is saved.
-     */
-    clearLibraryModal: function() {
-        $("input[name='Name']").val("");
-        $("input[name='Description']").val("");
-        $("input[name='Synopsis']").val("");
-    },
-
-    /**
-     * Prepare new library variables to be submitted to API.
-     */
-    serializeNewLibrary: function() {
-        return {
-            name: $("input[name='Name']").val(),
-            description: $("input[name='Description']").val(),
-            synopsis: $("input[name='Synopsis']").val()
-        };
-    },
-
-    /**
-     * Check whether entered values are valid.
-     */
-    validateNewLibrary: function(libraryDetails) {
-        return libraryDetails.name !== "";
-    },
-
     /**
      * Include or exclude deleted libraries in the view.
      */
     includeDeletedChecked: function(event) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (event.target.checked) {
             Galaxy.libraries.preferences.set({ with_deleted: true });
             Galaxy.libraries.libraryListView.fetchDeleted();
@@ -185,7 +120,7 @@ var LibraryToolbarView = Backbone.View.extend({
      * Include or exclude restricted libraries in the view.
      */
     excludeRestrictedChecked: function(event) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (event.target.checked) {
             Galaxy.libraries.preferences.set({ without_restricted: true });
         } else {
@@ -199,7 +134,7 @@ var LibraryToolbarView = Backbone.View.extend({
      * to query the collection of libraries.
      */
     searchLibraries: function(event) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var search_term = $(".library-search-input").val();
         this.options.search_term = search_term;
         Galaxy.libraries.libraryListView.searchLibraries(search_term);
@@ -212,17 +147,14 @@ var LibraryToolbarView = Backbone.View.extend({
                     <a class="btn btn-secondary mr-1" data-toggle="tooltip" data-placement="top" title="Go to first page" href="#">
                         <span class="fa fa-home"/>
                     </a>
-                    <a class="library-help-button btn btn-secondary mr-1" data-toggle="tooltip" title="See this screen annotated" href="https://galaxyproject.org/data-libraries/screen/list-of-libraries/" target="_blank">
-                        <span class="fa fa-question"/>
-                    </a>
                     <% if(admin_user === true) { %>
                         <button data-toggle="tooltip" data-placement="top" title="Create new library" id="create_new_library_btn" class="mr-1 btn btn-secondary" type="button">
-                            <span class="fa fa-plus"/>
+                            <span class="fa fa-plus" /> Library
                         </button>
                     <% } %>
-                    <div class="d-flex align-items-center library-paginator mr-1" />
+                    <div class="d-flex align-items-center mr-1" />
                         <form class="form-inline mr-1">
-                            <input type="text" class="form-control library-search-input mr-1" placeholder="Great Library" size="15">
+                            <input type="text" id="library-filter" class="form-control library-search-input mr-1" placeholder="Search" size="15">
                             <% if(admin_user === true) { %>
                                 <div class="form-check mr-1">
                                     <input class="form-check-input" id="include_deleted_chk" type="checkbox"/>
@@ -236,6 +168,12 @@ var LibraryToolbarView = Backbone.View.extend({
                         </form>
                     </div>
                     <div id="libraries_element" />
+
+                    <div class="d-flex justify-content-center align-items-center library-paginator mt-2 mb-2">
+                        <ul class="pagination paginator mr-1" />
+                        <input style="width: initial;" min="0" max="999" class="page_size form-control" type="number" value="<%- library_page_size %>" />
+                        <span class="text-muted ml-1 paginator-text" />
+                    </div>
                 </div>
             </div>`
         );
@@ -243,53 +181,76 @@ var LibraryToolbarView = Backbone.View.extend({
 
     templatePaginator: function() {
         return _.template(
-            [
-                '<ul class="pagination mr-1">',
-                "<% if ( ( show_page - 1 ) > 0 ) { %>",
-                "<% if ( ( show_page - 1 ) > page_count ) { %>", // we are on higher page than total page count
-                '<li class="page-item"><a class="page-link" href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>',
-                '<li class="page-item disabled"><a class="page-link" href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',
-                "<% } else { %>",
-                '<li class="page-item"><a class="page-link" href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>',
-                '<li class="page-item"><a class="page-link" href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>',
-                "<% } %>",
-                "<% } else { %>", // we are on the first page
-                '<li class="page-item disabled"><a class="page-link" href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>',
-                '<li class="page-item disabled"><a class="page-link" href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',
-                "<% } %>",
-                '<li class="page-item active">',
-                '<a class="page-link" href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>',
-                "</li>",
-                "<% if ( ( show_page ) < page_count ) { %>",
-                '<li class="page-item"><a class="page-link" href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>',
-                '<li class="page-item"><a class="page-link" href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',
-                "<% } else { %>",
-                '<li class="page-item disabled"><a class="page-link" href="#page/<% print( show_page  ) %>"><% print( show_page + 1 ) %></a></li>',
-                '<li class="page-item disabled"><a class="page-link" href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',
-                "<% } %>",
-                "</ul>",
-                '<span class="mr-1">',
-                ' <%- libraries_shown %> libraries shown <a href="" data-toggle="tooltip" data-placement="top" title="currently <%- library_page_size %> per page" class="page_size_prompt">(change)</a>',
-                "</span>",
-                '<span class="mr-1">',
-                " <%- total_libraries_count %> total",
-                "</span>"
-            ].join("")
+            `
+                        <% if ( ( show_page - 1 ) > 0 ) { %>
+                            <% if ( ( show_page - 1 ) > page_count ) { %> <!-- we are on higher page than total page count -->
+                               <li class="page-item">
+                                    <a class="page-link" href="#page/1">
+                                        <span class="fa fa-angle-double-left"></span>
+                                    </a>
+                                </li>
+                                <li class="page-item disabled">
+                                    <a class="page-link" href="#page/<% print( show_page ) %>">
+                                        <% print( show_page - 1 ) %>
+                                    </a>
+                                </li>
+                            <% } else { %>
+                                <li class="page-item">
+                                    <a class="page-link" href="#page/1">
+                                        <span class="fa fa-angle-double-left"></span>
+                                    </a>
+                                </li>
+                                <li class="page-item">
+                                    <a class="page-link" href="#page/<% print( show_page - 1 ) %>">
+                                        <% print( show_page - 1 ) %>
+                                    </a>
+                                </li>
+                            <% } %>
+                        <% } else { %> <!-- we are on the first page -->
+                           <li class="page-item disabled">
+                                <a class="page-link" href="#page/1">
+                                    <span class="fa fa-angle-double-left"></span>
+                                </a>
+                            </li>
+                            <li class="page-item disabled">
+                                <a class="page-link" href="#page/<% print( show_page ) %>">
+                                    <% print( show_page - 1 ) %>
+                                </a>
+                            </li>
+                        <% } %>
+                            <li class="page-item active">
+                                <a class="page-link" href="#page/<% print( show_page ) %>">
+                                    <% print( show_page ) %>
+                                </a>
+                            </li>
+                        <% if ( ( show_page ) < page_count ) { %>
+                            <li class="page-item">
+                                <a class="page-link" href="#page/<% print( show_page + 1 ) %>">
+                                    <% print( show_page + 1 ) %>
+                                </a>
+                            </li>
+                            <li class="page-item">
+                                <a class="page-link" href="#page/<% print( page_count ) %>">
+                                    <span class="fa fa-angle-double-right"></span>
+                                </a>
+                            </li>
+                        <% } else { %>
+                            <li class="page-item disabled">
+                                <a class="page-link" href="#page/<% print( show_page  ) %>">
+                                    <% print( show_page + 1 ) %>
+                                </a>
+                            </li>
+                            <li class="page-item disabled">
+                                <a class="page-link" href="#page/<% print( page_count ) %>">
+                                    <span class="fa fa-angle-double-right"></span>
+                                </a>
+                            </li>
+                        <% } %>
+                `
         );
     },
-
-    templateNewLibraryInModal: function() {
-        return _.template(
-            [
-                '<div id="new_library_modal">',
-                "<form>",
-                '<input type="text" name="Name" value="" placeholder="Name" autofocus>',
-                '<input type="text" name="Description" value="" placeholder="Description">',
-                '<input type="text" name="Synopsis" value="" placeholder="Synopsis">',
-                "</form>",
-                "</div>"
-            ].join("")
-        );
+    templatePaginatorText: function() {
+        return _.template(`per page, <%- total_libraries_count %> total`);
     }
 });
 
diff --git a/client/galaxy/scripts/mvc/library/library-model.js b/client/galaxy/scripts/mvc/library/library-model.js
index 6d53faa8a34..b1c91a25e40 100644
--- a/client/galaxy/scripts/mvc/library/library-model.js
+++ b/client/galaxy/scripts/mvc/library/library-model.js
@@ -91,7 +91,7 @@ var FolderContainer = Backbone.Model.extend({
         id: "unknown"
     },
     parse: function(obj) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         // empty the collection
         this.get("folder").reset();
         // response is not a simple array, it contains metadata
diff --git a/client/galaxy/scripts/mvc/list/list-view.js b/client/galaxy/scripts/mvc/list/list-view.js
index 25bb73ed901..69e0debbe9a 100644
--- a/client/galaxy/scripts/mvc/list/list-view.js
+++ b/client/galaxy/scripts/mvc/list/list-view.js
@@ -300,27 +300,22 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
             if (!actions.length) {
                 return $menu.empty();
             }
-
             var $newMenu = $(
-                [
-                    '<div class="list-action-menu btn-group">',
-                    '<button class="list-action-menu-btn btn btn-secondary dropdown-toggle" data-toggle="dropdown">',
-                    _l("For all selected"),
-                    "...",
-                    "</button>",
-                    '<ul class="dropdown-menu float-right" role="menu">',
-                    "</ul>",
-                    "</div>"
-                ].join("")
+                `<div class="list-action-menu btn-group">
+                    <button class="list-action-menu-btn btn btn-secondary dropdown-toggle" data-toggle="dropdown">
+                        ${_l("For all selected")}...
+                    </button>
+                    <div class="dropdown-menu float-right" role="menu"/>
+                </div>`
             );
             var $actions = actions.map(action => {
-                var html = ['<li><a href="javascript:void(0);">', action.html, "</a></li>"].join("");
+                var html = `<a class="dropdown-item" href="javascript:void(0);">${action.html}</a>`;
                 return $(html).click(ev => {
                     ev.preventDefault();
                     return action.func(ev);
                 });
             });
-            $newMenu.find("ul").append($actions);
+            $newMenu.find(".dropdown-menu").append($actions);
             $menu.replaceWith($newMenu);
             return $newMenu;
         },
diff --git a/client/galaxy/scripts/mvc/rules/rule-definitions.js b/client/galaxy/scripts/mvc/rules/rule-definitions.js
index c0cb365f121..e6fc8154036 100644
--- a/client/galaxy/scripts/mvc/rules/rule-definitions.js
+++ b/client/galaxy/scripts/mvc/rules/rule-definitions.js
@@ -18,7 +18,7 @@ const multiColumnsToString = function(targetColumns, colHeaders) {
 
 const removeColumns = function(columns, targetColumns) {
     const newColumns = [];
-    for (let index in columns) {
+    for (const index in columns) {
         if (targetColumns.indexOf(index) === -1) {
             newColumns.push(columns[index]);
         }
@@ -223,7 +223,7 @@ const RULES = {
                 const tags = sources[index]["tags"];
                 tags.sort();
                 let groupTagValue = rule.default_value;
-                for (let index in tags) {
+                for (const index in tags) {
                     const tag = tags[index];
                     if (tag.indexOf(groupTagPrefix) == 0) {
                         groupTagValue = tag.substr(groupTagPrefix.length);
@@ -402,7 +402,7 @@ const RULES = {
             const targets = rule.target_columns;
             function newRow(row) {
                 const newRow = [];
-                for (let index in row) {
+                for (const index in row) {
                     if (targets.indexOf(parseInt(index)) == -1) {
                         newRow.push(row[index]);
                     }
@@ -862,7 +862,7 @@ const colHeadersFor = function(data, columns) {
 };
 
 const applyRules = function(data, sources, columns, rules, headersPerRule = []) {
-    let colHeadersPerRule = Array.from(headersPerRule);
+    const colHeadersPerRule = Array.from(headersPerRule);
     let hasRuleError = false;
     for (var ruleIndex in rules) {
         const ruleHeaders = colHeadersFor(data, columns);
diff --git a/client/galaxy/scripts/mvc/tag.js b/client/galaxy/scripts/mvc/tag.js
index 5b42d64d9b5..eb150542695 100644
--- a/client/galaxy/scripts/mvc/tag.js
+++ b/client/galaxy/scripts/mvc/tag.js
@@ -142,7 +142,7 @@ var TagsEditor = Backbone.View.extend(baseMVC.LoggableMixin)
 
         /** @returns {String[]} all tags used by the current user */
         _getTagsUsed: function() {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             var self = this;
             return _.map(Galaxy.user.get("tags_used"), self._nameToHash);
         },
@@ -168,7 +168,7 @@ var TagsEditor = Backbone.View.extend(baseMVC.LoggableMixin)
          *  @param {String} newTag  the tag to add to the list of used
          */
         _addNewTagToTagsUsed: function(newTag) {
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             var tagsUsed = Galaxy.user.get("tags_used");
             if (!_.contains(tagsUsed, newTag)) {
                 tagsUsed.push(newTag);
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index c4e29fea8d8..ceb1a0dd109 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -17,7 +17,7 @@ import axios from "axios";
 
 export default FormBase.extend({
     initialize: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var self = this;
         this.deferred = new Deferred();
         FormBase.prototype.initialize.call(this, options);
@@ -26,7 +26,7 @@ export default FormBase.extend({
         this._update(this.model.get("initialmodel"));
 
         // listen to history panel
-        if (this.model.get("listen_to_history") && Galaxy && Galaxy.currHistoryPanel) {
+        if (this.model.get("listen_to_history") && Galaxy.currHistoryPanel) {
             this.listenTo(Galaxy.currHistoryPanel.collection, "change", () => {
                 self.model.get("onchange")();
             });
@@ -60,7 +60,7 @@ export default FormBase.extend({
         this.$el.off().hide();
         this.deferred.execute(() => {
             FormBase.prototype.remove.call(self);
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             Galaxy.emit.debug("tool-form-base::_destroy()", "Destroy view.");
         });
     },
@@ -75,15 +75,9 @@ export default FormBase.extend({
                 `<b>${options.name}</b> ${options.description} (Galaxy Version ${options.version})`,
             operations: !options.hide_operations && this._operations(),
             onchange: function() {
-                let Galaxy = getGalaxyInstance();
                 self.deferred.reset();
                 self.deferred.execute(process => {
                     self.model.get("postchange")(process, self);
-                    if (self.model.get("listen_to_history")) {
-                        process.then(() => {
-                            self.stopListening(Galaxy.currHistoryPanel.collection);
-                        });
-                    }
                 });
             }
         });
@@ -114,10 +108,10 @@ export default FormBase.extend({
     _operations: function() {
         var self = this;
         var options = this.model.attributes;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         // Buttons for adding and removing favorite.
-        let in_favorites = Galaxy.user.getFavorites().tools.indexOf(options.id) >= 0;
+        const in_favorites = Galaxy.user.getFavorites().tools.indexOf(options.id) >= 0;
         var favorite_button = new Ui.Button({
             icon: "fa-star-o",
             title: options.narrow ? null : "Favorite",
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
index 2ac0ec16e44..75c642e6ff6 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
@@ -17,7 +17,7 @@ import WorkflowIcons from "mvc/workflow/workflow-icons";
 
 var View = Backbone.View.extend({
     initialize: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal || new Modal.View();
         this.model = (options && options.model) || new Backbone.Model(options);
         this.deferred = new Deferred();
@@ -39,7 +39,7 @@ var View = Backbone.View.extend({
     /** Configures form/step options for each workflow step */
     _configure: function() {
         var self = this;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.forms = [];
         this.steps = [];
         this.links = [];
@@ -336,7 +336,7 @@ var View = Backbone.View.extend({
 
     /** Render job caching option */
     _renderUseCachedJob: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var extra_user_preferences = {};
         if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
             extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
@@ -370,7 +370,7 @@ var View = Backbone.View.extend({
 
     /** Render step */
     _renderStep: function(step) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var self = this;
         var form = null;
         this.deferred.execute(promise => {
@@ -529,7 +529,7 @@ var View = Backbone.View.extend({
 
     /** Refresh the history after job submission while form is shown */
     _refreshHistory: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var self = this;
         var history = Galaxy && Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model;
         if (this._refresh_history) {
@@ -561,7 +561,7 @@ var View = Backbone.View.extend({
 
     /** Validate and submit workflow */
     _submit: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var self = this;
         var history_form_data = this.history_form.data.create();
         var job_def = {
@@ -716,13 +716,13 @@ var View = Backbone.View.extend({
 
     /** Templates */
     _templateSuccess: function(response) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if ($.isArray(response) && response.length > 0) {
             let timesExecuted = "";
             // Default destination blurb, used for a single execution, same history.
             let destinationBlurb =
                 "You can check the status of queued jobs and view the resulting data by refreshing the History pane, if this has not already happened automatically.";
-            let newHistoryTarget =
+            const newHistoryTarget =
                 (response[0].history_id &&
                     Galaxy.currHistoryPanel &&
                     Galaxy.currHistoryPanel.model.id != response[0].history_id) ||
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index f5e11bfeaed..2eda949c313 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -12,23 +12,22 @@ import Modal from "mvc/ui/ui-modal";
 import ToolFormBase from "mvc/tool/tool-form-base";
 import Webhooks from "mvc/webhooks";
 
-var View = Backbone.View.extend({
+const View = Backbone.View.extend({
     initialize: function(options) {
-        let Galaxy = getGalaxyInstance();
-        var self = this;
+        const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal || new Modal.View();
         this.form = new ToolFormBase(
             Utils.merge(
                 {
                     listen_to_history: true,
                     always_refresh: false,
-                    buildmodel: function(process, form) {
-                        var options = form.model.attributes;
+                    buildmodel: (process, form) => {
+                        const options = form.model.attributes;
 
                         // build request url
-                        var build_url = "";
-                        var build_data = {};
-                        var job_id = options.job_id;
+                        let build_url = "";
+                        let build_data = {};
+                        const job_id = options.job_id;
                         if (job_id) {
                             build_url = `${getAppRoot()}api/jobs/${job_id}/build_for_rerun`;
                         } else {
@@ -42,18 +41,18 @@ var View = Backbone.View.extend({
                         Utils.get({
                             url: build_url,
                             data: build_data,
-                            success: function(data) {
+                            success: data => {
                                 if (!data.display) {
                                     window.location = getAppRoot();
                                     return;
                                 }
                                 form.model.set(data);
-                                self._customize(form);
+                                this._customize(form);
                                 Galaxy.emit.debug("tool-form-base::_buildModel()", "Initial tool model ready.", data);
                                 process.resolve();
                             },
-                            error: function(response, status) {
-                                var error_message = (response && response.err_msg) || "Uncaught error.";
+                            error: (response, status) => {
+                                const error_message = (response && response.err_msg) || "Uncaught error.";
                                 if (status == 401) {
                                     window.location = `${getAppRoot()}user/login?${$.param({
                                         redirect: `${getAppRoot()}?tool_id=${options.id}`
@@ -72,7 +71,7 @@ var View = Backbone.View.extend({
                                             title: _l("Tool request failed"),
                                             body: error_message,
                                             buttons: {
-                                                Close: function() {
+                                                Close: () => {
                                                     Galaxy.modal.hide();
                                                 }
                                             }
@@ -87,8 +86,8 @@ var View = Backbone.View.extend({
                             }
                         });
                     },
-                    postchange: function(process, form) {
-                        var current_state = {
+                    postchange: (process, form) => {
+                        const current_state = {
                             tool_id: form.model.get("id"),
                             tool_version: form.model.get("version"),
                             inputs: $.extend(true, {}, form.data.create())
@@ -99,13 +98,13 @@ var View = Backbone.View.extend({
                             type: "POST",
                             url: `${getAppRoot()}api/tools/${form.model.get("id")}/build`,
                             data: current_state,
-                            success: function(data) {
+                            success: data => {
                                 form.update(data);
                                 form.wait(false);
                                 Galaxy.emit.debug("tool-form::postchange()", "Received new model.", data);
                                 process.resolve();
                             },
-                            error: function(response) {
+                            error: response => {
                                 Galaxy.emit.debug("tool-form::postchange()", "Refresh request failed.", response);
                                 process.reject();
                             }
@@ -121,19 +120,18 @@ var View = Backbone.View.extend({
     },
 
     _customize: function(form) {
-        var self = this;
-        var options = form.model.attributes;
+        const options = form.model.attributes;
         // build execute button
-        var execute_button = new Ui.Button({
+        const execute_button = new Ui.Button({
             icon: "fa-check",
             tooltip: `Execute: ${options.name} (${options.version})`,
             title: _l("Execute"),
             cls: "btn btn-primary",
             wait_cls: "btn btn-info",
-            onclick: function() {
+            onclick: () => {
                 execute_button.wait();
                 form.portlet.disable();
-                self.submit(options, () => {
+                this.submit(options, () => {
                     execute_button.unwait();
                     form.portlet.enable();
                 });
@@ -143,7 +141,7 @@ var View = Backbone.View.extend({
 
         // remap feature
         if (options.job_id && options.job_remap) {
-            var label, help;
+            let label, help;
             if (options.job_remap === "job_produced_collection_elements") {
                 label = "Replace elements in collection ?";
                 help =
@@ -166,12 +164,12 @@ var View = Backbone.View.extend({
         }
 
         // Job Re-use Options
-        let Galaxy = getGalaxyInstance();
-        var extra_user_preferences = {};
+        const Galaxy = getGalaxyInstance();
+        let extra_user_preferences = {};
         if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
             extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
         }
-        var use_cached_job =
+        const use_cached_job =
             "use_cached_job|use_cached_job_checkbox" in extra_user_preferences
                 ? extra_user_preferences["use_cached_job|use_cached_job_checkbox"]
                 : false;
@@ -194,21 +192,22 @@ var View = Backbone.View.extend({
      * @param{function} callback  - Called when request has completed
      */
     submit: function(options, callback) {
-        let Galaxy = getGalaxyInstance();
-        var self = this;
-        var job_def = {
+        const Galaxy = getGalaxyInstance();
+        const history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
+        const job_def = {
+            history_id: history_id,
             tool_id: options.id,
             tool_version: options.version,
             inputs: this.form.data.create()
         };
         this.form.trigger("reset");
-        if (!self.validate(job_def)) {
+        if (!this.validate(job_def)) {
             Galaxy.emit.debug("tool-form::submit()", "Submission canceled. Validation failed.");
             callback && callback();
             return;
         }
         if (options.action !== `${getAppRoot()}tool_runner/index`) {
-            var $f = $("<form/>").attr({
+            const $f = $("<form/>").attr({
                 action: options.action,
                 method: options.method,
                 enctype: options.enctype
@@ -228,39 +227,43 @@ var View = Backbone.View.extend({
             type: "POST",
             url: `${getAppRoot()}api/tools`,
             data: job_def,
-            success: function(response) {
+            success: response => {
                 callback && callback();
-                self.$el.children().hide();
-                self.$el.append(self._templateSuccess(response, job_def));
+                this.$el.children().hide();
+                this.$el.append(this._templateSuccess(response, job_def));
+                this.$el.parent().scrollTop(0);
                 // Show Webhook if job is running
                 if (response.jobs && response.jobs.length > 0) {
-                    self.$el.append($("<div/>", { id: "webhook-view" }));
+                    this.$el.append($("<div/>", { id: "webhook-view" }));
                     new Webhooks.WebhookView({
                         type: "tool",
                         toolId: job_def.tool_id
                     });
                 }
-                Galaxy && Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.refreshContents();
+                if (Galaxy.currHistoryPanel) {
+                    this.form.stopListening(Galaxy.currHistoryPanel.collection);
+                    Galaxy.currHistoryPanel.refreshContents();
+                }
             },
-            error: function(response) {
+            error: response => {
                 callback && callback();
                 Galaxy.emit.debug("tool-form::submit", "Submission failed.", response);
-                var input_found = false;
+                let input_found = false;
                 if (response && response.err_data) {
-                    var error_messages = self.form.data.matchResponse(response.err_data);
-                    for (var input_id in error_messages) {
-                        self.form.highlight(input_id, error_messages[input_id]);
+                    const error_messages = this.form.data.matchResponse(response.err_data);
+                    for (const input_id in error_messages) {
+                        this.form.highlight(input_id, error_messages[input_id]);
                         input_found = true;
                         break;
                     }
                 }
                 if (!input_found) {
-                    self.modal.show({
+                    this.modal.show({
                         title: _l("Job submission failed"),
-                        body: self._templateError(job_def, response && response.err_msg),
+                        body: this._templateError(job_def, response && response.err_msg),
                         buttons: {
-                            Close: function() {
-                                self.modal.hide();
+                            Close: () => {
+                                this.modal.hide();
                             }
                         }
                     });
@@ -273,15 +276,15 @@ var View = Backbone.View.extend({
      * @param{dict}     job_def   - Job execution dictionary
      */
     validate: function(job_def) {
-        let Galaxy = getGalaxyInstance();
-        var job_inputs = job_def.inputs;
-        var batch_n = -1;
-        var batch_src = null;
-        for (var job_input_id in job_inputs) {
-            var input_value = job_inputs[job_input_id];
-            var input_id = this.form.data.match(job_input_id);
-            var input_field = this.form.field_list[input_id];
-            var input_def = this.form.input_list[input_id];
+        const Galaxy = getGalaxyInstance();
+        const job_inputs = job_def.inputs;
+        let batch_n = -1;
+        let batch_src = null;
+        for (const job_input_id in job_inputs) {
+            const input_value = job_inputs[job_input_id];
+            const input_id = this.form.data.match(job_input_id);
+            const input_field = this.form.field_list[input_id];
+            const input_def = this.form.input_list[input_id];
             if (!input_id || !input_def || !input_field) {
                 Galaxy.emit.debug("tool-form::validate()", "Retrieving input objects failed.");
                 continue;
@@ -291,19 +294,15 @@ var View = Backbone.View.extend({
                 return false;
             }
             if (input_field.validate) {
-                // wish there was a way to just reset this input field
-                const reset = () => {
-                    this.form.trigger("reset");
-                };
-                const validateObject = input_field.validate(reset);
-                if (!validateObject.valid) {
-                    this.form.highlight(input_id, validateObject.message);
+                const message = input_field.validate();
+                if (message) {
+                    this.form.highlight(input_id, message);
                     return false;
                 }
             }
             if (input_value && input_value.batch) {
-                var n = input_value.values.length;
-                var src = n > 0 && input_value.values[0] && input_value.values[0].src;
+                const n = input_value.values.length;
+                const src = n > 0 && input_value.values[0] && input_value.values[0].src;
                 if (src) {
                     if (batch_src === null) {
                         batch_src = src;
@@ -330,12 +329,12 @@ var View = Backbone.View.extend({
     },
 
     _getInputs: function(job_def) {
-        var inputs = [];
-        var index = {};
-        for (let i in job_def.inputs) {
-            let input = job_def.inputs[i];
+        const inputs = [];
+        const index = {};
+        for (const i in job_def.inputs) {
+            const input = job_def.inputs[i];
             if (input && $.isArray(input.values)) {
-                for (let j of input.values) {
+                for (const j of input.values) {
                     if (j.src && !index[j.id]) {
                         inputs.push(j);
                         index[j.id] = true;
@@ -346,36 +345,33 @@ var View = Backbone.View.extend({
         return inputs;
     },
 
-    _templateRow: function(list, title, max = 3) {
-        var blurb = "";
-        list.sort(function(a, b) {
-            return b.hid - a.hid;
-        });
+    _templateRow: function(list, title) {
+        let blurb = "";
         if (list.length > 0) {
             blurb += `<p>${title}:</p>`;
-            for (let item of list) {
-                let rowString = max > 0 ? `${item.hid}: ${_.escape(item.name)}` : "...";
-                blurb += `<p class="messagerow">
-                            <b>${rowString}</b>
-                          </p>`;
-                if (max-- <= 0) {
-                    break;
-                }
+            list.sort((a, b) => {
+                b.hid - a.hid;
+            });
+            blurb += `<ul>`;
+            for (const item of list) {
+                const rowString = `${item.hid}: ${_.escape(item.name)}`;
+                blurb += `<li><b>${rowString}</b></li>`;
             }
+            blurb += `</ul>`;
         }
         return blurb;
     },
 
     _templateSuccess: function(response, job_def) {
-        var njobs = response.jobs.length;
+        const njobs = response && response.jobs ? response.jobs.length : 0;
         if (njobs > 0) {
-            var inputs = this._getInputs(job_def);
-            var ninputs = inputs.length;
-            var noutputs = response.outputs.length;
-            var njobsText = njobs > 1 ? `${njobs} jobs` : `1 job`;
-            var ninputsText = ninputs > 1 ? `${ninputs} inputs` : `this input`;
-            var noutputsText = noutputs > 1 ? `${noutputs} outputs` : `this output`;
-            var tool_name = this.form.model.get("name");
+            const inputs = this._getInputs(job_def);
+            const ninputs = inputs.length;
+            const noutputs = response.outputs.length;
+            const njobsText = njobs > 1 ? `${njobs} jobs` : `1 job`;
+            const ninputsText = ninputs > 1 ? `${ninputs} inputs` : `this input`;
+            const noutputsText = noutputs > 1 ? `${noutputs} outputs` : `this output`;
+            const tool_name = this.form.model.get("name");
             return `<div class="donemessagelarge">
                         <p>
                             Executed <b>${tool_name}</b> and successfully added ${njobsText} to the queue.
diff --git a/client/galaxy/scripts/mvc/tool/tool-genomespace.js b/client/galaxy/scripts/mvc/tool/tool-genomespace.js
index 2c44b92cda7..a4523fac27a 100644
--- a/client/galaxy/scripts/mvc/tool/tool-genomespace.js
+++ b/client/galaxy/scripts/mvc/tool/tool-genomespace.js
@@ -4,7 +4,7 @@ import { getGalaxyInstance } from "app";
 // tool form templates
 export default {
     openFileBrowser: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var GS_UI_URL = Galaxy.config.genomespace_ui_url;
         var GS_UPLOAD_URL = `${GS_UI_URL}upload/loadUrlToGenomespace.html?getLocation=true`;
 
diff --git a/client/galaxy/scripts/mvc/tool/tools.js b/client/galaxy/scripts/mvc/tool/tools.js
index 034b0e5c2d2..d1831083fb9 100644
--- a/client/galaxy/scripts/mvc/tool/tools.js
+++ b/client/galaxy/scripts/mvc/tool/tools.js
@@ -367,7 +367,7 @@ var ToolSearch = Backbone.Model.extend({
      * Do the search and update the results.
      */
     do_search: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var query = this.attributes.query;
 
         // If query is too short, do not search.
@@ -436,16 +436,24 @@ var ToolPanel = Backbone.Model.extend({
 
         var // Helper to recursively parse tool panel.
             parse_elt = elt_dict => {
-                var type = elt_dict.model_class;
+                const type = elt_dict.model_class;
                 // There are many types of tools; for now, anything that ends in 'Tool'
-                // is treated as a generic tool.
+                // and is not a ExpressionTool is treated as a generic tool.
                 if (type.indexOf("Tool") === type.length - 4) {
-                    return self.attributes.tools.get(elt_dict.id);
+                    const tool = self.attributes.tools.get(elt_dict.id);
+                    if (type === "ExpressionTool") {
+                        tool.hide();
+                    }
+                    return tool;
                 } else if (type === "ToolSection") {
                     // Parse elements.
-                    var elems = _.map(elt_dict.elems, parse_elt);
+                    const elems = _.map(elt_dict.elems, parse_elt).filter(el => el.is_visible());
                     elt_dict.elems = elems;
-                    return new ToolSection(elt_dict);
+                    const section = new ToolSection(elt_dict);
+                    if (elems.length == 0) {
+                        section.hide();
+                    }
+                    return section;
                 } else if (type === "ToolSectionLabel") {
                     return new ToolSectionLabel(elt_dict);
                 }
@@ -529,7 +537,7 @@ var ToolLinkView = BaseView.extend({
         if (this.model.id === "upload1") {
             $link.find("a").on("click", e => {
                 e.preventDefault();
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 Galaxy.upload.show();
             });
         } else if (formStyle === "regular") {
@@ -537,7 +545,7 @@ var ToolLinkView = BaseView.extend({
             var self = this;
             $link.find("a").on("click", e => {
                 e.preventDefault();
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 Galaxy.router.push("/", {
                     tool_id: self.model.id,
                     version: self.model.get("version")
diff --git a/client/galaxy/scripts/mvc/toolshed/categories-view.js b/client/galaxy/scripts/mvc/toolshed/categories-view.js
index f54d0375609..226da29c9bc 100644
--- a/client/galaxy/scripts/mvc/toolshed/categories-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/categories-view.js
@@ -9,28 +9,23 @@ import "libs/jquery/jquery-ui";
 var ToolShedCategories = Backbone.View.extend({
     el: "#center",
 
-    defaults: {
-        tool_shed: "https://toolshed.g2.bx.psu.edu/"
-    },
-
     initialize: function(options) {
-        var shed = options.tool_shed.replace(/\//g, "%2f");
         this.options = _.defaults(this.options || options, this.defaults);
         this.model = new toolshed_model.Categories();
-        this.listenTo(this.model, "sync", this.render);
         this.model.url = `${this.model.url}?tool_shed_url=${this.options.tool_shed}`;
-        this.model.tool_shed = shed;
+        this.model.tool_shed = options.tool_shed.replace(/\//g, "%2f");
         this.model.fetch();
+        this.listenTo(this.model, "sync", this.render);
     },
 
     render: function(options) {
+        const category_list_template = this.templateCategoryList();
         this.options = _.extend(this.options, options);
         this.options.categories = this.model.models;
         this.options.queue = toolshed_util.queueLength();
-        var category_list_template = this.templateCategoryList;
         this.$el.html(category_list_template(this.options));
-        $("#center").css("overflow", "auto");
         this.bindEvents();
+        $("#center").css("overflow", "auto");
     },
 
     bindEvents: function() {
@@ -60,44 +55,42 @@ var ToolShedCategories = Backbone.View.extend({
         });
     },
 
-    templateCategoryList: _.template(
-        [
-            '<style type="text/css">',
-            ".ui-autocomplete { background-color: #fff; }",
-            "li.ui-menu-item { list-style-type: none; }",
-            "</style>",
-            '<div class="unified-panel-header" id="panel_header" unselectable="on">',
-            '<div class="unified-panel-header-inner" style="layout: inline;">Categories in <%= tool_shed.replace(/%2f/g, "/") %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>',
-            "</div>",
-            '<div class="unified-panel-body" id="list_categories">',
-            '<div id="standard-search" style="height: 2em; margin: 1em;">',
-            '<span class="ui-widget" >',
-            '<input class="search-box-input" id="search_box" data-shedurl="<%= tool_shed.replace(/%2f/g, "/") %>" name="search" placeholder="Search repositories by name or id" size="60" type="text" />',
-            "</span>",
-            "</div>",
-            '<div style="clear: both; margin-top: 1em;">',
-            '<table class="grid">',
-            '<thead id="grid-table-header">',
-            "<tr>",
-            "<th>Name</th>",
-            "<th>Description</th>",
-            "<th>Repositories</th>",
-            "</tr>",
-            "</thead>",
-            "<% _.each(categories, function(category) { %>",
-            "<tr>",
-            "<td>",
-            '<a href="#/category/s/<%= tool_shed %>/c/<%= category.get("id") %>/k/name/p/1/t/asc"><%= category.get("name") %></a>',
-            "</td>",
-            '<td><%= category.get("description") %></td>',
-            '<td><%= category.get("repositories") %></td>',
-            "</tr>",
-            "<% }); %>",
-            "</table>",
-            "</div>",
-            "</div>"
-        ].join("")
-    )
+    templateCategoryList: function() {
+        return _.template(
+            `<div class='shed-style-container'>
+                <div class='header'>
+                    <h2>Categories in <%= tool_shed.replace(/%2f/g, '/') %></h2>
+                    <span><a href='#/queue'>Repository Queue (<%= queue %>)</a></span>
+                    <span style='clear:both; '></span>
+                </div>
+                <div id='standard-search' style='height: 2em; margin: 1em;'>
+                    <span class='ui-widget' >
+                    <input class='search-box-input' id='search_box' data-shedurl='<%= tool_shed.replace(/%2f/g, '/') %>' name='search' placeholder='Search repositories' size='30' type='text' />
+                    </span>
+                </div>
+                <div style='clear: both; margin-top: 1em;'>
+                    <table class='grid'>
+                    <thead id='grid-table-header'>
+                    <tr>
+                        <th>Name</th>
+                        <th>Description</th>
+                        <th>Repositories</th>
+                    </tr>
+                    </thead>
+                    <% _.each(categories, function(category) { %>
+                    <tr>
+                        <td>
+                        <a href='#/category/s/<%= tool_shed %>/c/<%= category.get('id') %>/k/name/p/1/t/asc'><%= category.get('name') %></a>
+                        </td>
+                        <td><%= category.get('description') %></td>
+                        <td><%= category.get('repositories') %></td>
+                    </tr>
+                    <% }); %>
+                    </table>
+                </div>
+            </div>`
+        );
+    }
 });
 
 export default {
diff --git a/client/galaxy/scripts/mvc/toolshed/repo-status-view.js b/client/galaxy/scripts/mvc/toolshed/repo-status-view.js
index 1b02292fcd3..ebdd99624b5 100644
--- a/client/galaxy/scripts/mvc/toolshed/repo-status-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/repo-status-view.js
@@ -38,7 +38,7 @@ var ToolShedRepoStatusView = Backbone.View.extend({
 
     render: function(options) {
         this.options = _.extend(this.options, options);
-        var repo_status_template = this.templateRepoStatus;
+        var repo_status_template = this.templateRepoStatus();
         this.$el.html(
             repo_status_template({
                 title: _l("Repository Status"),
@@ -49,80 +49,82 @@ var ToolShedRepoStatusView = Backbone.View.extend({
         $("#center").css("overflow", "auto");
     },
 
-    templateRepoStatus: _.template(
-        [
-            '<div class="unified-panel-header" id="panel_header" unselectable="on">',
-            '<div class="unified-panel-header-inner"><%= title %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>',
-            "</div>",
-            '<style type="text/css">',
-            ".state-color-new,",
-            ".state-color-deactivated,",
-            ".state-color-uninstalled { border-color:#bfbfbf; background:#eee }",
-            ".state-color-cloning,",
-            ".state-color-setting-tool-versions,",
-            ".state-color-installing-repository-dependencies,",
-            ".state-color-installing-tool-dependencies,",
-            ".state-color-loading-proprietary-datatypes { border-color:#AAAA66; background:#FFFFCC }",
-            ".state-color-installed { border-color:#20b520; background:#b0f1b0 }",
-            ".state-color-error { border-color:#dd1b15; background:#f9c7c5 }",
-            "</style>",
-            '<table id="grid-table" class="grid">',
-            '<thead id="grid-table-header">',
-            "<tr>",
-            '<th id="null-header">Name<span class="sort-arrow"></span></th>',
-            '<th id="null-header">Description<span class="sort-arrow"></span></th>',
-            '<th id="null-header">Owner<span class="sort-arrow"></span></th>',
-            '<th id="null-header">Revision<span class="sort-arrow"></span></th>',
-            '<th id="null-header">Installation Status<span class="sort-arrow"></span></th>',
-            "</tr>",
-            "</thead>",
-            '<tbody id="grid-table-body">',
-            "<% _.each(repositories, function(repository) { %>",
-            "<tr>",
-            "<td>",
-            '<div id="" class="">',
-            '<label id="repo-name-<%= repository.get("id") %>" for="<%= repository.get("id") %>">',
-            '<%= repository.get("name") %>',
-            "</label>",
-            "</div>",
-            "</td>",
-            "<td>",
-            '<div id="" class="">',
-            '<label id="repo-desc-<%= repository.get("id") %>" for="<%= repository.get("id") %>">',
-            '<%= repository.get("description") %>',
-            "</label>",
-            "</div>",
-            "</td>",
-            "<td>",
-            '<div id="" class="">',
-            '<label id="repo-user-<%= repository.get("id") %>" for="<%= repository.get("id") %>">',
-            '<%= repository.get("owner") %>',
-            "</label>",
-            "</div>",
-            "</td>",
-            "<td>",
-            '<div id="" class="">',
-            '<label id="repo-changeset-<%= repository.get("id") %>" for="<%= repository.get("id") %>">',
-            '<%= repository.get("changeset_revision") %>',
-            "</label>",
-            "</div>",
-            "</td>",
-            "<td>",
-            '<div id="" class="">',
-            '<label id="RepositoryStatus-<%= repository.get("id") %>" for="<%= repository.get("id") %>">',
-            '<div class="repo-status count-box state-color-<%= repository.get("status").toLowerCase().replace(/ /g, "-") %>" id="RepositoryStatus-<%= repository.get("id") %>">',
-            '<%= repository.get("status") %>',
-            "</div>",
-            "</label>",
-            "</div>",
-            "</td>",
-            "</tr>",
-            "<% }); %>",
-            "</tbody>",
-            '<tfoot id="grid-table-footer"></tfoot>',
-            "</table>"
-        ].join("")
-    )
+    templateRepoStatus: function() {
+        return _.template(
+            `<div class="unified-panel-header" id="panel_header" unselectable="on">
+                <div class="unified-panel-header-inner"><%= title %>
+                    <a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a>
+                </div>
+            </div>
+            <style type="text/css">
+                .state-color-new,
+                .state-color-deactivated,
+                .state-color-uninstalled { border-color:#bfbfbf; background:#eee }
+                .state-color-cloning,
+                .state-color-setting-tool-versions,
+                .state-color-installing-repository-dependencies,
+                .state-color-installing-tool-dependencies,
+                .state-color-loading-proprietary-datatypes { border-color:#AAAA66; background:#FFFFCC }
+                .state-color-installed { border-color:#20b520; background:#b0f1b0 }
+                .state-color-error { border-color:#dd1b15; background:#f9c7c5 }
+            </style>
+            <table id="grid-table" class="grid">
+                <thead id="grid-table-header">
+                <tr>
+                    <th id="null-header">Name<span class="sort-arrow"></span></th>
+                    <th id="null-header">Description<span class="sort-arrow"></span></th>
+                    <th id="null-header">Owner<span class="sort-arrow"></span></th>
+                    <th id="null-header">Revision<span class="sort-arrow"></span></th>
+                    <th id="null-header">Installation Status<span class="sort-arrow"></span></th>
+                </tr>
+                </thead>
+                <tbody id="grid-table-body">
+                <% _.each(repositories, function(repository) { %>
+                <tr>
+                    <td>
+                    <div id="" class="">
+                    <label id="repo-name-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
+                    <%= repository.get("name") %>
+                    </label>
+                    </div>
+                    </td>
+                    <td>
+                    <div id="" class="">
+                    <label id="repo-desc-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
+                    <%= repository.get("description") %>
+                    </label>
+                    </div>
+                    </td>
+                    <td>
+                    <div id="" class="">
+                    <label id="repo-user-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
+                    <%= repository.get("owner") %>
+                    </label>
+                    </div>
+                    </td>
+                    <td>
+                    <div id="" class="">
+                    <label id="repo-changeset-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
+                    <%= repository.get("changeset_revision") %>
+                    </label>
+                    </div>
+                    </td>
+                    <td>
+                    <div id="" class="">
+                    <label id="RepositoryStatus-<%= repository.get("id") %>" for="<%= repository.get("id") %>">
+                    <div class="repo-status count-box state-color-<%= repository.get("status").toLowerCase().replace(/ /g, "-") %>" id="RepositoryStatus-<%= repository.get("id") %>">
+                    <%= repository.get("status") %>
+                    </div>
+                    </label>
+                    </div>
+                    </td>
+                </tr>
+                <% }); %>
+                </tbody>
+                <tfoot id="grid-table-footer"></tfoot>
+            </table>`
+        );
+    }
 });
 
 export default {
diff --git a/client/galaxy/scripts/mvc/toolshed/repositories-view.js b/client/galaxy/scripts/mvc/toolshed/repositories-view.js
index 3ee678dab4a..fca581d61f3 100644
--- a/client/galaxy/scripts/mvc/toolshed/repositories-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/repositories-view.js
@@ -14,9 +14,11 @@ var ToolShedCategoryContentsView = Backbone.View.extend({
         this.model = new toolshed_model.CategoryCollection();
         this.listenTo(this.model, "sync", this.render);
         var shed = params.tool_shed.replace(/\//g, "%2f");
-        this.model.url += `?tool_shed_url=${shed}&category_id=${params.category_id}&sort_key=${
-            params.sort_key
-        }&sort_order=${params.sort_order}&page=${params.page}`;
+        this.model.url += `?tool_shed_url=${shed}`;
+        this.model.url += `&category_id=${params.category_id}`;
+        this.model.url += `&sort_key=${params.sort_key}`;
+        this.model.url += `&sort_order=${params.sort_order}`;
+        this.model.url += `&page=${params.page}`;
         this.model.tool_shed = shed;
         this.model.category = params.category_id;
         this.model.fetch();
@@ -24,8 +26,8 @@ var ToolShedCategoryContentsView = Backbone.View.extend({
 
     render: function(options) {
         this.options = _.defaults(this.options || {}, options);
-        var category_contents_template = this.templateCategoryContents;
-        var page_navigation_template = this.templatePageNavigation;
+        var category_contents_template = this.templateCategoryContents();
+        var page_navigation_template = this.templatePageNavigation();
         var sorting = {
             class: { owner: "fa-sort", description: "fa-sort", name: "fa-sort" },
             direction: { owner: "asc", description: "asc", name: "asc" }
@@ -81,7 +83,7 @@ var ToolShedCategoryContentsView = Backbone.View.extend({
                 });
             },
             minLength: 3,
-            select: function(event, ui) {
+            select: (event, ui) => {
                 var tsr_id = ui.item.value;
                 var new_route = `repository/s/${this.model.tool_shed}/r/${tsr_id}`;
                 Backbone.history.navigate(new_route, {
@@ -114,105 +116,105 @@ var ToolShedCategoryContentsView = Backbone.View.extend({
         });
     },
 
-    templatePageNavigation: _.template(
-        [
-            '<div class="navigation">',
-            "<% if (page != 1) { %>",
-            '<a data-page="1" class="pagenav fa fa-fast-backward" />',
-            '<a data-page="<%= previous %>" class="pagenav fa fa-step-backward" />',
-            "<% } else { %>",
-            '<a data-page="1" class="pagenav-inactive fa fa-fast-backward" />',
-            '<a data-page="<%= previous %>" class="pagenav-inactive fa fa-step-backward" />',
-            "<% } %>",
-            "<% if (pages > 5) { %>",
-            "<% if (page != 1) { %>",
-            '<a data-page="1" class="pagenav fa"><a>1</a>',
-            "<% if (page != 2) { %>",
-            '<a class="fa">&hellip;</a>',
-            "<% } %>",
-            "<% } else { %>",
-            '<a data-page="1" class="pagenav-inactive fa"><a>1</a>',
-            "<% } %>",
-            "<% _.each(page_slice, function(i) { %>",
-            "<% if (i == page) { %>",
-            '<a data-page="<%= i %>" class="fa"><strong><%= i %></strong></a>',
-            "<% } else { %>",
-            '<a data-page="<%= i %>" class="pagenav fa"><%= i %></a>',
-            "<% } %>",
-            "<% }); %>",
-            "<% var last_pages = [pages - 2, pages - 1, pages]; %>",
-            "<% if (last_pages.indexOf(parseInt(page)) == -1) { %>",
-            '<a class="fa">&hellip;</a>',
-            '<a data-page="<%= pages %>" class="pagenav fa"><%= pages %></a>',
-            "<% } %>",
-            "<% } else { %>",
-            "<% for (i = 1; i <= pages; i++) { %>",
-            "<% if (i == page) { %>",
-            '<a data-page="<%= i %>" class="fa"><strong><%= i %></strong></a>',
-            "<% } else { %>",
-            '<a data-page="<%= i %>" class="pagenav fa"><%= i %></a>',
-            "<% } %>",
-            "<% } %>",
-            "<% } %>",
-            "<% if (page < pages) { %>",
-            '<a data-page="<%= next %>" class="pagenav fa fa-step-forward" />',
-            '<a data-page="<%= pages %>" class="pagenav fa fa-fast-forward" />',
-            "<% } else { %>",
-            '<a data-page="<%= next %>" class="pagenav-inactive fa fa-step-forward" />',
-            '<a data-page="<%= pages %>" class="pagenav-inactive fa fa-fast-forward" />',
-            "<% } %>",
-            "</div>"
-        ].join("")
-    ),
+    templatePageNavigation: function() {
+        return _.template(
+            `<div class="navigation">
+            <% if (page != 1) { %>
+            <a data-page="1" class="pagenav fa fa-fast-backward" />
+            <a data-page="<%= previous %>" class="pagenav fa fa-step-backward" />
+            <% } else { %>
+            <a data-page="1" class="pagenav-inactive fa fa-fast-backward" />
+            <a data-page="<%= previous %>" class="pagenav-inactive fa fa-step-backward" />
+            <% } %>
+            <% if (pages > 5) { %>
+            <% if (page != 1) { %>
+            <a data-page="1" class="pagenav fa"><a>1</a>
+            <% if (page != 2) { %>
+            <a class="fa">&hellip;</a>
+            <% } %>
+            <% } else { %>
+            <a data-page="1" class="pagenav-inactive fa"><a>1</a>
+            <% } %>
+            <% _.each(page_slice, function(i) { %>
+            <% if (i == page) { %>
+            <a data-page="<%= i %>" class="fa"><strong><%= i %></strong></a>
+            <% } else { %>
+            <a data-page="<%= i %>" class="pagenav fa"><%= i %></a>
+            <% } %>
+            <% }); %>
+            <% var last_pages = [pages - 2, pages - 1, pages]; %>
+            <% if (last_pages.indexOf(parseInt(page)) == -1) { %>
+            <a class="fa">&hellip;</a>
+            <a data-page="<%= pages %>" class="pagenav fa"><%= pages %></a>
+            <% } %>
+            <% } else { %>
+            <% for (i = 1; i <= pages; i++) { %>
+            <% if (i == page) { %>
+            <a data-page="<%= i %>" class="fa"><strong><%= i %></strong></a>
+            <% } else { %>
+            <a data-page="<%= i %>" class="pagenav fa"><%= i %></a>
+            <% } %>
+            <% } %>
+            <% } %>
+            <% if (page < pages) { %>
+            <a data-page="<%= next %>" class="pagenav fa fa-step-forward" />
+            <a data-page="<%= pages %>" class="pagenav fa fa-fast-forward" />
+            <% } else { %>
+            <a data-page="<%= next %>" class="pagenav-inactive fa fa-step-forward" />
+            <a data-page="<%= pages %>" class="pagenav-inactive fa fa-fast-forward" />
+            <% } %>
+            </div>`
+        );
+    },
 
-    templateCategoryContents: _.template(
-        [
-            '<style type="text/css">',
-            ".ui-autocomplete { background-color: #fff; }",
-            "li.ui-menu-item { list-style-type: none; }",
-            "div.navigation { width: 100%; text-align: center; }",
-            "div.navigation a { margin-left: 0.5em; margin-right: 0.5em; display: inline; text-decoration: underline; }",
-            "a.pagenav-inactive { opacity: 0.5; }",
-            "</style>",
-            '<div class="unified-panel-header" id="panel_header" unselectable="on">',
-            '<div class="unified-panel-header-inner">Repositories in <%= category.get("name") %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>',
-            "</div>",
-            '<div class="unified-panel-body" id="list_repositories">',
-            '<div id="standard-search" style="height: 2em; margin: 1em;">',
-            '<span class="ui-widget" >',
-            '<input class="search-box-input" id="search_box" name="search" data-shedurl="<%= tool_shed.replace(/%2f/g, "/") %>" placeholder="Search repositories by name or id" size="60" type="text" />',
-            "</span>",
-            "</div>",
-            "<% if (category.get('repository_count') > 25) { %>",
-            "<%= page_navigation %>",
-            "<% } %>",
-            '<div style="clear: both; margin-top: 1em;">',
-            '<table class="grid table-striped">',
-            '<thead id="grid-table-header">',
-            "<tr>",
-            '<th style="width: 10%;"><a class="fa fa-fw <%= sorting.class.owner %>" data-direction="<%= sorting.direction.owner %>" data-field="owner">Owner</a></th>',
-            '<th style="width: 15%;"><a class="fa fa-fw <%= sorting.class.name %>" data-direction="<%= sorting.direction.name %>" data-field="name">Name</a></th>',
-            '<th><a class="fa fa-fw <%= sorting.class.description %>" data-direction="<%= sorting.direction.description %>" data-field="description">Synopsis</a></th>',
-            '<th style="width: 10%;">Type</th>',
-            "</tr>",
-            "</thead>",
-            '<% _.each(category.get("repositories"), function(repository) { %>',
-            "<tr>",
-            "<td><%= repository.owner %></td>",
-            "<td>",
-            '<div style="float: left; margin-left: 1px;" class="menubutton split">',
-            '<a href="#/repository/s/<%= tool_shed %>/r/<%= repository.id %>"><%= repository.name %></a>',
-            "</div>",
-            "</td>",
-            "<td><%= repository.description %></td>",
-            "<td><%= repository.type %></td>",
-            "</tr>",
-            "<% }); %>",
-            "</table>",
-            "</div>",
-            "</div>"
-        ].join("")
-    )
+    templateCategoryContents: function() {
+        return _.template(
+            `<style type="text/css">
+            .ui-autocomplete { background-color: #fff; }
+            li.ui-menu-item { list-style-type: none; }
+            div.navigation { width: 100%; text-align: center; }
+            div.navigation a { margin-left: 0.5em; margin-right: 0.5em; display: inline; text-decoration: underline; }
+            a.pagenav-inactive { opacity: 0.5; }
+            </style>
+            <div class="unified-panel-header" id="panel_header" unselectable="on">
+            <div class="unified-panel-header-inner">Repositories in <%= category.get("name") %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>
+            </div>
+            <div class="unified-panel-body" id="list_repositories">
+            <div id="standard-search" style="height: 2em; margin: 1em;">
+            <span class="ui-widget" >
+            <input class="search-box-input" id="search_box" name="search" data-shedurl="<%= tool_shed.replace(/%2f/g, "/") %>" placeholder="Search repositories by name or id" size="60" type="text" />
+            </span>
+            </div>
+            <% if (category.get('repository_count') > 25) { %>
+            <%= page_navigation %>
+            <% } %>
+            <div style="clear: both; margin-top: 1em;">
+            <table class="grid table-striped">
+            <thead id="grid-table-header">
+            <tr>
+            <th style="width: 10%;"><a class="fa fa-fw <%= sorting.class.owner %>" data-direction="<%= sorting.direction.owner %>" data-field="owner">Owner</a></th>
+            <th style="width: 15%;"><a class="fa fa-fw <%= sorting.class.name %>" data-direction="<%= sorting.direction.name %>" data-field="name">Name</a></th>
+            <th><a class="fa fa-fw <%= sorting.class.description %>" data-direction="<%= sorting.direction.description %>" data-field="description">Synopsis</a></th>
+            <th style="width: 10%;">Type</th>
+            </tr>
+            </thead>
+            <% _.each(category.get("repositories"), function(repository) { %>
+            <tr>
+            <td><%= repository.owner %></td>
+            <td>
+            <div style="float: left; margin-left: 1px;" class="menubutton split">
+            <a href="#/repository/s/<%= tool_shed %>/r/<%= repository.id %>"><%= repository.name %></a>
+            </div>
+            </td>
+            <td><%= repository.description %></td>
+            <td><%= repository.type %></td>
+            </tr>
+            <% }); %>
+            </table>
+            </div>
+            </div>`
+        );
+    }
 });
 
 export default {
diff --git a/client/galaxy/scripts/mvc/toolshed/repository-queue-view.js b/client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
index 67104e85111..a00f7948c31 100644
--- a/client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
@@ -19,13 +19,11 @@ var View = Backbone.View.extend({
     },
 
     render: function(options) {
-        var repo_queue_template = this.templateRepoQueue;
+        var repo_queue_template = this.templateRepoQueue();
         var repositories = this.model.models;
         this.$el.html(
             repo_queue_template({
-                title: _l("Repository Installation Queue"),
                 repositories: repositories,
-                empty: _l("No repositories in queue."),
                 queue: toolshed_util.queueLength()
             })
         );
@@ -35,20 +33,23 @@ var View = Backbone.View.extend({
 
     bindEvents: function() {
         $(".install_one").on("click", ev => {
-            var repository_metadata = this.loadFromQueue($(ev.target).attr("data-repokey"));
+            const repository_metadata = this.loadFromQueue($(ev.target).attr("data-repokey"));
             this.installFromQueue(repository_metadata, $(ev.target).attr("data-repokey"));
         });
         $(".remove_one").on("click", ev => {
-            var queue_key = $(ev.target).attr("data-repokey");
-            var repo_queue = JSON.parse(window.localStorage.repositories);
+            const queue_key = $(ev.target).attr("data-repokey");
+            const repo_queue = JSON.parse(window.localStorage.repositories);
             if (repo_queue.hasOwnProperty(queue_key)) {
-                var repository_id = repo_queue[queue_key].repository.id;
+                this.removeRow(repo_queue[queue_key].id);
                 delete repo_queue[queue_key];
-                $(`#queued_repository_${repository_id}`).remove();
             }
             window.localStorage.repositories = JSON.stringify(repo_queue);
         });
         $("#clear_queue").on("click", () => {
+            const repo_queue = JSON.parse(window.localStorage.repositories);
+            for (const key of Object.keys(repo_queue)) {
+                this.removeRow(repo_queue[key].id);
+            }
             window.localStorage.repositories = "{}";
         });
         $("#from_workflow").on("click", () => {
@@ -59,6 +60,10 @@ var View = Backbone.View.extend({
         });
     },
 
+    removeRow: function(row_id) {
+        $(`#queued_repository_${row_id}`).remove();
+    },
+
     installFromQueue: function(repository_metadata, queue_key) {
         var params = {};
         params.install_tool_dependencies = repository_metadata.install_tool_dependencies;
@@ -107,48 +112,53 @@ var View = Backbone.View.extend({
         return this.defaults;
     },
 
-    templateRepoQueue: _.template(
-        [
-            '<div class="unified-panel-header" id="panel_header" unselectable="on">',
-            '<div class="unified-panel-header-inner"><%= title %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>',
-            "</div>",
-            '<div class="tab-pane" id="panel_header" id="repository_queue">',
-            '<table id="queued_repositories" class="grid" border="0" cellpadding="2" cellspacing="2" width="100%">',
-            '<thead id="grid-table-header">',
-            "<tr>",
-            '<th class="datasetRow">Name</th>',
-            '<th class="datasetRow">Owner</th>',
-            '<th class="datasetRow">Revision</th>',
-            '<th class="datasetRow">ToolShed</th>',
-            '<th class="datasetRow">Install</th>',
-            '<th class="datasetRow"><input class="btn btn-primary" type="submit" id="clear_queue" name="clear_queue" value="Clear queue" /></th>',
-            "</tr>",
-            "</thead>",
-            "<tbody>",
-            "<% if (repositories.length > 0) { %>",
-            "<% _.each(repositories, function(repository) { %>",
-            '<tr id="queued_repository_<%= repository.get("id") %>">',
-            '<td class="datasetRow"><%= repository.get("repository").name %></td>',
-            '<td class="datasetRow"><%= repository.get("repository").owner %></td>',
-            '<td class="datasetRow"><%= repository.get("changeset_revision") %></td>',
-            '<td class="datasetRow"><%= repository.get("tool_shed_url") %></td>',
-            '<td class="datasetRow">',
-            '<input class="btn btn-primary install_one" data-repokey="<%= repository.get("queue_key") %>" type="submit" id="install_repository_<%= repository.get("id") %>" name="install_repository" value="Install now" />',
-            "</td>",
-            '<td class="datasetRow">',
-            '<input class="btn btn-primary remove_one" data-repokey="<%= repository.get("queue_key") %>" type="submit" id="unqueue_repository_<%= repository.get("id") %>" name="unqueue_repository" value="Remove from queue" />',
-            "</td>",
-            "</tr>",
-            "<% }); %>",
-            "<% } else { %>",
-            '<tr><td colspan="6"><%= empty %></td></tr>',
-            "<% } %>",
-            "</tbody>",
-            "</table>",
-            '<input type="button" class="btn btn-primary" id="from_workflow" value="Add from workflow" />',
-            "</div>"
-        ].join("")
-    )
+    templateRepoQueue: function() {
+        return _.template(
+            `<div class='shed-style-container'>
+            <h2>
+            ${_l("Repository Queue")}
+            </h2>
+            <div class='tab-pane' id='panel_header' id='repository_queue'>
+            <table id='queued_repositories' class='grid' border='0' cellpadding='2' cellspacing='2' width='100%'>
+            <thead id='grid-table-header'>
+            <tr>
+            <th class='datasetRow'>Name</th>
+            <th class='datasetRow'>Owner</th>
+            <th class='datasetRow'>Revision</th>
+            <th class='datasetRow'>ToolShed</th>
+            <th class='datasetRow'>Install</th>
+            <th class='datasetRow'></th>
+            </tr>
+            </thead>
+            <tbody>
+            <% if (repositories.length > 0) { %>
+            <% _.each(repositories, function(repository) { %>
+            <tr id='queued_repository_<%= repository.get('id') %>'>
+            <td class='datasetRow'><%= repository.get('repository').name %></td>
+            <td class='datasetRow'><%= repository.get('repository').owner %></td>
+            <td class='datasetRow'><%= repository.get('changeset_revision') %></td>
+            <td class='datasetRow'><%= repository.get('tool_shed_url') %></td>
+            <td class='datasetRow'>
+            <input class='btn btn-primary install_one' data-repokey='<%= repository.get('queue_key') %>' type='submit' id='install_repository_<%= repository.get('id') %>' name='install_repository' value='Install now' />
+            </td>
+            <td class='datasetRow'>
+            <input class='btn btn-primary remove_one' data-repokey='<%= repository.get('queue_key') %>' type='submit' id='unqueue_repository_<%= repository.get('id') %>' name='unqueue_repository' value='Remove from queue' />
+            </td>
+            </tr>
+            <% }); %>
+            <% } else { %>
+            <tr><td colspan='6'>
+            ${_l("No repositories in queue.")}
+            </td></tr>
+            <% } %>
+            </tbody>
+            </table>
+            <input type='button' class='btn btn-primary' id='from_workflow' value='Add from workflow' />
+            <input class='btn btn-primary' type='submit' id='clear_queue' name='clear_queue' value='Clear queue' />
+            </div>
+            </div>`
+        );
+    }
 });
 
 export default {
diff --git a/client/galaxy/scripts/mvc/toolshed/repository-view.js b/client/galaxy/scripts/mvc/toolshed/repository-view.js
index 96a2a7602e5..b5ab7af65b5 100644
--- a/client/galaxy/scripts/mvc/toolshed/repository-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/repository-view.js
@@ -25,7 +25,7 @@ var ToolShedRepositoryView = Backbone.View.extend({
     },
 
     render: function(options) {
-        var repo_details_template = this.templateRepoDetails;
+        var repo_details_template = this.templateRepoDetails();
         var models = this.model.models[0];
         this.options = {
             repository: models.get("repository"),
@@ -45,13 +45,13 @@ var ToolShedRepositoryView = Backbone.View.extend({
         this.options.current_metadata = this.options.repository.metadata[this.options.current_changeset];
         this.options.current_metadata.tool_shed_url = this.model.tool_shed_url;
         this.options.tools = this.options.current_metadata.tools;
-        this.options.repository_dependencies_template = this.templateRepoDependencies;
-        this.options.repository_dependency_template = this.templateRepoDependency;
-        this.options.tps_template_global_select = this.templateGlobalSectionSelect;
-        this.options.tps_template_global_create = this.templateGlobalSectionCreate;
-        this.options.tps_template_tool_select = this.templateToolSectionSelect;
-        this.options.tps_template_tool_create = this.templateToolSectionCreate;
-        this.options.panel_section_options = this.templatePanelSelectOptions;
+        this.options.repository_dependencies_template = this.templateRepoDependencies();
+        this.options.repository_dependency_template = this.templateRepoDependency();
+        this.options.tps_template_global_select = this.templateGlobalSectionSelect();
+        this.options.tps_template_global_create = this.templateGlobalSectionCreate();
+        this.options.tps_template_tool_select = this.templateToolSectionSelect();
+        this.options.tps_template_tool_create = this.templateToolSectionCreate();
+        this.options.panel_section_options = this.templatePanelSelectOptions();
         this.options.tool_dependencies = models.get("tool_dependencies");
         this.options.shed_tool_conf = this.templateShedToolConf({
             shed_tool_confs: models.get("shed_conf")
@@ -376,7 +376,7 @@ var ToolShedRepositoryView = Backbone.View.extend({
 
     toolTPSSelectionEvents: function() {
         $(".tool_panel_section_picker").on("change", ev => {
-            let element = $(ev.target);
+            const element = $(ev.target);
             var new_value = element.find("option:selected").val();
             var default_tps = $("#tool_panel_section_select")
                 .find("option:selected")
@@ -389,248 +389,248 @@ var ToolShedRepositoryView = Backbone.View.extend({
         });
     },
 
-    templateRepoDetails: _.template(
-        [
-            '<div class="unified-panel-header" id="panel_header" unselectable="on">',
-            '<div class="unified-panel-header-inner">Repository information for&nbsp;<strong><%= repository.name %></strong>&nbsp;from&nbsp;<strong><%= repository.owner %></strong><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>',
-            "</div>",
-            '<div class="unified-panel-body" id="repository_details" data-tsrid="<%= repository.id %>">',
-            '<form id="repository_installation" name="install_repository" method="post" action="<%= api_url %>">',
-            '<input type="hidden" id="repositories" name="<%= repository.id %>" value="ID" />',
-            '<input type="hidden" id="tool_shed_url" name="tool_shed_url" value="<%= tool_shed %>" />',
-            '<div class="toolForm">',
-            '<div class="toolFormTitle">Changeset</div>',
-            '<div class="toolFormBody changeset">',
-            '<select id="changeset" name="changeset" style="margin: 5px;">',
-            "<% _.each(Object.keys(repository.metadata), function(changeset) { %>",
-            '<% if (changeset == current_changeset) { var selected = "selected "; } else { var selected = ""; } %>',
-            '<option <%= selected %>value="<%= changeset.split(":")[1] %>"><%= changeset %></option>',
-            "<% }); %>",
-            "</select>",
-            '<input class="btn btn-primary preview-button" data-tsrid="<%= current_metadata.repository.id %>" type="submit" id="install_repository" name="install_repository" value="Install this revision now" />',
-            '<input class="btn btn-primary preview-button" type="button" id="queue_install" name="queue_install" value="Install this revision later" />',
-            '<div class="toolParamHelp" style="clear: both;">Please select a revision and review the settings below before installing.</div>',
-            "</div>",
-            "</div>",
-            "<%= shed_tool_conf %>",
-            "<% if (current_metadata.has_repository_dependencies) { %>",
-            '<div class="toolFormTitle">Repository dependencies for <strong id="current_changeset"><%= current_changeset %></strong></div>',
-            '<div class="toolFormBody">',
-            '<p id="install_repository_dependencies_checkbox">',
-            '<input type="checkbox" checked id="install_repository_dependencies" />',
-            '<label for="install_repository_dependencies">Install repository dependencies</label>',
-            "</p>",
-            "<% current_metadata.repository_dependency_template = repository_dependency_template; %>",
-            '<div class="tables container-table" id="repository_dependencies">',
-            '<div class="expandLink">',
-            '<a class="toggle_folder" data_target="repository_dependencies_table">',
-            "Repository dependencies &ndash; <em>installation of these additional repositories is required</em>",
-            "</a>",
-            "</div>",
-            "<%= repository_dependencies_template(current_metadata) %>",
-            "</div>",
-            "</div>",
-            "<% } %>",
-            "<% if (current_metadata.includes_tool_dependencies) { %>",
-            '<div class="toolFormTitle">Tool dependencies</div>',
-            '<div class="toolFormBody">',
-            '<p id="install_resolver_dependencies_checkbox">',
-            '<input type="checkbox" checked id="install_resolver_dependencies" />',
-            '<label for="install_resolver_dependencies">Install resolver dependencies</label>',
-            "</p>",
-            '<p id="install_tool_dependencies_checkbox">',
-            '<input type="checkbox" checked id="install_tool_dependencies" />',
-            '<label for="install_tool_dependencies">Install tool dependencies</label>',
-            "</p>",
-            '<div class="tables container-table" id="tool_dependencies">',
-            '<div class="expandLink">',
-            '<a class="toggle_folder" data_target="tool_dependencies_table">',
-            "Tool dependencies &ndash; <em>repository tools require handling of these dependencies</em>",
-            "</a>",
-            "</div>",
-            '<table class="tables container-table" id="tool_dependencies_table" border="0" cellpadding="2" cellspacing="2" width="100%">',
-            "<thead>",
-            '<tr style="display: table-row;" class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">',
-            '<th style="padding-left: 40px;">Name</th>',
-            "<th>Version</th>",
-            "<th>Type</th>",
-            "</tr>",
-            "</thead>",
-            '<tbody id="tool_deps">',
-            "<% _.each(tool_dependencies[current_changeset], function(dependency) { %>",
-            '<tr class="datasetRow tool_dependency_row" style="display: table-row;">',
-            '<td style="padding-left: 40px;">',
-            "<%= dependency.name %></td>",
-            "<td><%= dependency.version %></td>",
-            "<td><%= dependency.type %></td>",
-            "</tr>",
-            "<% }); %>",
-            "</tbody>",
-            "</table>",
-            "</div>",
-            "</div>",
-            "<% } %>",
-            "<% if (current_metadata.includes_tools_for_display_in_tool_panel) { %>",
-            '<div class="toolFormTitle">Tools &ndash; <em>click the name to preview the tool and use the pop-up menu to inspect all metadata</em></div>',
-            '<div class="toolFormBody">',
-            '<div class="tables container-table" id="tools_toggle">',
-            '<table class="tables container-table" id="valid_tools" border="0" cellpadding="2" cellspacing="2" width="100%">',
-            "<thead>",
-            '<tr style="display: table-row;" class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">',
-            '<th style="padding-left: 40px;">Name</th>',
-            "<th>Description</th>",
-            "<th>Version</th>",
-            "<th><%= tps_template_global_select({panel_section_dict: panel_section_dict, panel_section_options: panel_section_options}) %></tr>",
-            "</thead>",
-            '<tbody id="tools_in_repo">',
-            "<% _.each(current_metadata.tools, function(tool) { %>",
-            '<tr id="libraryItem-<%= tool.clean %>" class="tool_row" style="display: table-row;" style="width: 15%">',
-            '<td style="padding-left: 40px;">',
-            '<div id="tool-<%= tool.clean %>" class="menubutton split popup" style="float: left;">',
-            '<a class="tool_form view-info" data-toggle="modal" data-target="toolform_<%= tool.clean %>" data-clean="<%= tool.clean %>" data-guid="<%= tool.guid %>" data-name="<%= tool.name %>" data-desc="<%= tool.description %>"><%= tool["name"] %></a>',
-            "</div>",
-            "</td>",
-            "<td><%= tool.description %></td>",
-            '<td style="width: 15%"><%= tool.version %></td>',
-            '<td style="width: 35%" id="tool_tps_<%= tool.clean %>">',
-            "<%= tps_template_tool_select({tool: tool, panel_section_dict: panel_section_dict, panel_section_options: panel_section_options}) %>",
-            "</td>",
-            "</tr>",
-            "<% }); %>",
-            "</tbody>",
-            "</table>",
-            "</div>",
-            "</div>",
-            "<% } %>",
-            "</form>",
-            "</div>"
-        ].join("")
-    ),
+    templateRepoDetails: function() {
+        return _.template(
+            `<div class="unified-panel-header" id="panel_header" unselectable="on">
+            <div class="unified-panel-header-inner">Repository information for&nbsp;<strong><%= repository.name %></strong>&nbsp;from&nbsp;<strong><%= repository.owner %></strong><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>
+            </div>
+            <div class="unified-panel-body" id="repository_details" data-tsrid="<%= repository.id %>">
+            <form id="repository_installation" name="install_repository" method="post" action="<%= api_url %>">
+            <input type="hidden" id="repositories" name="<%= repository.id %>" value="ID" />
+            <input type="hidden" id="tool_shed_url" name="tool_shed_url" value="<%= tool_shed %>" />
+            <div class="toolForm">
+            <div class="toolFormTitle">Changeset</div>
+            <div class="toolFormBody changeset">
+            <select id="changeset" name="changeset" style="margin: 5px;">
+            <% _.each(Object.keys(repository.metadata), function(changeset) { %>
+            <% if (changeset == current_changeset) { var selected = "selected "; } else { var selected = ""; } %>
+            <option <%= selected %>value="<%= changeset.split(":")[1] %>"><%= changeset %></option>
+            <% }); %>
+            </select>
+            <input class="btn btn-primary preview-button" data-tsrid="<%= current_metadata.repository.id %>" type="submit" id="install_repository" name="install_repository" value="Install this revision now" />
+            <input class="btn btn-primary preview-button" type="button" id="queue_install" name="queue_install" value="Install this revision later" />
+            <div class="toolParamHelp" style="clear: both;">Please select a revision and review the settings below before installing.</div>
+            </div>
+            </div>
+            <%= shed_tool_conf %>
+            <% if (current_metadata.has_repository_dependencies) { %>
+            <div class="toolFormTitle">Repository dependencies for <strong id="current_changeset"><%= current_changeset %></strong></div>
+            <div class="toolFormBody">
+            <p id="install_repository_dependencies_checkbox">
+            <input type="checkbox" checked id="install_repository_dependencies" />
+            <label for="install_repository_dependencies">Install repository dependencies</label>
+            </p>
+            <% current_metadata.repository_dependency_template = repository_dependency_template; %>
+            <div class="tables container-table" id="repository_dependencies">
+            <div class="expandLink">
+            <a class="toggle_folder" data_target="repository_dependencies_table">
+            Repository dependencies &ndash; <em>installation of these additional repositories is required</em>
+            </a>
+            </div>
+            <%= repository_dependencies_template(current_metadata) %>
+            </div>
+            </div>
+            <% } %>
+            <% if (current_metadata.includes_tool_dependencies) { %>
+            <div class="toolFormTitle">Tool dependencies</div>
+            <div class="toolFormBody">
+            <p id="install_resolver_dependencies_checkbox">
+            <input type="checkbox" checked id="install_resolver_dependencies" />
+            <label for="install_resolver_dependencies">Install resolver dependencies</label>
+            </p>
+            <p id="install_tool_dependencies_checkbox">
+            <input type="checkbox" checked id="install_tool_dependencies" />
+            <label for="install_tool_dependencies">Install tool dependencies</label>
+            </p>
+            <div class="tables container-table" id="tool_dependencies">
+            <div class="expandLink">
+            <a class="toggle_folder" data_target="tool_dependencies_table">
+            Tool dependencies &ndash; <em>repository tools require handling of these dependencies</em>
+            </a>
+            </div>
+            <table class="tables container-table" id="tool_dependencies_table" border="0" cellpadding="2" cellspacing="2" width="100%">
+            <thead>
+            <tr style="display: table-row;" class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">
+            <th style="padding-left: 40px;">Name</th>
+            <th>Version</th>
+            <th>Type</th>
+            </tr>
+            </thead>
+            <tbody id="tool_deps">
+            <% _.each(tool_dependencies[current_changeset], function(dependency) { %>
+            <tr class="datasetRow tool_dependency_row" style="display: table-row;">
+            <td style="padding-left: 40px;">
+            <%= dependency.name %></td>
+            <td><%= dependency.version %></td>
+            <td><%= dependency.type %></td>
+            </tr>
+            <% }); %>
+            </tbody>
+            </table>
+            </div>
+            </div>
+            <% } %>
+            <% if (current_metadata.includes_tools_for_display_in_tool_panel) { %>
+            <div class="toolFormTitle">Tools &ndash; <em>click the name to preview the tool and use the pop-up menu to inspect all metadata</em></div>
+            <div class="toolFormBody">
+            <div class="tables container-table" id="tools_toggle">
+            <table class="tables container-table" id="valid_tools" border="0" cellpadding="2" cellspacing="2" width="100%">
+            <thead>
+            <tr style="display: table-row;" class="datasetRow" parent="0" id="libraryItem-rt-f9cad7b01a472135">
+            <th style="padding-left: 40px;">Name</th>
+            <th>Description</th>
+            <th>Version</th>
+            <th><%= tps_template_global_select({panel_section_dict: panel_section_dict, panel_section_options: panel_section_options}) %></tr>
+            </thead>
+            <tbody id="tools_in_repo">
+            <% _.each(current_metadata.tools, function(tool) { %>
+            <tr id="libraryItem-<%= tool.clean %>" class="tool_row" style="display: table-row;" style="width: 15%">
+            <td style="padding-left: 40px;">
+            <div id="tool-<%= tool.clean %>" class="menubutton split popup" style="float: left;">
+            <a class="tool_form view-info" data-toggle="modal" data-target="toolform_<%= tool.clean %>" data-clean="<%= tool.clean %>" data-guid="<%= tool.guid %>" data-name="<%= tool.name %>" data-desc="<%= tool.description %>"><%= tool["name"] %></a>
+            </div>
+            </td>
+            <td><%= tool.description %></td>
+            <td style="width: 15%"><%= tool.version %></td>
+            <td style="width: 35%" id="tool_tps_<%= tool.clean %>">
+            <%= tps_template_tool_select({tool: tool, panel_section_dict: panel_section_dict, panel_section_options: panel_section_options}) %>
+            </td>
+            </tr>
+            <% }); %>
+            </tbody>
+            </table>
+            </div>
+            </div>
+            <% } %>
+            </form>
+            </div>`
+        );
+    },
 
-    templateRepoDependencies: _.template(
-        [
-            '<div class="toolFormTitle">Repository Dependencies</div>',
-            '<div class="toolFormBody tables container-table" id="repository_dependencies">',
-            "<ul>",
-            "<li>Repository installation requires the following",
-            "<% if (has_repository_dependencies) { %>",
-            "<% _.each(repository_dependencies, function(dependency) { %>",
-            "<% dependency.repository_dependency_template = repository_dependency_template; %>",
-            "<%= repository_dependency_template(dependency) %>",
-            "<% }); %>",
-            "<% } %>",
-            "</li>",
-            "</ul>",
-            "</div>"
-        ].join("")
-    ),
+    templateRepoDependencies: function() {
+        return _.template(
+            `<div class="toolFormTitle">Repository Dependencies</div>
+            <div class="toolFormBody tables container-table" id="repository_dependencies">
+            <ul>
+            <li>Repository installation requires the following
+            <% if (has_repository_dependencies) { %>
+            <% _.each(repository_dependencies, function(dependency) { %>
+            <% dependency.repository_dependency_template = repository_dependency_template; %>
+            <%= repository_dependency_template(dependency) %>
+            <% }); %>
+            <% } %>
+            </li>
+            </ul>
+            </div>`
+        );
+    },
 
-    templateRepoDependency: _.template(
-        [
-            '<li id="metadata_<%= id %>" class="datasetRow repository_dependency_row">',
-            "Repository <b><%= repository.name %></b> revision <b><%= changeset_revision %></b> owned by <b><%= repository.owner %></b>",
-            "<% if (has_repository_dependencies) { %>",
-            '<ul class="child_dependencies">',
-            "<% _.each(repository_dependencies, function(dependency) { %>",
-            "<% dependency.repository_dependency_template = repository_dependency_template; %>",
-            "<%= repository_dependency_template(dependency) %>",
-            "<% }); %>",
-            "</ul>",
-            "<% } %>",
-            "</li>"
-        ].join("")
-    ),
+    templateRepoDependency: function() {
+        return _.template(
+            `<li id="metadata_<%= id %>" class="datasetRow repository_dependency_row">
+            Repository <b><%= repository.name %></b> revision <b><%= changeset_revision %></b> owned by <b><%= repository.owner %></b>
+            <% if (has_repository_dependencies) { %>
+            <ul class="child_dependencies">
+            <% _.each(repository_dependencies, function(dependency) { %>
+            <% dependency.repository_dependency_template = repository_dependency_template; %>
+            <%= repository_dependency_template(dependency) %>
+            <% }); %>
+            </ul>
+            <% } %>
+            </li>`
+        );
+    },
 
-    templateShedToolConf: _.template(
-        [
-            '<div class="toolFormTitle">Shed tool configuration file:</div>',
-            '<div class="toolFormBody">',
-            '<div class="form-row">',
-            '<select name="shed_tool_conf">',
-            "<% _.each(shed_tool_confs.options, function(conf) { %>",
-            '<option value="<%= conf.value %>"><%= conf.label %></option>',
-            "<% }); %>",
-            "</select>",
-            '<div class="toolParamHelp" style="clear: both;">Select the file whose <b>tool_path</b> setting you want used for installing repositories.</div>',
-            "</div>",
-            "</div>"
-        ].join("")
-    ),
+    templateShedToolConf: function() {
+        return _.template(
+            `<div class="toolFormTitle">Shed tool configuration file:</div>
+            <div class="toolFormBody">
+            <div class="form-row">
+            <select name="shed_tool_conf">
+            <% _.each(shed_tool_confs.options, function(conf) { %>
+            <option value="<%= conf.value %>"><%= conf.label %></option>
+            <% }); %>
+            </select>
+            <div class="toolParamHelp" style="clear: both;">Select the file whose <b>tool_path</b> setting you want used for installing repositories.</div>
+            </div>
+            </div>`
+        );
+    },
 
-    templateToolDependency: _.template(
-        [
-            "<% if (has_repository_dependencies) { %>",
-            "<% _.each(repository_dependencies, function(dependency) { %>",
-            "<% if (dependency.includes_tool_dependencies) { %>",
-            "<% dependency.tool_dependency_template = tool_dependency_template %>",
-            "<%= tool_dependency_template(dependency) %>",
-            "<% } %>",
-            "<% }); %>",
-            "<% } %>"
-        ].join("")
-    ),
+    // templateToolDependency: function(){
+    //     return _.template(
+    //         `<% if (has_repository_dependencies) { %>
+    //         <% _.each(repository_dependencies, function(dependency) { %>
+    //         <% if (dependency.includes_tool_dependencies) { %>
+    //         <% dependency.tool_dependency_template = tool_dependency_template %>
+    //         <%= tool_dependency_template(dependency) %>
+    //         <% } %>
+    //         <% }); %>
+    //         <% } %>`
+    //     );
+    // },
 
-    templateGlobalSectionCreate: _.template(
-        [
-            '<div id="tool_panel_section">',
-            '<div class="form-row" id="new_tps">',
-            '<input id="new_tool_panel_section" name="new_tool_panel_section" type="textfield" value="" size="40"/>',
-            '<input class="btn btn-primary global-select-tps-button" type="button" id="select_existing" value="Select existing" />',
-            '<div class="toolParamHelp" style="clear: both;">',
-            "Add a new tool panel section to contain the installed tools (optional).",
-            "</div>",
-            "</div>",
-            "</div>"
-        ].join("")
-    ),
+    templateGlobalSectionCreate: function() {
+        return _.template(
+            `<div id="tool_panel_section">
+            <div class="form-row" id="new_tps">
+            <input id="new_tool_panel_section" name="new_tool_panel_section" type="textfield" value="" size="40"/>
+            <input class="btn btn-primary global-select-tps-button" type="button" id="select_existing" value="Select existing" />
+            <div class="toolParamHelp" style="clear: both;">
+            Add a new tool panel section to contain the installed tools (optional).
+            </div>
+            </div>
+            </div>`
+        );
+    },
 
-    templateGlobalSectionSelect: _.template(
-        [
-            '<div id="tool_panel_section">',
-            '<div class="toolFormTitle">Tool Panel Section</div>',
-            '<div class="toolFormBody">',
-            '<div class="tab-pane" id="select_tps">',
-            '<select name="<%= name %>" id="<%= panel_section_dict.id %>">',
-            "<%= panel_section_options({sections: panel_section_dict.sections}) %>",
-            "</select>",
-            '<input class="btn btn-primary global-create-tps-button" type="button" id="create_new" value="Create new" />',
-            '<div class="toolParamHelp" style="clear: both;">',
-            "Select an existing tool panel section to contain the installed tools (optional).",
-            "</div>",
-            "</div>",
-            "</div>",
-            "</div>"
-        ].join("")
-    ),
+    templateGlobalSectionSelect: function() {
+        return _.template(
+            `<div id="tool_panel_section">
+            <div class="toolFormTitle">Tool Panel Section</div>
+            <div class="toolFormBody">
+            <div class="tab-pane" id="select_tps">
+            <select name="<%= name %>" id="<%= panel_section_dict.id %>">
+            <%= panel_section_options({sections: panel_section_dict.sections}) %>
+            </select>
+            <input class="btn btn-primary global-create-tps-button" type="button" id="create_new" value="Create new" />
+            <div class="toolParamHelp" style="clear: both;">
+            Select an existing tool panel section to contain the installed tools (optional).
+            </div>
+            </div>
+            </div>
+            </div>`
+        );
+    },
 
-    templateToolSectionCreate: _.template(
-        [
-            '<div id="new_tps_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="form-row">',
-            '<input data-toolguid="<%= tool.guid %>" class="tool_panel_section_picker" size="40" name="new_tool_panel_section" id="new_tool_panel_section_<%= tool.clean %>" type="text">',
-            '<input id="per_tool_select_<%= tool.clean %>" class="btn btn-primary select-tps-button" data-toolguid="<%= tool.guid %>" value="Select existing" id="select_existing_<%= tool.clean %>" type="button">',
-            "</div>"
-        ].join("")
-    ),
+    templateToolSectionCreate: function() {
+        return _.template(
+            `<div id="new_tps_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="form-row">
+            <input data-toolguid="<%= tool.guid %>" class="tool_panel_section_picker" size="40" name="new_tool_panel_section" id="new_tool_panel_section_<%= tool.clean %>" type="text">
+            <input id="per_tool_select_<%= tool.clean %>" class="btn btn-primary select-tps-button" data-toolguid="<%= tool.guid %>" value="Select existing" id="select_existing_<%= tool.clean %>" type="button">
+            </div>`
+        );
+    },
 
-    templateToolSectionSelect: _.template(
-        [
-            '<div id="select_tps_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="tps_creator">',
-            '<select default="active" style="width: 30em;" data-toolguid="<%= tool.guid %>" class="tool_panel_section_picker" name="tool_panel_section_id" id="tool_panel_section_select_<%= tool.clean %>">',
-            "<%= panel_section_options({sections: panel_section_dict.sections}) %>",
-            "</select>",
-            '<input id="per_tool_create_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="btn btn-primary create-tps-button" data-toolguid="<%= tool.guid %>" value="Create new" id="create_new_<%= tool.clean %>" type="button">',
-            '<div style="clear: both;" class="toolParamHelp"></div>',
-            "</div>"
-        ].join("")
-    ),
+    templateToolSectionSelect: function() {
+        return _.template(
+            `<div id="select_tps_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="tps_creator">
+            <select default="active" style="width: 30em;" data-toolguid="<%= tool.guid %>" class="tool_panel_section_picker" name="tool_panel_section_id" id="tool_panel_section_select_<%= tool.clean %>">
+            <%= panel_section_options({sections: panel_section_dict.sections}) %>
+            </select>
+            <input id="per_tool_create_<%= tool.clean %>" data-clean="<%= tool.clean %>" class="btn btn-primary create-tps-button" data-toolguid="<%= tool.guid %>" value="Create new" id="create_new_<%= tool.clean %>" type="button">
+            <div style="clear: both;" class="toolParamHelp"></div>
+            </div>`
+        );
+    },
 
-    templatePanelSelectOptions: _.template(
-        [
-            "<% _.each(sections, function(section) { %>",
-            '<option value="<%= section.id %>"><%= section.name %></option>',
-            "<% }); %>"
-        ].join("")
-    )
+    templatePanelSelectOptions: function() {
+        return _.template(
+            `<% _.each(sections, function(section) { %>
+            <option value="<%= section.id %>"><%= section.name %></option>
+            <% }); %>`
+        );
+    }
 });
 
 export default {
diff --git a/client/galaxy/scripts/mvc/toolshed/shed-list-view.js b/client/galaxy/scripts/mvc/toolshed/shed-list-view.js
index b2d9b6ea8bd..e092ffae6f8 100644
--- a/client/galaxy/scripts/mvc/toolshed/shed-list-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/shed-list-view.js
@@ -1,19 +1,11 @@
 import Backbone from "backbone";
+import $ from "jquery";
 import _ from "underscore";
 import _l from "utils/localization";
 import toolshed_model from "mvc/toolshed/toolshed-model";
 import toolshed_util from "mvc/toolshed/util";
 
-var View = Backbone.View.extend({
-    defaults: {
-        tool_sheds: [
-            {
-                url: "https://toolshed.g2.bx.psu.edu/",
-                name: "Galaxy Main Tool Shed"
-            }
-        ]
-    },
-
+var ShedListView = Backbone.View.extend({
     initialize: function(options) {
         this.options = _.defaults(this.options || {}, this.defaults);
         this.model = new toolshed_model.ShedsCollection();
@@ -25,7 +17,7 @@ var View = Backbone.View.extend({
 
     render: function(options) {
         this.options = _.defaults(this.options || {}, options, this.defaults);
-        var toolshed_list_template = this.templateToolshedList;
+        var toolshed_list_template = this.templateToolshedList();
         this.$el.html(
             toolshed_list_template({
                 title: _l("Configured Galaxy Tool Sheds"),
@@ -33,33 +25,29 @@ var View = Backbone.View.extend({
                 queue: toolshed_util.queueLength()
             })
         );
+        $("#center").css("overflow", "auto");
     },
 
-    templateToolshedList: _.template(
-        [
-            '<div class="unified-panel-header" id="panel_header" unselectable="on">',
-            '<div class="unified-panel-header-inner"><%= title %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>',
-            "</div>",
-            '<div class="unified-panel-body" id="list_toolsheds">',
-            '<div class="form-row">',
-            '<table class="grid">',
-            "<% _.each(tool_sheds, function(shed) { %>",
-            '<tr class="libraryTitle">',
-            "<td>",
-            '<div style="float: left; margin-left: 1px;" class="menubutton split">',
-            '<a class="view-info shed-selector" href="#/categories/s/<%= shed.get("url") %>"><%= shed.get("name") %></a>',
-            "</div>",
-            "</td>",
-            "</tr>",
-            "<% }); %>",
-            "</table>",
-            "</div>",
-            '<div style="clear: both"></div>',
-            "</div>"
-        ].join("")
-    )
+    templateToolshedList: function() {
+        return _.template(
+            `<div class='shed-style-container'>
+                <div class='header'>
+                <h2>
+                ${_l("Configured Tool Sheds")}
+                </h2>
+                <span><a href='#/queue'>Repository Queue (<%= queue %>)</a></span>
+                <div style='clear:both;'></div>
+                </div'>
+                <% _.each(tool_sheds, function(shed) { %>
+                    <div>
+                    <a href='#/categories/s/<%= shed.get('url') %>'><%= shed.get('name') %></a>
+                    </div>
+                <% }); %>
+                </div>`
+        );
+    }
 });
 
 export default {
-    ShedListView: View
+    ShedListView: ShedListView
 };
diff --git a/client/galaxy/scripts/mvc/toolshed/workflows-view.js b/client/galaxy/scripts/mvc/toolshed/workflows-view.js
index cf662a3916e..e88192ce711 100644
--- a/client/galaxy/scripts/mvc/toolshed/workflows-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/workflows-view.js
@@ -19,7 +19,7 @@ var View = Backbone.View.extend({
     },
 
     render: function(options) {
-        var workflows_missing_tools = this.templateWorkflows;
+        var workflows_missing_tools = this.templateWorkflows();
         var workflows = this.model.models;
         this.$el.html(
             workflows_missing_tools({
@@ -75,57 +75,57 @@ var View = Backbone.View.extend({
         $("#from_workflow").on("click", this.loadWorkflows);
     },
 
-    templateWorkflows: _.template(
-        [
-            '<div class="unified-panel-header" id="panel_header" unselectable="on">',
-            '<div class="unified-panel-header-inner"><%= title %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>',
-            "</div>",
-            '<style type="text/css">',
-            ".workflow_names, .workflow_tools { list-style-type: none; } ul.workflow_tools, ul.workflow_names {  padding-left: 0px; }",
-            "</style>",
-            '<table id="workflows_missing_tools" class="grid" border="0" cellpadding="2" cellspacing="2" width="100%">',
-            '<thead id="grid-table-header">',
-            "<tr>",
-            '<th class="datasetRow">Workflows</th>',
-            '<th class="datasetRow">Tool IDs</th>',
-            '<th class="datasetRow">Shed</th>',
-            '<th class="datasetRow">Name</th>',
-            '<th class="datasetRow">Owner</th>',
-            '<th class="datasetRow">Actions</th>',
-            "</tr>",
-            "</thead>",
-            "<tbody>",
-            "<% _.each(workflows, function(workflow) { %>",
-            "<tr>",
-            '<td class="datasetRow">',
-            '<ul class="workflow_names">',
-            '<% _.each(workflow.get("workflows"), function(name) { %>',
-            '<li class="workflow_names"><%= name %></li>',
-            "<% }); %>",
-            "</ul>",
-            "</td>",
-            '<td class="datasetRow">',
-            '<ul class="workflow_tools">',
-            '<% _.each(workflow.get("tools"), function(tool) { %>',
-            '<li class="workflow_tools"><%= tool %></li>',
-            "<% }); %>",
-            "</ul>",
-            "</td>",
-            '<td class="datasetRow"><%= workflow.get("shed") %></td>',
-            '<td class="datasetRow"><%= workflow.get("repository") %></td>',
-            '<td class="datasetRow"><%= workflow.get("owner") %></td>',
-            '<td class="datasetRow">',
-            '<ul class="workflow_tools">',
-            '<li class="workflow_tools">',
-            '<input type="button" class="show_wf_repo btn btn-primary" data-shed="<%= workflow.get("shed") %>" data-owner="<%= workflow.get("owner") %>" data-repo="<%= workflow.get("repository") %>" data-toolids="<%= workflow.get("tools").join(",") %>" value="Show Repository" /></li>',
-            "</ul>",
-            "</td>",
-            "</tr>",
-            "<% }); %>",
-            "</ul>",
-            "</div>"
-        ].join("")
-    )
+    templateWorkflows: function() {
+        _.template(
+            `<div class="unified-panel-header" id="panel_header" unselectable="on">
+            <div class="unified-panel-header-inner"><%= title %><a class="ml-auto" href="#/queue">Repository Queue (<%= queue %>)</a></div>
+            </div>
+            <style type="text/css">
+            .workflow_names, .workflow_tools { list-style-type: none; } ul.workflow_tools, ul.workflow_names {  padding-left: 0px; }
+            </style>
+            <table id="workflows_missing_tools" class="grid" border="0" cellpadding="2" cellspacing="2" width="100%">
+            <thead id="grid-table-header">
+            <tr>
+            <th class="datasetRow">Workflows</th>
+            <th class="datasetRow">Tool IDs</th>
+            <th class="datasetRow">Shed</th>
+            <th class="datasetRow">Name</th>
+            <th class="datasetRow">Owner</th>
+            <th class="datasetRow">Actions</th>
+            </tr>
+            </thead>
+            <tbody>
+            <% _.each(workflows, function(workflow) { %>
+            <tr>
+            <td class="datasetRow">
+            <ul class="workflow_names">
+            <% _.each(workflow.get("workflows"), function(name) { %>
+            <li class="workflow_names"><%= name %></li>
+            <% }); %>
+            </ul>
+            </td>
+            <td class="datasetRow">
+            <ul class="workflow_tools">
+            <% _.each(workflow.get("tools"), function(tool) { %>
+            <li class="workflow_tools"><%= tool %></li>
+            <% }); %>
+            </ul>
+            </td>
+            <td class="datasetRow"><%= workflow.get("shed") %></td>
+            <td class="datasetRow"><%= workflow.get("repository") %></td>
+            <td class="datasetRow"><%= workflow.get("owner") %></td>
+            <td class="datasetRow">
+            <ul class="workflow_tools">
+            <li class="workflow_tools">
+            <input type="button" class="show_wf_repo btn btn-primary" data-shed="<%= workflow.get("shed") %>" data-owner="<%= workflow.get("owner") %>" data-repo="<%= workflow.get("repository") %>" data-toolids="<%= workflow.get("tools").join(",") %>" value="Show Repository" /></li>
+            </ul>
+            </td>
+            </tr>
+            <% }); %>
+            </ul>
+            </div>`
+        );
+    }
 });
 
 export default {
diff --git a/client/galaxy/scripts/mvc/tours.js b/client/galaxy/scripts/mvc/tours.js
index 8bf7559d064..eaca3c05fce 100644
--- a/client/galaxy/scripts/mvc/tours.js
+++ b/client/galaxy/scripts/mvc/tours.js
@@ -12,7 +12,7 @@ import { getAppRoot } from "onload/loadConfig";
 import "libs/bootstrap-tour";
 
 // bootstrap-tour configures a window.Tour object; keep a local ref.
-let Tour = window.Tour;
+const Tour = window.Tour;
 
 // For buttons to show, we need to add them to bootstrap/popper's sanitizing filters.
 $.fn.tooltip.Constructor.Default.whiteList.button = ["data-role"];
@@ -206,10 +206,10 @@ export var ToursView = Backbone.View.extend({
 });
 
 export function giveTourWithData(data) {
-    let hookedTourData = hooked_tour_from_data(data);
+    const hookedTourData = hooked_tour_from_data(data);
     window.sessionStorage.setItem("activeGalaxyTour", JSON.stringify(data));
     // Store tour steps in sessionStorage to easily persist w/o hackery.
-    let tour = new Tour(_.extend({ steps: hookedTourData.steps }, tour_opts));
+    const tour = new Tour(_.extend({ steps: hookedTourData.steps }, tour_opts));
     // Always clean restart, since this is a new, explicit execution.
     tour.init();
     tour.goTo(0);
diff --git a/client/galaxy/scripts/mvc/ui/error-modal.js b/client/galaxy/scripts/mvc/ui/error-modal.js
index 6318e2087fc..f38414683ac 100644
--- a/client/galaxy/scripts/mvc/ui/error-modal.js
+++ b/client/galaxy/scripts/mvc/ui/error-modal.js
@@ -35,7 +35,7 @@ var DETAILS_MSG = _l("The following information can assist the developers in fin
 
 /** private helper that builds the modal and handles adding details */
 function _errorModal(message, title, details) {
-    let Galaxy = getGalaxyInstance();
+    const Galaxy = getGalaxyInstance();
     // create and return the modal, adding details button only if needed
     Galaxy.modal.show({
         title: title,
@@ -75,7 +75,7 @@ function errorModal(message, title, details) {
         return;
     }
 
-    let Galaxy = getGalaxyInstance();
+    const Galaxy = getGalaxyInstance();
     message = _l(message);
     title = _l(title) || _l("Error:");
     if (Galaxy && Galaxy.modal) {
@@ -113,7 +113,7 @@ function ajaxErrorModal(model, xhr, options, message, title) {
 
 /** build details which may help debugging the ajax call */
 function _ajaxDetails(model, xhr, options) {
-    let Galaxy = getGalaxyInstance();
+    const Galaxy = getGalaxyInstance();
     return {
         //TODO: still can't manage Raven id
         raven: _.result(window.Raven, "lastEventId"),
diff --git a/client/galaxy/scripts/mvc/ui/popup-menu.js b/client/galaxy/scripts/mvc/ui/popup-menu.js
index 5e27f02dca1..6166a6e078e 100644
--- a/client/galaxy/scripts/mvc/ui/popup-menu.js
+++ b/client/galaxy/scripts/mvc/ui/popup-menu.js
@@ -5,7 +5,7 @@
 import $ from "jquery";
 import _ from "underscore";
 import Backbone from "backbone";
-var PopupMenu = Backbone.View.extend({
+const PopupMenu = Backbone.View.extend({
     //TODO: maybe better as singleton off the Galaxy obj
     /** Cache the desired button element and options, set up the button click handler
      *  NOTE: attaches this view as HTML/jQ data on the button for later use.
@@ -20,11 +20,10 @@ var PopupMenu = Backbone.View.extend({
         this.$button.data("popupmenu", this);
 
         // set up button click -> open menu behavior
-        var menu = this;
         this.$button.click(event => {
             // if there's already a menu open, remove it
             $(".popmenu-wrapper").remove();
-            menu._renderAndShow(event);
+            this._renderAndShow(event);
             return false;
         });
     },
@@ -51,23 +50,18 @@ var PopupMenu = Backbone.View.extend({
 
         // set up behavior on each link/anchor elem
         if (this.options.length) {
-            var menu = this;
-            //precondition: there should be one option per li
-            this.$el.find("li").each(function(i, li) {
-                var option = menu.options[i];
-
+            this.$(".popupmenu-option").each((i, el) => {
+                const option = this.options[i];
                 // if the option has 'func', call that function when the anchor is clicked
                 if (option.func) {
-                    $(this)
-                        .children("a.popupmenu-option")
-                        .click(event => {
-                            option.func.call(menu, event, option);
-                            // We must preventDefault otherwise clicking "cancel"
-                            // on a purge or something still navigates and causes
-                            // the action.
-                            event.preventDefault();
-                            // bubble up so that an option click will call the close behavior
-                        });
+                    $(el).click(event => {
+                        option.func.call(this, event, option);
+                        // We must preventDefault otherwise clicking "cancel"
+                        // on a purge or something still navigates and causes
+                        // the action.
+                        event.preventDefault();
+                        // bubble up so that an option click will call the close behavior
+                    });
                 }
             });
         }
@@ -75,42 +69,33 @@ var PopupMenu = Backbone.View.extend({
     },
 
     template: function(id, options) {
-        return ['<ul id="', id, '-menu" class="dropdown-menu">', this._templateOptions(options), "</ul>"].join("");
+        return `<div id="${id}-menu" class="dropdown-menu">
+                    ${this._templateOptions(options)}
+                </div>`;
     },
 
     _templateOptions: function(options) {
         if (!options.length) {
-            return "<li>(no options)</li>";
+            return '<div class="dropdown-header">(no options)</div>';
         }
         return _.map(options, option => {
             if (option.divider) {
-                return '<li class="divider"></li>';
+                return '<div class="popupmenu-option dropdown-divider"/>';
             } else if (option.header) {
-                return ['<li class="head"><a href="javascript:void(0);">', option.html, "</a></li>"].join("");
+                return `<div class="popupmenu-option dropdown-header">${option.html}</div>`;
             }
-            var href = option.href || "javascript:void(0);";
-            var target = option.target ? ` target="${option.target}"` : "";
-
-            var check = option.checked ? '<span class="fa fa-check"></span>' : "";
-
-            return [
-                '<li><a class="popupmenu-option" href="',
-                href,
-                '"',
-                target,
-                ">",
-                check,
-                option.html,
-                "</a></li>"
-            ].join("");
+            const href = option.href || "javascript:void(0);";
+            const target = option.target ? `target="${option.target}"` : "";
+            const check = option.checked ? '<span class="fa fa-check mr-1"/>' : "";
+            return `<a class="popupmenu-option dropdown-item" href="${href}" ${target}>${check}${option.html}</a>`;
         }).join("");
     },
 
     // get the absolute position/offset for the menu
     _getShownPosition: function(clickEvent) {
         // display menu horiz. centered on click...
-        var menuWidth = this.$el.width();
-        var x = clickEvent.pageX - menuWidth / 2;
+        const menuWidth = this.$el.width();
+        let x = clickEvent.pageX - menuWidth / 2;
 
         // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )
         x = Math.min(x, $(document).scrollLeft() + $(window).width() - menuWidth - 5);
@@ -124,11 +109,14 @@ var PopupMenu = Backbone.View.extend({
     // bind an event handler to all available frames so that when anything is clicked
     // the menu is removed from the DOM and the event handler unbinds itself
     _setUpCloseBehavior: function() {
-        var menu = this;
         //TODO: alternately: focus hack, blocking overlay, jquery.blockui
 
         // function to close popup and unbind itself
-        function closePopup(event) {
+        const closePopup = event => {
+            //do nothing if header item is clicked
+            if (event.target.classList.contains("dropdown-header")) {
+                return;
+            }
             $(document).off("click.close_popup");
             try {
                 if (window && window.parent !== window) {
@@ -147,19 +135,19 @@ var PopupMenu = Backbone.View.extend({
                     console.debug(err);
                 }
             }
-            menu.remove();
-        }
+            this.remove();
+        };
 
-        $("html").one("click.close_popup", closePopup);
+        $("html").on("click.close_popup", closePopup);
         try {
             if (window && window.parent !== window) {
                 $(window.parent.document)
                     .find("html")
-                    .one("click.close_popup", closePopup);
+                    .on("click.close_popup", closePopup);
             } else {
                 $("iframe#galaxy_main")
                     .contents()
-                    .one("click.close_popup", closePopup);
+                    .on("click.close_popup", closePopup);
             }
         } catch (err) {
             if (err instanceof DOMException) {
@@ -190,7 +178,7 @@ var PopupMenu = Backbone.View.extend({
 
     // search for a menu option by its html
     findIndexByHtml: function(html) {
-        for (var i = 0; i < this.options.length; i++) {
+        for (let i = 0; i < this.options.length; i++) {
             if (_.has(this.options[i], "html") && this.options[i].html === html) {
                 return i;
             }
@@ -213,134 +201,5 @@ PopupMenu.create = function _create($button, options) {
     return new PopupMenu($button, options);
 };
 
-// -----------------------------------------------------------------------------
-// the following class functions are bridges from the original make_popupmenu and make_popup_menus
-// to the newer backbone.js PopupMenu
-
-/** Create a PopupMenu from simple map initial_options activated by clicking button_element.
- *      Converts initial_options to object array used by PopupMenu.
- *  @param {jQuery|DOMElement} button_element element which, when clicked, activates menu
- *  @param {Object} initial_options map of key -> values, where
- *      key is option text, value is fn to call when option is clicked
- *  @returns {PopupMenu} the PopupMenu created
- */
-PopupMenu.make_popupmenu = (button_element, initial_options) => {
-    var convertedOptions = [];
-    _.each(initial_options, (optionVal, optionKey) => {
-        var newOption = { html: optionKey };
-
-        // keys with null values indicate: header
-        if (optionVal === null) {
-            // !optionVal? (null only?)
-            newOption.header = true;
-
-            // keys with function values indicate: a menu option
-        } else if ($.type(optionVal) === "function") {
-            newOption.func = optionVal;
-        }
-        //TODO:?? any other special optionVals?
-        // there was no divider option originally
-        convertedOptions.push(newOption);
-    });
-    return new PopupMenu($(button_element), convertedOptions);
-};
-
-/** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.
- *  @param {jQuery} $parent the element that contains the links to convert to options
- *  @param {String} selector jq selector string to find links
- *  @returns {Object[]} the options array to initialize a PopupMenu
- */
-//TODO: lose parent and selector, pass in array of links, use map to return options
-PopupMenu.convertLinksToOptions = ($parent, selector) => {
-    $parent = $($parent);
-    selector = selector || "a";
-    var options = [];
-    $parent.find(selector).each((elem, i) => {
-        var option = {};
-        var $link = $(elem);
-
-        // convert link text to the option text (html) and the href into the option func
-        option.html = $link.text();
-        if ($link.attr("href")) {
-            var linkHref = $link.attr("href");
-            var linkTarget = $link.attr("target");
-            var confirmText = $link.attr("confirm");
-
-            option.func = () => {
-                // if there's a "confirm" attribute, throw up a confirmation dialog, and
-                //  if the user cancels - do nothing
-                if (confirmText && !confirm(confirmText)) {
-                    return;
-                }
-
-                // if there's no confirm attribute, or the user accepted the confirm dialog:
-                switch (linkTarget) {
-                    // relocate the center panel
-                    case "_parent":
-                        window.parent.location = linkHref;
-                        break;
-
-                    // relocate the entire window
-                    case "_top":
-                        window.top.location = linkHref;
-                        break;
-
-                    // relocate this panel
-                    default:
-                        window.location = linkHref;
-                }
-            };
-        }
-        options.push(option);
-    });
-    return options;
-};
-
-/** Create a single popupmenu from existing DOM button and anchor elements
- *  @param {jQuery} $buttonElement the element that when clicked will open the menu
- *  @param {jQuery} $menuElement the element that contains the anchors to convert into a menu
- *  @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options
- *  @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu
- */
-PopupMenu.fromExistingDom = ($buttonElement, $menuElement, menuElementLinkSelector) => {
-    $buttonElement = $($buttonElement);
-    $menuElement = $($menuElement);
-    var options = PopupMenu.convertLinksToOptions($menuElement, menuElementLinkSelector);
-    // we're done with the menu (having converted it to an options map)
-    $menuElement.remove();
-    return new PopupMenu($buttonElement, options);
-};
-
-/** Create all popupmenus within a document or a more specific element
- *  @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)
- *  @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to "div[popupmenu]")
- *  @param {Function} buttonSelectorBuildFn the function to build the jq button selector.
- *      Will be passed $menuElement, parent.
- *      (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )
- *  @returns {PopupMenu[]} array of popupmenus created
- */
-PopupMenu.make_popup_menus = (parent, menuSelector, buttonSelectorBuildFn) => {
-    parent = parent || document;
-    // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'
-    //  which contains the id of the button that activates the menu
-    menuSelector = menuSelector || "div[popupmenu]";
-    // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button
-    buttonSelectorBuildFn = buttonSelectorBuildFn || (($menuElement, parent) => `#${$menuElement.attr("popupmenu")}`);
-
-    // aggregate and return all PopupMenus
-    var popupMenusCreated = [];
-    $(parent)
-        .find(menuSelector)
-        .each(function() {
-            var $menuElement = $(this);
-
-            var $buttonElement = $(parent).find(buttonSelectorBuildFn($menuElement, parent));
-
-            popupMenusCreated.push(PopupMenu.fromDom($buttonElement, $menuElement));
-            $buttonElement.addClass("popup");
-        });
-    return popupMenusCreated;
-};
-
 // =============================================================================
 export default PopupMenu;
diff --git a/client/galaxy/scripts/mvc/ui/ui-buttons.js b/client/galaxy/scripts/mvc/ui/ui-buttons.js
index e4612492d8f..512d6a3ec52 100644
--- a/client/galaxy/scripts/mvc/ui/ui-buttons.js
+++ b/client/galaxy/scripts/mvc/ui/ui-buttons.js
@@ -262,7 +262,7 @@ var ButtonMenu = Backbone.View.extend({
                 .html(options.title);
         this.$menu && this.$menu.remove();
         if (this.collection.length > 0) {
-            this.$menu = $("<ul/>")
+            this.$menu = $("<div/>")
                 .addClass("menu dropdown-menu dropdown-menu-right")
                 .addClass(`pull-${this.model.get("pull")}`)
                 .attr("role", "menu");
@@ -290,8 +290,8 @@ var ButtonMenu = Backbone.View.extend({
                             suboptions.onclick();
                         }
                     });
-                this.$menu.append($("<li/>").append($link));
-                suboptions.divider && this.$menu.append($("<li/>").addClass("divider"));
+                this.$menu.append($link);
+                suboptions.divider && this.$menu.append($("<div/>").addClass("divider"));
             }
         });
     },
diff --git a/client/galaxy/scripts/mvc/ui/ui-frames.js b/client/galaxy/scripts/mvc/ui/ui-frames.js
index cc01c957fd3..86ba1e7795d 100644
--- a/client/galaxy/scripts/mvc/ui/ui-frames.js
+++ b/client/galaxy/scripts/mvc/ui/ui-frames.js
@@ -156,7 +156,7 @@ var View = Backbone.View.extend({
      *              argument that is the frame's content DOM element
      */
     add: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (this.frame_counter >= this.options.frame_max) {
             Galaxy.modal.show({
                 title: _l("Warning"),
diff --git a/client/galaxy/scripts/mvc/ui/ui-misc.js b/client/galaxy/scripts/mvc/ui/ui-misc.js
index 1e83c10575b..45727ff342f 100644
--- a/client/galaxy/scripts/mvc/ui/ui-misc.js
+++ b/client/galaxy/scripts/mvc/ui/ui-misc.js
@@ -257,13 +257,13 @@ export var Upload = Backbone.View.extend({
  * what we need where we need it, allowing for better package optimization.
  */
 
-export let Button = Buttons.Button;
-export let ButtonCheck = Buttons.ButtonCheck;
-export let ButtonMenu = Buttons.ButtonMenu;
-export let ButtonLink = Buttons.ButtonLink;
-export let Checkbox = Options.Checkbox;
-export let RadioButton = Options.RadioButton;
-export let Radio = Options.Radio;
+export const Button = Buttons.Button;
+export const ButtonCheck = Buttons.ButtonCheck;
+export const ButtonMenu = Buttons.ButtonMenu;
+export const ButtonLink = Buttons.ButtonLink;
+export const Checkbox = Options.Checkbox;
+export const RadioButton = Options.RadioButton;
+export const Radio = Options.Radio;
 export { Select, Slider, Drilldown };
 
 export default {
diff --git a/client/galaxy/scripts/mvc/ui/ui-modal.js b/client/galaxy/scripts/mvc/ui/ui-modal.js
index 6f494c74a91..25dc0aa7679 100644
--- a/client/galaxy/scripts/mvc/ui/ui-modal.js
+++ b/client/galaxy/scripts/mvc/ui/ui-modal.js
@@ -55,6 +55,7 @@ export var View = Backbone.View.extend({
                 this.hide(true);
             });
         }
+        this.$el.find(".title").focus();
     },
 
     /**
@@ -80,6 +81,9 @@ export var View = Backbone.View.extend({
         // link elements
         this.$header = this.$(".modal-header");
         this.$dialog = this.$(".modal-dialog");
+        if (this.options.extra_class) {
+            this.$dialog.addClass(this.options.extra_class);
+        }
         this.$body = this.$(".modal-body");
         this.$footer = this.$(".modal-footer");
         this.$backdrop = this.$(".modal-backdrop");
@@ -195,7 +199,7 @@ export var View = Backbone.View.extend({
             '<div class="modal-dialog">' +
             '<div class="modal-content">' +
             '<div class="modal-header">' +
-            '<h4 class="title"/>' +
+            '<h4 class="title" tabindex="0"/>' +
             "</div>" +
             '<div class="modal-body"/>' +
             '<div class="modal-footer">' +
diff --git a/client/galaxy/scripts/mvc/ui/ui-options.js b/client/galaxy/scripts/mvc/ui/ui-options.js
index 03fe661287a..d8cc303e002 100644
--- a/client/galaxy/scripts/mvc/ui/ui-options.js
+++ b/client/galaxy/scripts/mvc/ui/ui-options.js
@@ -298,7 +298,7 @@ RadioButton.View = Base.extend({
 
     /** Main template function */
     _template: function() {
-        return $("<div/>").addClass("btn-group ui-radiobutton d-flex");
+        return $("<div/>").addClass("btn-group ui-radiobutton");
     }
 });
 
diff --git a/client/galaxy/scripts/mvc/ui/ui-popover.js b/client/galaxy/scripts/mvc/ui/ui-popover.js
index 151be0c2694..009360982a9 100644
--- a/client/galaxy/scripts/mvc/ui/ui-popover.js
+++ b/client/galaxy/scripts/mvc/ui/ui-popover.js
@@ -21,7 +21,7 @@ export default Backbone.View.extend({
      * Show popover
      */
     show: function($content) {
-        let btn = "<i class='fa fa-times-circle'/>";
+        const btn = "<i class='fa fa-times-circle'/>";
         $(this.$target).popover({
             title: `${this.options.title} ${btn}`,
             placement: this.options.placement,
@@ -33,7 +33,7 @@ export default Backbone.View.extend({
 
         // add event to hide if click is outside of popup and not on container
         var self = this;
-        let $popover = $(this.$target.data("bs.popover").tip);
+        const $popover = $(this.$target.data("bs.popover").tip);
         $popover.find(".popover-header > i").on("click", () => this.hide());
         $("body").on(`mousedown.${this.uid}`, e => {
             if (!$($popover).is(e.target) && $($popover).has(e.target).length === 0) {
diff --git a/client/galaxy/scripts/mvc/ui/ui-rules-edit.js b/client/galaxy/scripts/mvc/ui/ui-rules-edit.js
index 74f36d4ae17..8ae520efacb 100644
--- a/client/galaxy/scripts/mvc/ui/ui-rules-edit.js
+++ b/client/galaxy/scripts/mvc/ui/ui-rules-edit.js
@@ -2,7 +2,6 @@ import Backbone from "backbone";
 import { getAppRoot } from "onload/loadConfig";
 import axios from "axios";
 import _l from "utils/localization";
-// import Utils from "utils/utils";
 import Ui from "mvc/ui/ui-misc";
 import Vue from "vue";
 import ListCollectionCreator from "mvc/collection/list-collection-creator";
@@ -12,15 +11,12 @@ import RulesDisplay from "components/RulesDisplay.vue";
  * Bridge rule based builder and the tool form.
  */
 var View = Backbone.View.extend({
-    // initialize
     initialize: function(options) {
-        // link this
-        this.options = options;
+        this.model = new Backbone.Model();
         this.target = options.target;
-        this.reset = null;
         const view = this;
 
-        // create insert new list element button
+        // create insert edit button
         this.browse_button = new Ui.Button({
             title: _l("Edit"),
             icon: "fa fa-edit",
@@ -76,7 +72,7 @@ var View = Backbone.View.extend({
     _showRuleEditor: function(elements) {
         const elementsType = "collection_contents";
         const importType = "collections";
-        let value = this._value;
+        const value = this._value;
         const options = {
             saveRulesFn: rules => this._handleRulesSave(rules),
             initialRules: value
@@ -105,9 +101,8 @@ var View = Backbone.View.extend({
         `;
     },
 
-    /** Return/Set currently selected genomespace filename */
+    /** Return/Set current value */
     value: function(new_value) {
-        // check if new_value is defined
         if (new_value !== undefined) {
             this._setValue(new_value);
         } else {
@@ -115,33 +110,31 @@ var View = Backbone.View.extend({
         }
     },
 
-    // update
+    /** Update input element options */
     update: function(input_def) {
         this.target = input_def.target;
     },
 
-    // get value
+    /** Returns current value */
     _getValue: function() {
         return this._value;
     },
 
-    // set value
+    /** Sets current value */
     _setValue: function(new_value) {
         if (new_value) {
             if (typeof new_value == "string") {
                 new_value = JSON.parse(new_value);
             }
             this._value = new_value;
+            this.model.trigger("error", null);
             this.trigger("change");
             this.instance.inputRules = new_value;
-            if (this.reset) {
-                this.reset();
-                this.reset = null;
-            }
         }
     },
 
-    validate: function(reset) {
+    /** Validate input element value */
+    validate: function() {
         const value = this._value;
         let message = null;
         if (!value || value.rules.length === 0) {
@@ -149,15 +142,14 @@ var View = Backbone.View.extend({
         } else if (value.mapping.length === 0) {
             message = "No collection identifiers defined, specify at least one collection identifier.";
         } else {
-            for (let rule of value.rules) {
+            for (const rule of value.rules) {
                 if (rule.error) {
                     message = "One or more rules in error.";
                     break;
                 }
             }
         }
-        this.reset = reset;
-        return { valid: !message, message: message };
+        return message;
     }
 });
 
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-content.js b/client/galaxy/scripts/mvc/ui/ui-select-content.js
index 3f3aae33364..d9baa250c59 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-content.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-content.js
@@ -8,15 +8,16 @@ import Select from "mvc/ui/ui-select-default";
 import { getGalaxyInstance } from "app";
 
 /** Batch mode variations */
-var Batch = { DISABLED: "disabled", ENABLED: "enabled", LINKED: "linked" };
+const Batch = { DISABLED: "disabled", ENABLED: "enabled", LINKED: "linked" };
 
 /** List of available content selectors options */
-var Configurations = {
+const Configurations = {
     data: [
         {
             src: "hda",
             icon: "fa-file-o",
             tooltip: _l("Single dataset"),
+            library: true,
             multiple: false,
             batch: Batch.DISABLED
         },
@@ -122,9 +123,9 @@ var Configurations = {
 };
 
 /** View for hda and hdca content selector ui elements */
-var View = Backbone.View.extend({
+const View = Backbone.View.extend({
     initialize: function(options) {
-        var self = this;
+        const self = this;
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -157,7 +158,7 @@ var View = Backbone.View.extend({
         };
 
         // add drag-drop event handlers
-        let element = this.$el.get(0);
+        const element = this.$el.get(0);
         element.addEventListener("dragenter", e => {
             this.lastenter = e.target;
             self.$el.addClass("ui-dragover");
@@ -171,15 +172,15 @@ var View = Backbone.View.extend({
         element.addEventListener("drop", e => {
             e.preventDefault();
             try {
-                let drop_data = JSON.parse(e.dataTransfer.getData("text"))[0];
+                const drop_data = JSON.parse(e.dataTransfer.getData("text"))[0];
                 this._handleDropValues(drop_data);
             } catch (e) {
                 this._handleDropStatus("danger");
             }
         });
 
-        // track current history elements
-        this.history = {};
+        // track current cache elements
+        this.cache = {};
 
         // add listeners
         this.listenTo(this.model, "change:data", this._changeData, this);
@@ -223,19 +224,20 @@ var View = Backbone.View.extend({
 
     /** Return the currently selected dataset values */
     value: function(new_value) {
-        let galaxy = getGalaxyInstance();
+        const galaxy = getGalaxyInstance();
         new_value !== undefined && this.model.set("value", new_value);
-        var current = this.model.get("current");
+        const current = this.model.get("current");
         if (this.config[current]) {
-            var id_list = this.fields[current].value();
+            let id_list = this.fields[current].value();
             if (id_list !== null) {
                 id_list = $.isArray(id_list) ? id_list : [id_list];
                 if (id_list.length > 0) {
-                    var result = this._batch({ values: [] });
-                    for (var i in id_list) {
-                        var details = this.history[`${id_list[i]}_${this.config[current].src}`];
+                    const result = this._batch({ values: [] });
+                    for (const i in id_list) {
+                        const details = this.cache[`${id_list[i]}_${this.config[current].src}`];
                         if (details) {
-                            result.values.push(details);
+                            const unpatchedValue = this._unpatchValue(details);
+                            result.values.push(unpatchedValue);
                         } else {
                             galaxy.emit.debug(
                                 "ui-select-content::value()",
@@ -256,9 +258,9 @@ var View = Backbone.View.extend({
 
     /** Change of current select field */
     _changeCurrent: function() {
-        var self = this;
+        const self = this;
         _.each(this.fields, (field, i) => {
-            let cnf = self.config[i];
+            const cnf = self.config[i];
             if (self.model.get("current") == i) {
                 field.$el.show();
                 _.each(self.$batch, ($batchfield, batchmode) => {
@@ -268,7 +270,7 @@ var View = Backbone.View.extend({
                         $batchfield.hide();
                     }
                 });
-                if (cnf.showdialog) {
+                if (cnf.src == "hda") {
                     self.button_dialog.show();
                 } else {
                     self.button_dialog.hide();
@@ -287,11 +289,11 @@ var View = Backbone.View.extend({
 
     /** Change of type */
     _changeType: function() {
-        let self = this;
-        let galaxy = getGalaxyInstance();
+        const self = this;
+        const galaxy = getGalaxyInstance();
 
         // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]
-        var config_id =
+        const config_id =
             (this.model.get("flavor") ? `${this.model.get("flavor")}_` : "") +
             String(this.model.get("type")) +
             (this.model.get("multiple") ? "_multiple" : "");
@@ -303,9 +305,9 @@ var View = Backbone.View.extend({
         }
 
         // prepare extension component of error message
-        var data = self.model.get("data");
-        var extensions = Utils.textify(this.model.get("extensions"));
-        var src_labels = this.model.get("src_labels");
+        const data = self.model.get("data");
+        const extensions = Utils.textify(this.model.get("extensions"));
+        const src_labels = this.model.get("src_labels");
 
         // build radio button for data selectors
         this.fields = [];
@@ -346,23 +348,23 @@ var View = Backbone.View.extend({
             tooltip: "Browse Datasets",
             cls: "ml-2",
             onclick: () => {
-                let current = this.model.get("current");
-                let cnf = this.config[current];
+                const current = this.model.get("current");
+                const cnf = this.config[current];
                 galaxy.data.dialog(
                     response => {
                         this._handleDropValues(response, false);
                     },
                     {
                         multiple: cnf.multiple,
-                        format: null,
-                        library: false
+                        library: !!cnf.library,
+                        format: null
                     }
                 );
             }
         });
 
         // append views
-        let $fields = $("<div/>").addClass("w-100");
+        const $fields = $("<div/>").addClass("w-100");
         this.$el
             .empty()
             .addClass("d-flex flex-row")
@@ -382,7 +384,7 @@ var View = Backbone.View.extend({
 
     /** Change of wait flag */
     _changeWait: function() {
-        var self = this;
+        const self = this;
         _.each(this.fields, field => {
             field[self.model.get("wait") ? "wait" : "unwait"]();
         });
@@ -390,9 +392,9 @@ var View = Backbone.View.extend({
 
     /** Change of available options */
     _changeData: function() {
-        var options = this.model.get("data");
-        var self = this;
-        var select_options = {};
+        const options = this.model.get("data");
+        const self = this;
+        const select_options = {};
         _.each(options, (items, src) => {
             select_options[src] = [];
             _.each(items, item => {
@@ -401,9 +403,10 @@ var View = Backbone.View.extend({
                     keep: item.keep,
                     label: `${item.hid}: ${item.name}`,
                     value: item.id,
+                    origin: item.origin,
                     tags: item.tags
                 });
-                self.history[`${item.id}_${src}`] = item;
+                self.cache[`${item.id}_${src}`] = item;
             });
         });
         _.each(this.config, (c, i) => {
@@ -413,19 +416,19 @@ var View = Backbone.View.extend({
 
     /** Change of incoming value */
     _changeValue: function() {
-        var new_value = this.model.get("value");
+        const new_value = this.model.get("value");
         if (new_value && new_value.values && new_value.values.length > 0) {
             // create list with content ids
-            var list = [];
+            const list = [];
             _.each(new_value.values, value => {
                 list.push(value.id);
             });
             // sniff first suitable field type from config list
-            var src = new_value.values[0].src;
-            var multiple = new_value.values.length > 1;
-            for (var i = 0; i < this.config.length; i++) {
-                var field = this.fields[i];
-                var c = this.config[i];
+            const src = new_value.values[0].src;
+            const multiple = new_value.values.length > 1;
+            for (let i = 0; i < this.config.length; i++) {
+                const field = this.fields[i];
+                const c = this.config[i];
                 if (c.src == src && [multiple, true].indexOf(c.multiple) !== -1) {
                     this.model.set("current", i);
                     field.value(list);
@@ -444,27 +447,50 @@ var View = Backbone.View.extend({
         return v.history_content_type == "dataset_collection" ? "hdca" : "hda";
     },
 
+    /** Library datasets are displayed and selected together with history datasets **/
+    _patchValue: function(v) {
+        if (v.src == "ldda") {
+            v.src = "hda";
+            v.origin = "ldda";
+            v.id = `${v.origin}${v.id}`;
+        }
+    },
+
+    /** Restores original value e.g. after patching library datasets **/
+    _unpatchValue: function(v) {
+        if (v.origin) {
+            const d = Object.assign({}, v);
+            d.id = d.id.substr(d.origin.length);
+            d.src = d.origin;
+            return d;
+        }
+        return v;
+    },
+
     /** Add values from drag/drop */
     _handleDropValues: function(drop_data, drop_partial = true) {
-        let data = this.model.get("data");
-        let current = this.model.get("current");
-        let config = this.config[current];
-        let field = this.fields[current];
+        const self = this;
+        const data = this.model.get("data");
+        const current = this.model.get("current");
+        const config = this.config[current];
+        const field = this.fields[current];
         if (data) {
-            let values = $.isArray(drop_data) ? drop_data : [drop_data];
+            const values = $.isArray(drop_data) ? drop_data : [drop_data];
             if (values.length > 0) {
                 let data_changed = false;
                 _.each(values, v => {
-                    let new_id = v.id;
-                    let new_src = (v.src = this._getSource(v));
-                    let new_value = { id: new_id, src: new_src };
+                    self._patchValue(v);
+                    const new_id = v.id;
+                    const new_src = (v.src = this._getSource(v));
+                    const new_value = { id: new_id, src: new_src };
                     if (!_.findWhere(data[new_src], new_value)) {
                         data_changed = true;
                         data[new_src].push({
                             id: new_id,
                             src: new_src,
                             hid: v.hid || "Selected",
-                            name: v.hid ? v.name : new_id,
+                            name: v.name ? v.name : new_id,
+                            origin: v.origin,
                             keep: true,
                             tags: []
                         });
@@ -473,10 +499,10 @@ var View = Backbone.View.extend({
                 if (data_changed) {
                     this._changeData();
                 }
-                let first_id = values[0].id;
-                let first_src = values[0].src;
+                const first_id = values[0].id;
+                const first_src = values[0].src;
                 if (config.src == first_src && drop_partial) {
-                    var current_value = field.value();
+                    let current_value = field.value();
                     if (current_value && config.multiple) {
                         _.each(values, v => {
                             if (current_value.indexOf(v.id) == -1) {
@@ -499,7 +525,7 @@ var View = Backbone.View.extend({
 
     /** Highlight drag result */
     _handleDropStatus: function(status) {
-        var self = this;
+        const self = this;
         this.$el.removeClass("ui-dragover").addClass(`ui-dragover-${status}`);
         setTimeout(() => {
             self.$el.removeClass(`ui-dragover-${status}`);
@@ -509,10 +535,10 @@ var View = Backbone.View.extend({
     /** Assists in identifying the batch mode */
     _batch: function(result) {
         result["batch"] = false;
-        var current = this.model.get("current");
-        var config = this.config[current];
+        const current = this.model.get("current");
+        const config = this.config[current];
         if (config.src == "hdca") {
-            var hdca = this.history[`${this.fields[current].value()}_hdca`];
+            const hdca = this.cache[`${this.fields[current].value()}_hdca`];
             if (hdca && hdca.map_over_type) {
                 result["batch"] = true;
             }
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-default.js b/client/galaxy/scripts/mvc/ui/ui-select-default.js
index b8da1914a54..3060ee846e6 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-default.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js
@@ -165,7 +165,7 @@ var View = Backbone.View.extend({
             this.data2 = [];
             this.data2index = {};
             _.each(this.data, (option, index) => {
-                let d = {
+                const d = {
                     order: index,
                     id: option.value,
                     text: option.label,
@@ -201,7 +201,7 @@ var View = Backbone.View.extend({
                 },
                 formatResult: result => {
                     let extraTagWarning = "";
-                    let filteredTags = _.filter(result.tags, t => this.matched_tags.hasOwnProperty(t));
+                    const filteredTags = _.filter(result.tags, t => this.matched_tags.hasOwnProperty(t));
                     if (filteredTags.length > 5) {
                         extraTagWarning = `&nbsp;<div class="label label-warning">${filteredTags.length -
                             5} more tags</div>`;
diff --git a/client/galaxy/scripts/mvc/ui/ui-select.js b/client/galaxy/scripts/mvc/ui/ui-select.js
index bc9d7be5485..ead66ad4df5 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select.js
@@ -153,11 +153,11 @@ var View = Backbone.View.extend({
         if (!this.options.multiple) {
             if (this.select_data) {
                 this.select_data.map(value => {
-                    let mx = this.options.maximumTextLength + 3;
+                    const mx = this.options.maximumTextLength + 3;
                     if (value.text && value.text.length > mx) {
                         let pos = value.text.indexOf(`(${value.id})`);
                         pos = pos != -1 && pos < mx ? pos : mx;
-                        let sub = value.text.substring(0, pos).replace(/[ .]*$/, "");
+                        const sub = value.text.substring(0, pos).replace(/[ .]*$/, "");
                         value.text = `${sub}...(${value.id})`;
                     }
                 });
diff --git a/client/galaxy/scripts/mvc/ui/ui-slider.js b/client/galaxy/scripts/mvc/ui/ui-slider.js
index f2c48634b7d..f1050baf374 100644
--- a/client/galaxy/scripts/mvc/ui/ui-slider.js
+++ b/client/galaxy/scripts/mvc/ui/ui-slider.js
@@ -1,11 +1,9 @@
-import $ from "jquery";
 import Backbone from "backbone";
 
 import Utils from "utils/utils";
 
-var View = Backbone.View.extend({
+const View = Backbone.View.extend({
     initialize: function(options) {
-        var self = this;
         this.model =
             (options && options.model) ||
             new Backbone.Model({
@@ -26,51 +24,24 @@ var View = Backbone.View.extend({
         this.$slider = this.$(".ui-form-slider-element");
 
         // add text field event
-        var pressed = [];
         this.$text
-            .on("change", function() {
-                self.value($(this).val());
+            .on("change", e => {
+                this.value(e.currentTarget.value);
             })
-            .on("keyup", e => {
-                pressed[e.which] = false;
-            })
-            .on("keydown", function(e) {
-                var v = e.which;
-                pressed[v] = true;
-                if (self.model.get("is_workflow") && pressed[16] && v == 52) {
-                    self.value("$");
-                    event.preventDefault();
-                } else if (
-                    !(
-                        v == 8 ||
-                        v == 9 ||
-                        v == 13 ||
-                        v == 37 ||
-                        v == 39 ||
-                        (v >= 48 && v <= 57) ||
-                        (v >= 96 && v <= 105) ||
-                        ((v == 190 || v == 110) &&
-                            $(this)
-                                .val()
-                                .indexOf(".") == -1 &&
-                            self.model.get("precise")) ||
-                        ((v == 189 || v == 109) &&
-                            $(this)
-                                .val()
-                                .indexOf("-") == -1) ||
-                        self._isParameter($(this).val()) ||
-                        pressed[91] ||
-                        pressed[17]
-                    )
-                ) {
-                    event.preventDefault();
+            .on("input", e => {
+                const input = e.currentTarget;
+                if (this._isParameter(input.value)) {
+                    return;
+                } else if (!this.model.get("precise")) {
+                    input.value = input.value.split(".")[0];
                 }
+                input.value = input.value.replace(/[^0-9eE.-]/g, "");
             });
 
         // build slider, cannot be rebuild in render
-        var opts = this.model.attributes;
+        const opts = this.model.attributes;
         this.has_slider = opts.max !== null && opts.min !== null && opts.max > opts.min;
-        var step = opts.step;
+        let step = opts.step;
         if (!step) {
             if (opts.precise && this.has_slider) {
                 step = (opts.max - opts.min) / opts.split;
@@ -80,7 +51,7 @@ var View = Backbone.View.extend({
         }
         if (this.has_slider) {
             this.$slider.slider({ min: opts.min, max: opts.max, step: step }).on("slide", (event, ui) => {
-                self.value(ui.value);
+                this.value(ui.value);
             });
         }
 
@@ -90,7 +61,7 @@ var View = Backbone.View.extend({
     },
 
     render: function() {
-        var value = this.model.get("value");
+        const value = this.model.get("value");
         if (this.has_slider) {
             this.$slider.slider("value", value);
             this.$slider.show();
@@ -107,9 +78,9 @@ var View = Backbone.View.extend({
     /** Set and return the current value */
     value: function(new_val) {
         if (new_val !== undefined) {
-            let options = this.model.attributes;
-            let original_val = new_val;
-            let is_value = new_val !== null && new_val !== "" && !this._isParameter(new_val);
+            const options = this.model.attributes;
+            const original_val = new_val;
+            const is_value = new_val !== null && new_val !== "" && !this._isParameter(new_val);
             if (is_value) {
                 if (isNaN(new_val)) {
                     new_val = 0;
@@ -127,8 +98,8 @@ var View = Backbone.View.extend({
             this.model.set("value", new_val);
             this.model.trigger("change");
             options.onchange(new_val);
-            let has_changed = is_value && parseInt(original_val) !== parseInt(new_val);
-            let message = has_changed ? "This value was invalid or out-of-range. It has been auto-corrected." : null;
+            const has_changed = is_value && parseInt(original_val) !== parseInt(new_val);
+            const message = has_changed ? "This value was invalid or out-of-range. It has been auto-corrected." : null;
             this.model.trigger("error", message);
         }
         return this.model.get("value");
diff --git a/client/galaxy/scripts/mvc/ui/ui-tabs.js b/client/galaxy/scripts/mvc/ui/ui-tabs.js
index b84d4d58b77..c188ca7521c 100644
--- a/client/galaxy/scripts/mvc/ui/ui-tabs.js
+++ b/client/galaxy/scripts/mvc/ui/ui-tabs.js
@@ -161,6 +161,7 @@ export var View = Backbone.View.extend({
                 $("<a/>")
                     .addClass("nav-link")
                     .attr("id", `tab-title-link-${options.id}`)
+                    .attr("href", "javascript:void(0);")
             );
         var $href = $tmpl.find("a");
         options.icon &&
diff --git a/client/galaxy/scripts/mvc/upload/collection/collection-view.js b/client/galaxy/scripts/mvc/upload/collection/collection-view.js
index 880fefc84dd..358d982310f 100644
--- a/client/galaxy/scripts/mvc/upload/collection/collection-view.js
+++ b/client/galaxy/scripts/mvc/upload/collection/collection-view.js
@@ -248,7 +248,7 @@ export default Backbone.View.extend({
         this.counter.announce--;
         this.counter.success++;
         this._updateScreen();
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.currHistoryPanel.refreshContents();
     },
 
@@ -276,7 +276,7 @@ export default Backbone.View.extend({
     },
 
     _eventBuild: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var allHids = [];
         _.forEach(this.collection.models, upload => {
             allHids.push.apply(allHids, upload.get("hids"));
diff --git a/client/galaxy/scripts/mvc/upload/collection/rules-input-view.js b/client/galaxy/scripts/mvc/upload/collection/rules-input-view.js
index 63545509dd7..ddf1ecf2312 100644
--- a/client/galaxy/scripts/mvc/upload/collection/rules-input-view.js
+++ b/client/galaxy/scripts/mvc/upload/collection/rules-input-view.js
@@ -78,14 +78,14 @@ export default Backbone.View.extend({
 
     _renderSelectedType: function() {
         const selectionType = this.selectionType;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (selectionType == "dataset") {
             if (!this.datasetSelectorView) {
                 this.selectedDatasetId = null;
                 const history = Galaxy && Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model;
                 const historyContentModels = history.contents.models;
                 const options = [];
-                for (let historyContentModel of historyContentModels) {
+                for (const historyContentModel of historyContentModels) {
                     const attr = historyContentModel.attributes;
                     if (attr.history_content_type !== "dataset") {
                         continue;
@@ -113,7 +113,7 @@ export default Backbone.View.extend({
     },
 
     _onDataset: function(selectedDatasetId) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.selectedDatasetId = selectedDatasetId;
         if (!selectedDatasetId) {
             this._setPreview("");
@@ -146,7 +146,7 @@ export default Backbone.View.extend({
     _buildSelection: function(content) {
         const selectionType = this.selectionType;
         const selection = {};
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (selectionType == "dataset" || selectionType == "paste") {
             selection.selectionType = "raw";
             selection.content = content;
diff --git a/client/galaxy/scripts/mvc/upload/composite/composite-view.js b/client/galaxy/scripts/mvc/upload/composite/composite-view.js
index 50a75706056..dbae23f2cd4 100644
--- a/client/galaxy/scripts/mvc/upload/composite/composite-view.js
+++ b/client/galaxy/scripts/mvc/upload/composite/composite-view.js
@@ -23,6 +23,13 @@ export default Backbone.View.extend({
         this.setElement(this._template());
 
         // create button section
+        this.btnReset = new Ui.Button({
+            id: "btn-reset",
+            title: _l("Reset"),
+            onclick: function() {
+                self._eventReset();
+            }
+        });
         this.btnStart = new Ui.Button({
             title: _l("Start"),
             onclick: function() {
@@ -37,7 +44,7 @@ export default Backbone.View.extend({
         });
 
         // append buttons to dom
-        _.each([this.btnStart, this.btnClose], button => {
+        _.each([this.btnReset, this.btnStart, this.btnClose], button => {
             self.$(".upload-buttons").prepend(button.$el);
         });
 
@@ -55,7 +62,8 @@ export default Backbone.View.extend({
                     _.each(details.composite_files, item => {
                         self.collection.add({
                             id: self.collection.size(),
-                            file_desc: item.description || item.name
+                            file_desc: item.description || item.name,
+                            optional: item.optional
                         });
                     });
                 }
@@ -105,7 +113,11 @@ export default Backbone.View.extend({
             this.select_genome.enable();
             this.select_extension.enable();
         }
-        if (this.collection.where({ status: "ready" }).length == this.collection.length && this.collection.length > 0) {
+        if (
+            this.collection.where({ status: "ready" }).length + this.collection.where({ optional: true }).length ==
+                this.collection.length &&
+            this.collection.length > 0
+        ) {
             this.btnStart.enable();
             this.btnStart.$el.addClass("btn-primary");
         } else {
@@ -151,6 +163,16 @@ export default Backbone.View.extend({
         });
     },
 
+    /** Remove all */
+    _eventReset: function() {
+        if (this.collection.where({ status: "running" }).length == 0) {
+            this.collection.reset();
+            this.select_extension.value(this.options.default_extension);
+            this.select_genome.value(this.options.default_genome);
+            this.render();
+        }
+    },
+
     /** Refresh progress state */
     _eventProgress: function(percentage) {
         this.collection.each(it => {
@@ -160,7 +182,7 @@ export default Backbone.View.extend({
 
     /** Refresh success state */
     _eventSuccess: function(message) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.collection.each(it => {
             it.set("status", "success");
         });
diff --git a/client/galaxy/scripts/mvc/upload/default/default-row.js b/client/galaxy/scripts/mvc/upload/default/default-row.js
index caf4d328c1b..ae9825adfea 100644
--- a/client/galaxy/scripts/mvc/upload/default/default-row.js
+++ b/client/galaxy/scripts/mvc/upload/default/default-row.js
@@ -84,7 +84,7 @@ export default Backbone.View.extend({
         // handle extension info popover
         this.$(".upload-extension-info")
             .on("click", e => {
-                let upload_ext = this.upload_extension;
+                const upload_ext = this.upload_extension;
                 if (upload_ext) {
                     if (upload_ext.extension_popup.visible) {
                         upload_ext.extension_popup.hide();
diff --git a/client/galaxy/scripts/mvc/upload/default/default-view.js b/client/galaxy/scripts/mvc/upload/default/default-view.js
index 7278c4d544a..2c772fc6aa8 100644
--- a/client/galaxy/scripts/mvc/upload/default/default-view.js
+++ b/client/galaxy/scripts/mvc/upload/default/default-view.js
@@ -260,7 +260,7 @@ export default Backbone.View.extend({
 
     /** Success */
     _eventSuccess: function(index, message) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var it = this.collection.get(index);
         it.set({ percentage: 100, status: "success" });
         this.ui_button.model.set("percentage", this._uploadPercentage(100, it.get("file_size")));
@@ -373,7 +373,7 @@ export default Backbone.View.extend({
             this._uploadFtp();
 
             // queue remaining files
-            let Galaxy = getGalaxyInstance();
+            const Galaxy = getGalaxyInstance();
             this.uploadbox.start({
                 id: Galaxy.user.id,
                 chunk_upload_size: this.app.options.chunk_upload_size
diff --git a/client/galaxy/scripts/mvc/upload/upload-ftp.js b/client/galaxy/scripts/mvc/upload/upload-ftp.js
index 41f2b3d7081..98f59d512d6 100644
--- a/client/galaxy/scripts/mvc/upload/upload-ftp.js
+++ b/client/galaxy/scripts/mvc/upload/upload-ftp.js
@@ -2,7 +2,6 @@
 import _ from "underscore";
 import $ from "jquery";
 import Backbone from "backbone";
-import { getAppRoot } from "onload/loadConfig";
 import { getGalaxyInstance } from "app";
 import Utils from "utils/utils";
 import UploadUtils from "mvc/upload/upload-utils";
@@ -15,7 +14,7 @@ export default Backbone.View.extend({
             class_remove: "upload-icon-button fa fa-check-square-o",
             class_partial: "upload-icon-button fa fa-minus-square-o",
             help_enabled: true,
-            oidc_text: `<br/>If you are signed-in to Galaxy using a third-party identity and you <strong>don't have a Galaxy password</strong> please go to <a href="${getAppRoot()}user/reset_password" target="_blank">this</a> page and request a password for your Galaxy account.`,
+            oidc_text: `<br/>If you are signed-in to Galaxy using a third-party identity and you <strong>do not have a Galaxy password</strong> please use the reset password option in the login form with your email to create a password for your account.`,
             help_text: `This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>${
                 options.ftp_upload_site
             }</strong> using your Galaxy credentials.
@@ -27,7 +26,7 @@ export default Backbone.View.extend({
         }).set(options);
 
         this.collection = this.model.get("collection");
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (Galaxy.config.enable_oidc) {
             this.model.set("help_text", this.model.get("help_text") + this.model.get("oidc_text"));
         }
diff --git a/client/galaxy/scripts/mvc/upload/upload-model.js b/client/galaxy/scripts/mvc/upload/upload-model.js
index 96489cca825..356670d7d12 100644
--- a/client/galaxy/scripts/mvc/upload/upload-model.js
+++ b/client/galaxy/scripts/mvc/upload/upload-model.js
@@ -5,6 +5,7 @@ var Model = Backbone.Model.extend({
         genome: "?",
         url_paste: "",
         status: "init",
+        optional: false,
         info: null,
         file_name: "",
         file_mode: "",
diff --git a/client/galaxy/scripts/mvc/upload/upload-settings.js b/client/galaxy/scripts/mvc/upload/upload-settings.js
index 240a3452025..6923b0d9863 100644
--- a/client/galaxy/scripts/mvc/upload/upload-settings.js
+++ b/client/galaxy/scripts/mvc/upload/upload-settings.js
@@ -40,7 +40,7 @@ export default Backbone.View.extend({
             var $checkbox = $("<div/>")
                 .addClass(`upload-${parameter.id} fa`)
                 .addClass((self.model.get(parameter.id) && self.options.class_check) || self.options.class_uncheck);
-            let $row = $("<tr/>")
+            const $row = $("<tr/>")
                 .append($("<td/>").append($checkbox))
                 .append($("<td/>").append(parameter.title))
                 .on("click", () => {
diff --git a/client/galaxy/scripts/mvc/upload/upload-view.js b/client/galaxy/scripts/mvc/upload/upload-view.js
index 9061a31ca3e..4063b2eb017 100644
--- a/client/galaxy/scripts/mvc/upload/upload-view.js
+++ b/client/galaxy/scripts/mvc/upload/upload-view.js
@@ -65,7 +65,7 @@ export default Backbone.View.extend({
 
     /** Show/hide upload dialog */
     show: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var self = this;
         if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) {
             window.setTimeout(() => {
@@ -114,7 +114,7 @@ export default Backbone.View.extend({
 
     /** Refresh user and current history */
     currentHistory: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         return this.current_user && Galaxy.currHistoryPanel.model.get("id");
     },
 
@@ -173,6 +173,8 @@ export default Backbone.View.extend({
                                 file: it.get("file_data")
                             });
                     }
+                } else if (it.get("optional")) {
+                    continue;
                 } else {
                     data.error_message = "Upload content incomplete.";
                     it.set("status", "error");
diff --git a/client/galaxy/scripts/mvc/user/user-custom-builds.js b/client/galaxy/scripts/mvc/user/user-custom-builds.js
index aaf4005d801..4ae6dc844b4 100644
--- a/client/galaxy/scripts/mvc/user/user-custom-builds.js
+++ b/client/galaxy/scripts/mvc/user/user-custom-builds.js
@@ -19,7 +19,7 @@ var Collection = Backbone.Collection.extend({
 
 var View = Backbone.View.extend({
     initialize: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var self = this;
         this.active_tab = "user";
         var history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
diff --git a/client/galaxy/scripts/mvc/user/user-model.js b/client/galaxy/scripts/mvc/user/user-model.js
index 8de2b2e1343..afea7d350dc 100644
--- a/client/galaxy/scripts/mvc/user/user-model.js
+++ b/client/galaxy/scripts/mvc/user/user-model.js
@@ -55,13 +55,13 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
         },
 
         updatePreferences: function(name, new_value) {
-            let preferences = this.get("preferences");
+            const preferences = this.get("preferences");
             preferences[name] = JSON.stringify(new_value);
             this.preferences = preferences;
         },
 
         getFavorites: function() {
-            let preferences = this.get("preferences");
+            const preferences = this.get("preferences");
             if (preferences && preferences.favorites) {
                 return JSON.parse(preferences.favorites);
             } else {
@@ -72,7 +72,7 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
         },
 
         updateFavorites: function(object_type, new_favorites) {
-            let favorites = this.getFavorites();
+            const favorites = this.getFavorites();
             favorites[object_type] = new_favorites[object_type];
             this.updatePreferences("favorites", favorites);
         },
diff --git a/client/galaxy/scripts/mvc/user/user-preferences.js b/client/galaxy/scripts/mvc/user/user-preferences.js
index 70f1f88d590..71e42f3aba0 100644
--- a/client/galaxy/scripts/mvc/user/user-preferences.js
+++ b/client/galaxy/scripts/mvc/user/user-preferences.js
@@ -10,16 +10,16 @@ import Ui from "mvc/ui/ui-misc";
 import QueryStringParsing from "utils/query-string-parsing";
 
 /** Contains descriptive dictionaries describing user forms */
-var Model = Backbone.Model.extend({
+const Model = Backbone.Model.extend({
     initialize: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         options = options || {};
         options.user_id = options.user_id || Galaxy.user.id;
         this.set({
             user_id: options.user_id,
             information: {
                 title: _l("Manage information"),
-                description: "Edit your email, addresses and custom parameters or change your username.",
+                description: "Edit your email, addresses and custom parameters or change your public name.",
                 url: `api/users/${options.user_id}/information/inputs`,
                 icon: "fa-user",
                 redirect: "user"
@@ -90,6 +90,15 @@ var Model = Backbone.Model.extend({
                 submit_title: "Create a new key",
                 submit_icon: "fa-check"
             },
+            cloud_auth: {
+                title: _l("Manage Cloud Authorization"),
+                description: _l(
+                    "Add or modify the configuration that grants Galaxy to access your cloud-based resources."
+                ),
+                icon: "fa-cloud",
+                submit_title: "Create a new key",
+                submit_icon: "fa-check"
+            },
             toolbox_filters: {
                 title: _l("Manage Toolbox filters"),
                 description: _l("Customize your Toolbox by displaying or omitting sets of Tools."),
@@ -140,7 +149,7 @@ var Model = Backbone.Model.extend({
 });
 
 /** View of the main user preference panel with links to individual user forms */
-var View = Backbone.View.extend({
+const View = Backbone.View.extend({
     title: _l("User Preferences"),
     active_tab: "user",
     initialize: function() {
@@ -150,48 +159,48 @@ var View = Backbone.View.extend({
     },
 
     render: function() {
-        var self = this;
-        let Galaxy = getGalaxyInstance();
-        var config = Galaxy.config;
+        const Galaxy = getGalaxyInstance();
+        const config = Galaxy.config;
         $.getJSON(`${getAppRoot()}api/users/${Galaxy.user.id}`, data => {
-            self.$preferences = $("<div/>")
+            this.$preferences = $("<div/>")
                 .append($("<h2/>").append("User preferences"))
                 .append($("<p/>").append(`You are logged in as <strong>${_.escape(data.email)}</strong>.`))
-                .append((self.$table = $("<table/>")));
-            var message = QueryStringParsing.get("message");
-            var status = QueryStringParsing.get("status");
+                .append((this.$table = $("<table/>")));
+            const message = QueryStringParsing.get("message");
+            const status = QueryStringParsing.get("status");
             if (message && status) {
-                self.$preferences.prepend(new Ui.Message({ message: message, status: status }).$el);
+                this.$preferences.prepend(new Ui.Message({ message: message, status: status }).$el);
             }
             if (!config.use_remote_user) {
-                self._addLink("information");
-                self._addLink("password");
+                this._addLink("information");
+                this._addLink("password");
             }
             if (config.enable_communication_server) {
-                self._addLink("communication");
+                this._addLink("communication");
             }
-            self._addLink("custom_builds");
-            self._addLink("permissions");
-            self._addLink("make_data_private");
-            self._addLink("api_key");
+            this._addLink("custom_builds");
+            this._addLink("permissions");
+            this._addLink("make_data_private");
+            this._addLink("api_key");
+            this._addLink("cloud_auth");
             if (config.enable_openid) {
-                self._addLink("genomespace");
+                this._addLink("genomespace");
             }
             if (config.has_user_tool_filters) {
-                self._addLink("toolbox_filters");
+                this._addLink("toolbox_filters");
             }
             if (Galaxy.session_csrf_token) {
-                self._addLink("logout");
+                this._addLink("logout");
             }
-            self.$preferences.append(self._templateFooter(data));
-            self.$el.empty().append(self.$preferences);
+            this.$preferences.append(this._templateFooter(data));
+            this.$el.empty().append(this.$preferences);
         });
     },
 
     _addLink: function(action) {
-        var options = this.model.get(action);
-        var $row = $(this._templateLink(options));
-        var $a = $row.find("a");
+        const options = this.model.get(action);
+        const $row = $(this._templateLink(options));
+        const $a = $row.find("a");
         if (options.onclick) {
             $a.on("click", () => {
                 options.onclick();
@@ -215,7 +224,7 @@ var View = Backbone.View.extend({
     },
 
     _templateFooter: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         return `<p class="mt-2">You are using <strong>${
             options.nice_total_disk_usage
         }</strong> of disk space in this Galaxy instance. ${
diff --git a/client/galaxy/scripts/mvc/visualization/chart/chart-client.js b/client/galaxy/scripts/mvc/visualization/chart/chart-client.js
index 3f4195bd21e..47d6a4d7158 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/chart-client.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/chart-client.js
@@ -12,7 +12,7 @@ import Menu from "mvc/visualization/chart/views/menu";
 
 export default Backbone.View.extend({
     initialize: function(options) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.modal = Galaxy && Galaxy.modal ? Galaxy.modal : new Modal.View();
         this.setElement(
             $("<div/>")
@@ -45,7 +45,7 @@ export default Backbone.View.extend({
                 this.chart.trigger("redraw");
             })
             .fail(response => {
-                let message = response.responseJSON && response.responseJSON.err_msg;
+                const message = response.responseJSON && response.responseJSON.err_msg;
                 this.errormessage = message || "Import failed for unkown reason.";
             });
     }
diff --git a/client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js b/client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
index d834364e737..78547e41830 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
@@ -12,7 +12,7 @@ function createPNG(options) {
 }
 
 function _downloadData(imageData, filename) {
-    let link = document.createElement("a");
+    const link = document.createElement("a");
     link.download = filename;
     link.href = imageData;
     link.click();
@@ -47,7 +47,7 @@ function _toImage($el, x_offset, y_offset, newContext) {
 
 /** Convert canvas to png */
 function _canvas2png(options) {
-    let $canvas = options.$el.find(".charts-viewer-canvas");
+    const $canvas = options.$el.find(".charts-viewer-canvas");
     try {
         if ($canvas.width() !== 0 && $canvas.height() !== 0) {
             var newCanvas = document.createElement("canvas");
@@ -91,7 +91,7 @@ function _svg2png(options) {
     source.src = "data:image/svg+xml;base64," + window.btoa(xml.string);
     source.onload = function() {
         context.drawImage(source, 0, 0, canvas.width, canvas.height);
-        let imageData = canvas.toDataURL("image/png");
+        const imageData = canvas.toDataURL("image/png");
         _downloadPNGData(imageData, options.title);
         $container.remove();
     };
diff --git a/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js b/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
index 74dca068758..6c61f1b7a97 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
@@ -86,9 +86,9 @@ var request = function(options) {
             for (let i = 0; i < results.length; i++) {
                 results[i] = [];
             }
-            for (let i in response.data) {
+            for (const i in response.data) {
                 var row = response.data[i];
-                for (let j in row) {
+                for (const j in row) {
                     var v = row[j];
                     if (v !== undefined && v != 2147483647 && j < column_length) {
                         results[j].push(v);
@@ -96,7 +96,7 @@ var request = function(options) {
                 }
             }
             console.debug("tabular-datasets::_fetch() - Fetching complete.");
-            for (let i in results) {
+            for (const i in results) {
                 var column = column_list[i];
                 var block_id = _block_id(dataset_id, column);
                 _cache[block_id] = results[i];
diff --git a/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js b/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
index 67f2f6bebfa..80efaa12c2c 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
@@ -142,7 +142,7 @@ var wait = function(chart, success, error) {
 
 /** Refresh history panel */
 var refreshHdas = function() {
-    let Galaxy = getGalaxyInstance();
+    const Galaxy = getGalaxyInstance();
     if (Galaxy && Galaxy.currHistoryPanel) {
         Galaxy.currHistoryPanel.refreshContents();
     }
diff --git a/client/galaxy/scripts/mvc/visualization/chart/utilities/series.js b/client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
index 117d7fdc24d..1f335089f25 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
@@ -5,8 +5,8 @@ import * as d3 from "d3";
 function getDomains(groups, keys) {
     function _apply(operator, key) {
         let value;
-        for (let group_index in groups) {
-            let value_sub = d3[operator](groups[group_index].values, function(d) {
+        for (const group_index in groups) {
+            const value_sub = d3[operator](groups[group_index].values, function(d) {
                 return d[key];
             });
             value = value === undefined ? value_sub : Math[operator](value, value_sub);
@@ -34,11 +34,11 @@ function makeSeries(groups, keys) {
             var point = [];
             if (keys) {
                 for (var key_index in keys) {
-                    let column_index = keys[key_index];
+                    const column_index = keys[key_index];
                     point.push(group.values[value_index][column_index]);
                 }
             } else {
-                for (let column_index in group.values[value_index]) {
+                for (const column_index in group.values[value_index]) {
                     point.push(group.values[value_index][column_index]);
                 }
             }
@@ -109,12 +109,12 @@ function makeUniqueCategories(groups, with_index) {
         }
     }
     // convert group values into category indeces
-    for (let i in groups) {
-        let group = groups[i];
-        for (let j in group.values) {
-            let value_dict = group.values[j];
-            for (let key in categories) {
-                let value = String(value_dict[key]);
+    for (const i in groups) {
+        const group = groups[i];
+        for (const j in group.values) {
+            const value_dict = group.values[j];
+            for (const key in categories) {
+                const value = String(value_dict[key]);
                 value_dict[key] = categories[key][value];
             }
         }
diff --git a/client/galaxy/scripts/mvc/visualization/chart/views/menu.js b/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
index 04025678b67..b5b2914a129 100644
--- a/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
+++ b/client/galaxy/scripts/mvc/visualization/chart/views/menu.js
@@ -124,7 +124,7 @@ export default Backbone.View.extend({
         });
         this.buttons = [this.left_button, this.right_button, this.execute_button, this.export_button, this.save_button];
         this.setElement("<div/>");
-        for (let b of this.buttons) {
+        for (const b of this.buttons) {
             this.$el.append(b.$el);
         }
         this.listenTo(this.model, "change", () => this.render());
diff --git a/client/galaxy/scripts/mvc/webhooks.js b/client/galaxy/scripts/mvc/webhooks.js
index 9d333dcd31c..b5713de87af 100644
--- a/client/galaxy/scripts/mvc/webhooks.js
+++ b/client/galaxy/scripts/mvc/webhooks.js
@@ -54,7 +54,7 @@ const load = options => {
 
 function filterType(data, type) {
     return data.models.filter(item => {
-        let itype = item.get("type");
+        const itype = item.get("type");
         if (itype) {
             return itype.indexOf(type) !== -1;
         } else {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index 8bf330abe72..10b55a62020 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -56,7 +56,7 @@ var Tool = Backbone.View.extend({
                     form.model.get("postchange")(process, form);
                 },
                 postchange: function(process, form) {
-                    let Galaxy = getGalaxyInstance();
+                    const Galaxy = getGalaxyInstance();
                     var options = form.model.attributes;
                     var current_state = {
                         tool_id: options.id,
@@ -201,7 +201,7 @@ function _visit(head, head_list, output_id, options) {
 
 function _makeRenameHelp(name_labels) {
     let help_section = `This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid input variables are:`;
-    let li = `
+    const li = `
         <ul>
             ${name_labels
                 .map(
@@ -224,10 +224,10 @@ function _makeSection(output_id, label, options) {
     var node = options.node;
     var workflow = options.workflow;
 
-    for (let key in datatypes) {
+    for (const key in datatypes) {
         extensions.push({ 0: datatypes[key], 1: datatypes[key] });
     }
-    for (let key in node.input_terminals) {
+    for (const key in node.input_terminals) {
         name_label_map.push({ name: node.input_terminals[key].name, label: node.input_terminals[key].label });
     }
     var rename_help = _makeRenameHelp(name_label_map);
@@ -276,7 +276,13 @@ function _makeSection(output_id, label, options) {
                 ignore: "__empty__",
                 value: "__empty__",
                 options: extensions,
-                help: "This action will change the datatype of the output to the indicated value."
+                help: "This action will change the datatype of the output to the indicated datatype.",
+                onchange: function(new_value) {
+                    if (new_value === "__empty__") {
+                        new_value = null;
+                    }
+                    workflow.updateDatatype(node, output_id, new_value);
+                }
             },
             {
                 action: "TagDatasetAction",
@@ -379,8 +385,8 @@ function _addSections(form) {
             help:
                 "Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."
         });
-        for (let output_id in node.output_terminals) {
-            let label = node.output_terminals[output_id].label || output_id;
+        for (const output_id in node.output_terminals) {
+            const label = node.output_terminals[output_id].label || output_id;
             inputs.push(_makeSection(output_id, label, options));
         }
     }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index a9db9f71352..adaf86871bb 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -54,6 +54,10 @@ class Workflow {
             return false;
         }
     }
+    updateDatatype(node, outputName, newDatatype) {
+        node.changeOutputDatatype(outputName, newDatatype);
+        return true;
+    }
     create_node(type, title_text, content_id) {
         var node = this.app.prebuildNode(type, title_text, content_id);
         this.add_node(node);
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index c1dbbdb23a2..4ac55fb2815 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -60,6 +60,23 @@ var Node = Backbone.Model.extend({
         }
         return changed;
     },
+    changeOutputDatatype: function(outputName, datatype) {
+        const output_terminal = this.output_terminals[outputName];
+        const output = this.nodeView.outputViews[outputName].output;
+        output_terminal.force_datatype = datatype;
+        output.force_datatype = datatype;
+        if (datatype) {
+            this.post_job_actions["ChangeDatatypeAction" + outputName] = {
+                action_arguments: { newtype: datatype },
+                action_type: "ChangeDatatypeAction",
+                output_name: outputName
+            };
+        } else {
+            delete this.post_job_actions["ChangeDatatypeAction" + outputName];
+        }
+        this.markChanged();
+        output_terminal.destroyInvalidConnections();
+    },
     connectedOutputTerminals: function() {
         return this._connectedTerminals(this.output_terminals);
     },
@@ -276,6 +293,10 @@ var Node = Backbone.Model.extend({
                 // the output already exists, but the output formats may have changed.
                 // Therefore we update the datatypes and destroy invalid connections.
                 node.output_terminals[output.name].datatypes = output.extensions;
+                node.output_terminals[output.name].force_datatype = output.force_datatype;
+                if (node.type == "parameter_input") {
+                    node.output_terminals[output.name].attributes.type = output.type;
+                }
                 node.output_terminals[output.name].destroyInvalidConnections();
             }
         });
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index 550149d40ba..3c89c1aa6d1 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -165,7 +165,7 @@ var Terminal = Backbone.Model.extend({
         let output_val = val;
         if (this.multiple) {
             // emulate list input
-            let description = new CollectionTypeDescription("list");
+            const description = new CollectionTypeDescription("list");
             if (val.collectionType === description.collectionType) {
                 // No mapping over necessary
                 return;
@@ -195,9 +195,9 @@ var Terminal = Backbone.Model.extend({
     },
 
     resetCollectionTypeSource: function() {
-        let node = this.node;
+        const node = this.node;
         _.each(node.output_terminals, function(output_terminal) {
-            let type_source = output_terminal.attributes.collection_type_source;
+            const type_source = output_terminal.attributes.collection_type_source;
             if (type_source && output_terminal.attributes.collection_type) {
                 output_terminal.attributes.collection_type = null;
                 output_terminal.update(output_terminal.attributes);
@@ -212,6 +212,7 @@ var OutputTerminal = Terminal.extend({
     initialize: function(attr) {
         Terminal.prototype.initialize.call(this, attr);
         this.datatypes = attr.datatypes;
+        this.force_datatype = attr.force_datatype;
     },
 
     resetMappingIfNeeded: function() {
@@ -354,19 +355,8 @@ var BaseInputTerminal = Terminal.extend({
                 return new ConnectionAcceptable(true, null);
             }
             var cat_outputs = [];
-            cat_outputs = cat_outputs.concat(other.datatypes);
-            if (other.node.post_job_actions) {
-                for (var pja_i in other.node.post_job_actions) {
-                    var pja = other.node.post_job_actions[pja_i];
-                    if (
-                        pja.action_type == "ChangeDatatypeAction" &&
-                        (pja.output_name === "" || pja.output_name == other.name) &&
-                        pja.action_arguments
-                    ) {
-                        cat_outputs.push(pja.action_arguments.newtype);
-                    }
-                }
-            }
+            const other_datatypes = other.force_datatype ? [other.force_datatype] : other.datatypes;
+            cat_outputs = cat_outputs.concat(other_datatypes);
             // FIXME: No idea what to do about case when datatype is 'input'
             for (var other_datatype_i in cat_outputs) {
                 var other_datatype = cat_outputs[other_datatype_i];
@@ -426,7 +416,7 @@ var InputTerminal = BaseInputTerminal.extend({
                         "Cannot attach collections to data parameters with individual data inputs already attached."
                     );
                 }
-                if (otherCollectionType.collectionType.endsWith("paired")) {
+                if (otherCollectionType.collectionType && otherCollectionType.collectionType.endsWith("paired")) {
                     return new ConnectionAcceptable(
                         false,
                         "Cannot attach paired inputs to multiple data parameters, only lists may be treated this way."
@@ -435,6 +425,10 @@ var InputTerminal = BaseInputTerminal.extend({
             }
             if (thisMapOver.isCollection && thisMapOver.canMatch(otherCollectionType)) {
                 return this._producesAcceptableDatatype(other);
+            } else if (this.multiple && new CollectionTypeDescription("list").canMatch(otherCollectionType)) {
+                // This handles the special case of a list input being connected to a multiple="true" data input.
+                // Nested lists would be correctly mapped over by the above condition.
+                return this._producesAcceptableDatatype(other);
             } else {
                 //  Need to check if this would break constraints...
                 var mappingConstraints = this._mappingConstraints();
@@ -506,7 +500,7 @@ var InputCollectionTerminal = BaseInputTerminal.extend({
         if (!other) {
             return;
         } else {
-            let node = this.node;
+            const node = this.node;
             _.each(node.output_terminals, function(output_terminal) {
                 if (output_terminal.attributes.collection_type_source && !connector.dragging) {
                     if (other.isMappedOver()) {
@@ -611,6 +605,7 @@ var OutputCollectionTerminal = Terminal.extend({
     initialize: function(attr) {
         Terminal.prototype.initialize.call(this, attr);
         this.datatypes = attr.datatypes;
+        this.force_datatype = attr.force_datatype;
         if (attr.collection_type) {
             this.collectionType = new CollectionTypeDescription(attr.collection_type);
         } else {
@@ -634,7 +629,7 @@ var OutputCollectionTerminal = Terminal.extend({
             newCollectionType = ANY_COLLECTION_TYPE_DESCRIPTION;
         }
 
-        let oldCollectionType = this.collectionType;
+        const oldCollectionType = this.collectionType;
         this.collectionType = newCollectionType;
         // we need to iterate over a copy, as we slice this.connectors in the process of destroying connections
         var connectors = this.connectors.slice(0);
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index 46a548beb10..0d57a097973 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -5,7 +5,7 @@ import Backbone from "backbone";
 // TODO; tie into Galaxy state?
 window.workflow_globals = window.workflow_globals || {};
 
-var DataInputView = Backbone.View.extend({
+const DataInputView = Backbone.View.extend({
     className: "form-row dataRow input-data-row",
 
     initialize: function(options) {
@@ -35,7 +35,7 @@ var DataInputView = Backbone.View.extend({
     }
 });
 
-var DataOutputView = Backbone.View.extend({
+const DataOutputView = Backbone.View.extend({
     className: "form-row dataRow",
 
     initialize: function(options) {
@@ -43,18 +43,18 @@ var DataOutputView = Backbone.View.extend({
         this.terminalElement = options.terminalElement;
         this.nodeView = options.nodeView;
 
-        var output = this.output;
-        var label = output.label || output.name;
-        var node = this.nodeView.node;
+        const output = this.output;
+        let label = output.label || output.name;
+        const node = this.nodeView.node;
 
-        var isInput = output.extensions.indexOf("input") >= 0 || output.extensions.indexOf("input_collection") >= 0;
+        const isInput = output.extensions.indexOf("input") >= 0 || output.extensions.indexOf("input_collection") >= 0;
         if (!isInput) {
-            label = `${label} (${output.extensions.join(", ")})`;
+            label = `${label} (${output.force_datatype || output.extensions.join(", ")})`;
         }
         this.$el.html(label);
         this.calloutView = null;
         if (["tool", "subworkflow"].indexOf(node.type) >= 0) {
-            var calloutView = new OutputCalloutView({
+            const calloutView = new OutputCalloutView({
                 label: label,
                 output: output,
                 node: node
@@ -86,7 +86,7 @@ var DataOutputView = Backbone.View.extend({
     }
 });
 
-var ParameterOutputView = Backbone.View.extend({
+const ParameterOutputView = Backbone.View.extend({
     className: "form-row dataRow",
 
     initialize: function(options) {
@@ -94,28 +94,20 @@ var ParameterOutputView = Backbone.View.extend({
         this.terminalElement = options.terminalElement;
         this.nodeView = options.nodeView;
 
-        var output = this.output;
-        var label = output.label || output.name;
-        var node = this.nodeView.node;
+        const output = this.output;
+        const label = output.label || output.name;
+        const node = this.nodeView.node;
 
         this.$el.html(label);
         this.calloutView = null;
         if (["tool", "subworkflow"].indexOf(node.type) >= 0) {
-            var calloutView = new OutputCalloutView({
+            const calloutView = new OutputCalloutView({
                 label: label,
                 output: output,
                 node: node
             });
             this.calloutView = calloutView;
             this.$el.append(calloutView.el);
-            this.$el.hover(
-                () => {
-                    calloutView.hoverImage();
-                },
-                () => {
-                    calloutView.resetImage();
-                }
-            );
         }
         this.$el.css({
             position: "absolute",
@@ -141,21 +133,21 @@ var ParameterOutputView = Backbone.View.extend({
     }
 });
 
-var OutputCalloutView = Backbone.View.extend({
+const OutputCalloutView = Backbone.View.extend({
     tagName: "div",
 
     initialize: function(options) {
         this.label = options.label;
         this.node = options.node;
         this.output = options.output;
-        var view = this;
-        var node = this.node;
+        const view = this;
+        const node = this.node;
         this.$el
             .attr("class", `callout-terminal ${this.label}`)
             .css({ display: "none" })
             .append(
                 $("<icon class='mark-terminal fa fa-asterisk'/>").click(() => {
-                    var outputName = view.output.name;
+                    const outputName = view.output.name;
                     if (node.isWorkflowOutput(outputName)) {
                         node.removeWorkflowOutput(outputName);
                         view.$("icon").removeClass("mark-terminal-active");
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index b5dc65a0596..1eaa4d3d4f0 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -84,24 +84,33 @@ export default Backbone.View.extend({
         return terminalView;
     },
 
-    addDataOutput: function(output) {
-        var terminalViewClass = TerminalViews.OutputTerminalView;
-        var outputViewClass = DataViews.DataOutputView;
+    terminalViewForOutput: function(output) {
+        let terminalViewClass = TerminalViews.OutputTerminalView;
         if (output.collection) {
             terminalViewClass = TerminalViews.OutputCollectionTerminalView;
         } else if (output.parameter) {
             terminalViewClass = TerminalViews.OutputParameterTerminalView;
-            outputViewClass = DataViews.ParameterOutputView;
         }
-        var terminalView = new terminalViewClass({
+        const terminalView = new terminalViewClass({
             node: this.node,
             output: output
         });
-        var outputView = new outputViewClass({
+        return terminalView;
+    },
+
+    outputViewforOutput: function(output, terminalView) {
+        const outputViewClass = output.parameter ? DataViews.ParameterOutputView : DataViews.DataOutputView;
+        const outputView = new outputViewClass({
             output: output,
             terminalElement: terminalView.el,
             nodeView: this
         });
+        return outputView;
+    },
+
+    addDataOutput: function(output) {
+        const terminalView = this.terminalViewForOutput(output);
+        const outputView = this.outputViewforOutput(output, terminalView);
         this.outputViews[output.name] = outputView;
         this.tool_body.append(outputView.$el.append(terminalView.terminalElements()));
     },
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 460f1f3198f..00be7196c0c 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -143,11 +143,11 @@ var BaseInputTerminalView = TerminalView.extend({
         }
     },
     onHover: function() {
-        let element = this.el;
-        let terminal = element.terminal;
+        const element = this.el;
+        const terminal = element.terminal;
         // If connected, create a popup to allow disconnection
         if (terminal.connectors.length > 0) {
-            let t = $("<div/>")
+            const t = $("<div/>")
                 .addClass("delete-terminal")
                 .click(() => {
                     $.each(terminal.connectors, (_, x) => {
@@ -291,7 +291,8 @@ var OutputTerminalView = BaseOutputTerminalView.extend({
         var type = output.extensions;
         var terminal = new Terminals.OutputTerminal({
             element: this.el,
-            datatypes: type
+            datatypes: type,
+            force_datatype: output.force_datatype
         });
         return terminal;
     }
@@ -307,7 +308,8 @@ var OutputCollectionTerminalView = BaseOutputTerminalView.extend({
             element: this.el,
             collection_type: collection_type,
             collection_type_source: collection_type_source,
-            datatypes: output.extensions
+            datatypes: output.extensions,
+            force_datatype: output.force_datatype
         });
         return terminal;
     }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index 7c166b83eae..b6bde09ec82 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js
@@ -68,30 +68,6 @@ export default Backbone.View.extend({
         var self = (window.workflow_globals.app = this);
         this.options = options;
         this.urls = (options && options.urls) || {};
-        var close_editor = () => {
-            self.workflow.check_changes_in_active_form();
-            if (self.workflow && self.workflow.has_changes) {
-                var do_close = () => {
-                    window.onbeforeunload = undefined;
-                    window.document.location = self.urls.workflow_index;
-                };
-                show_modal(
-                    "Close workflow editor",
-                    "There are unsaved changes to your workflow which will be lost.",
-                    {
-                        Cancel: hide_modal,
-                        "Save Changes": function() {
-                            save_current_workflow(null, do_close);
-                        }
-                    },
-                    {
-                        "Don't Save": do_close
-                    }
-                );
-            } else {
-                window.document.location = self.urls.workflow_index;
-            }
-        };
         var workflow_index = self.urls.workflow_index;
         var save_current_workflow = (eventObj, success_callback) => {
             show_message("Saving workflow", "progress");
@@ -272,8 +248,8 @@ export default Backbone.View.extend({
         this.type_to_type = this.datatypes_mapping.class_to_classes;
 
         this.get_workflow_versions = function() {
-            let _workflow_version_dropdown = {};
-            let workflow_versions = JSON.parse(
+            const _workflow_version_dropdown = {};
+            const workflow_versions = JSON.parse(
                 $.ajax({
                     url: `${getAppRoot()}api/workflows/${self.options.id}/versions`,
                     async: false
@@ -281,8 +257,8 @@ export default Backbone.View.extend({
             );
 
             for (let i = 0; i < workflow_versions.length; i++) {
-                let current_wf = workflow_versions[i];
-                let version_text = `Version ${current_wf["version"]}, ${current_wf["steps"]} steps`;
+                const current_wf = workflow_versions[i];
+                let version_text = `Version ${current_wf.version}, ${current_wf.steps} steps`;
                 let selected = false;
                 if (i == self.workflow.workflow_version) {
                     version_text = `${version_text} (active)`;
@@ -297,7 +273,7 @@ export default Backbone.View.extend({
         };
 
         this.build_version_select = function() {
-            let versions = this.get_workflow_versions();
+            const versions = this.get_workflow_versions();
             $("#workflow-version-switch").empty();
             $.each(versions, function(k, v) {
                 $("#workflow-version-switch").append(
@@ -311,7 +287,9 @@ export default Backbone.View.extend({
                 $("#workflow-version-switch").unbind("change");
                 if (this.value != self.workflow.workflow_version) {
                     if (self.workflow && self.workflow.has_changes) {
-                        let r = confirm("There are unsaved changes to your workflow which will be lost. Continue ?");
+                        const r = window.confirm(
+                            "There are unsaved changes to your workflow which will be lost. Continue ?"
+                        );
                         if (r == false) {
                             // We rebuild the version select list, to reset the selected version
                             self.build_version_select();
@@ -378,12 +356,12 @@ export default Backbone.View.extend({
         // Load workflow definition
         this.load_workflow(self.options.id, self.options.version);
         if (make_popupmenu) {
+            $("#workflow-run-button").click(
+                () => (window.location = `${getAppRoot()}workflows/run?id=${self.options.id}`)
+            );
+            $("#workflow-save-button").click(() => save_current_workflow());
             make_popupmenu($("#workflow-options-button"), {
-                Save: save_current_workflow,
                 "Save As": workflow_save_as,
-                Run: function() {
-                    window.location = `${getAppRoot()}workflows/run?id=${self.options.id}`;
-                },
                 "Edit Attributes": function() {
                     self.workflow.clear_active_node();
                 },
@@ -391,8 +369,7 @@ export default Backbone.View.extend({
                 Download: {
                     url: `${getAppRoot()}api/workflows/${self.options.id}/download?format=json-download`,
                     action: function() {}
-                },
-                Close: close_editor
+                }
             });
         }
 
@@ -528,7 +505,7 @@ export default Backbone.View.extend({
                     cls: "ui-button-icon-plain",
                     tooltip: _l("Copy and insert individual steps"),
                     onclick: function() {
-                        let Galaxy = getGalaxyInstance();
+                        const Galaxy = getGalaxyInstance();
                         if (workflow.step_count < 2) {
                             self.copy_into_workflow(workflow.id, workflow.name);
                         } else {
@@ -716,7 +693,7 @@ export default Backbone.View.extend({
                     if (pja.action_arguments) {
                         $.each(pja.action_arguments, (k, action_argument) => {
                             if (typeof action_argument === "string") {
-                                let arg_matches = action_argument.match(parameter_re);
+                                const arg_matches = action_argument.match(parameter_re);
                                 if (arg_matches) {
                                     matches = matches.concat(arg_matches);
                                 }
@@ -754,7 +731,7 @@ export default Backbone.View.extend({
         const cls = "right-content";
         var id = `${cls}-${node.id}`;
         var $container = $(`#${cls}`);
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (content && $container.find(`#${id}`).length === 0) {
             var $el = $(`<div id="${id}" class="${cls}"/>`);
             content.node = node;
@@ -799,6 +776,7 @@ export default Backbone.View.extend({
         // Fix width to computed width
         // Now add floats
         var buttons = $("<div class='buttons' style='float: right;'></div>");
+        buttons.append($(`<div class="sr-only"><a href="#right">Node Details</a></div>`));
         if (type !== "subworkflow") {
             buttons.append(
                 $("<div/>")
diff --git a/client/galaxy/scripts/mvc/workflow/workflow.js b/client/galaxy/scripts/mvc/workflow/workflow.js
index 720d9bea4dc..9530a6836f1 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow.js
@@ -81,7 +81,7 @@ const WorkflowItemView = Backbone.View.extend({
     },
 
     copyWorkflow: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         const oldName = this.model.get("name");
         $.getJSON(`${this.model.urlRoot}/${this.model.id}/download`, wfJson => {
             let newName = `Copy of ${oldName}`;
@@ -108,9 +108,9 @@ const WorkflowItemView = Backbone.View.extend({
     },
 
     _rowTemplate: function() {
-        let Galaxy = getGalaxyInstance();
-        let show = this.model.get("show_in_tool_panel");
-        let wfId = this.model.id;
+        const Galaxy = getGalaxyInstance();
+        const show = this.model.get("show_in_tool_panel");
+        const wfId = this.model.id;
         const checkboxHtml = `<input id="show-in-tool-panel" type="checkbox" class="show-in-tool-panel" ${
             show ? `checked="${show}"` : ""
         } value="${wfId}">`;
@@ -138,8 +138,8 @@ const WorkflowItemView = Backbone.View.extend({
     },
 
     renderTagEditor: function() {
-        let el = $(this.el).find(".tags-display")[0];
-        let propsData = {
+        const el = $(this.el).find(".tags-display")[0];
+        const propsData = {
             model: this.model,
             disabled: false,
             context: "workflow"
@@ -149,8 +149,8 @@ const WorkflowItemView = Backbone.View.extend({
 
     /** Template for user actions for workflows */
     _templateActions: function() {
-        let Galaxy = getGalaxyInstance();
-        if (this.model.get("owner") === Galaxy.user.attributes.username) {
+        const Galaxy = getGalaxyInstance();
+        if (this.model.get("owner") == Galaxy.user.attributes.username) {
             return `<div class="dropdown-menu">
                         <a class="dropdown-item" href="${getAppRoot()}workflow/editor?id=${this.model.id}">Edit</a>
                         <a class="dropdown-item" href="${getAppRoot()}workflows/run?id=${this.model.id}">Run</a>
@@ -158,24 +158,24 @@ const WorkflowItemView = Backbone.View.extend({
                         <a class="dropdown-item" href="${getAppRoot()}api/workflows/${
                 this.model.id
             }/download?format=json-download">Download</a>
-                        <a class="dropdown-item" id="copy-workflow" style="cursor: pointer;">Copy</a>
-                        <a class="dropdown-item" id="rename-workflow" style="cursor: pointer;">Rename</a>
+                        <a class="dropdown-item" id="copy-workflow">Copy</a>
+                        <a class="dropdown-item" id="rename-workflow">Rename</a>
                         <a class="dropdown-item" href="${getAppRoot()}workflow/display_by_id?id=${
                 this.model.id
             }">View</a>
-                        <a class="dropdown-item" id="delete-workflow" style="cursor: pointer;">Delete</a>
+                        <a class="dropdown-item" id="delete-workflow">Delete</a>
                     </div>`;
         } else {
-            return `<ul class="dropdown-menu">
-                        <li><a href="${getAppRoot()}workflow/display_by_username_and_slug?username=${this.model.get(
+            return `<div class="dropdown-menu">
+                        <a class="dropdown-item" href="${getAppRoot()}workflow/display_by_username_and_slug?username=${this.model.get(
                 "owner"
-            )}&slug=${this.model.get("slug")}">View</a></li>
-                        <li><a href="${getAppRoot()}workflows/run?id=${this.model.id}">Run</a></li>
-                        <li><a id="copy-workflow" style="cursor: pointer;">Copy</a></li>
-                        <li><a class="link-confirm-shared-${
+            )}&slug=${this.model.get("slug")}">View</a>
+                        <a class="dropdown-item" href="${getAppRoot()}workflows/run?id=${this.model.id}">Run</a>
+                        <a class="dropdown-item" id="copy-workflow">Copy</a>
+                        <a class="dropdown-item link-confirm-shared-${
                             this.model.id
                         }" href="${getAppRoot()}workflow/sharing?unshare_me=True&id=${this.model.id}">Remove</a></li>
-                    </ul>`;
+                    </div>`;
         }
     }
 });
diff --git a/client/galaxy/scripts/nls/fr/locale.js b/client/galaxy/scripts/nls/fr/locale.js
index 8c0c3ecfaf8..3e0f8c1ad91 100644
--- a/client/galaxy/scripts/nls/fr/locale.js
+++ b/client/galaxy/scripts/nls/fr/locale.js
@@ -306,9 +306,9 @@ define({
     // ---------------------------------------------------------------------------- history-list
     Histories: false,
     // ---------------------------------------------------------------------------- shed-list-view
-    "Configured Galaxy Tool Sheds": false,
+    "Configured Tool Sheds": false,
     // ---------------------------------------------------------------------------- repository-queue-view
-    "Repository Installation Queue": false,
+    "Repository Queue": false,
     // ---------------------------------------------------------------------------- repo-status-view
     "Repository Status": false,
     // ---------------------------------------------------------------------------- workflows-view
diff --git a/client/galaxy/scripts/nls/locale.js b/client/galaxy/scripts/nls/locale.js
index 285a390b929..bd635ce8e4b 100644
--- a/client/galaxy/scripts/nls/locale.js
+++ b/client/galaxy/scripts/nls/locale.js
@@ -306,9 +306,9 @@ define({
         // ---------------------------------------------------------------------------- history-list
         Histories: false,
         // ---------------------------------------------------------------------------- shed-list-view
-        "Configured Galaxy Tool Sheds": false,
+        "Configured Tool Sheds": false,
         // ---------------------------------------------------------------------------- repository-queue-view
-        "Repository Installation Queue": false,
+        "Repository Queue": false,
         // ---------------------------------------------------------------------------- repo-status-view
         "Repository Status": false,
         // ---------------------------------------------------------------------------- workflows-view
diff --git a/client/galaxy/scripts/onload/defaultAppFactory.js b/client/galaxy/scripts/onload/defaultAppFactory.js
index 82d76276607..778a95412f6 100644
--- a/client/galaxy/scripts/onload/defaultAppFactory.js
+++ b/client/galaxy/scripts/onload/defaultAppFactory.js
@@ -9,8 +9,8 @@ import { setGalaxyInstance } from "app";
  */
 export const defaultAppFactory = (config, label = "Galaxy") => {
     return setGalaxyInstance(GalaxyApp => {
-        let { options, bootstrapped } = config;
-        let app = new GalaxyApp(options, bootstrapped);
+        const { options, bootstrapped } = config;
+        const app = new GalaxyApp(options, bootstrapped);
         app.debug(`${label} app`);
         return app;
     });
diff --git a/client/galaxy/scripts/onload/getRootFromIndexLink.js b/client/galaxy/scripts/onload/getRootFromIndexLink.js
index 09c2d884655..e0e6cc88142 100644
--- a/client/galaxy/scripts/onload/getRootFromIndexLink.js
+++ b/client/galaxy/scripts/onload/getRootFromIndexLink.js
@@ -5,7 +5,7 @@
 import { serverPath } from "utils/serverPath";
 
 export function getRootFromIndexLink(defaultRoot = "/") {
-    let links = document.getElementsByTagName("link");
-    let indexLink = Array.from(links).find(link => link.rel == "index");
+    const links = document.getElementsByTagName("link");
+    const indexLink = Array.from(links).find(link => link.rel == "index");
     return indexLink && indexLink.href ? serverPath(indexLink.href) : defaultRoot;
 }
diff --git a/client/galaxy/scripts/onload/globalInits/initSentry.js b/client/galaxy/scripts/onload/globalInits/initSentry.js
index 7fafc9194c7..26a606447dc 100644
--- a/client/galaxy/scripts/onload/globalInits/initSentry.js
+++ b/client/galaxy/scripts/onload/globalInits/initSentry.js
@@ -10,7 +10,7 @@ export const initSentry = (galaxy, config) => {
     console.log("initSentry");
 
     if (config.sentry) {
-        let { sentry_dsn_public, email } = config.sentry;
+        const { sentry_dsn_public, email } = config.sentry;
         Raven.config(sentry_dsn_public).install();
         if (email) {
             Raven.setUser({ email });
diff --git a/client/galaxy/scripts/onload/globalInits/panelManagement.js b/client/galaxy/scripts/onload/globalInits/panelManagement.js
index 032c07841d9..39c51254caf 100644
--- a/client/galaxy/scripts/onload/globalInits/panelManagement.js
+++ b/client/galaxy/scripts/onload/globalInits/panelManagement.js
@@ -8,7 +8,7 @@ export function panelManagement(panelConfig) {
     console.log("panelManagement");
     console.log("(looks like it's assinging some global handlers to window to manage the left and right panel views?)");
 
-    let { left_panel, right_panel, rightPanelSelector, leftPanelSelector } = panelConfig;
+    const { left_panel, right_panel, rightPanelSelector, leftPanelSelector } = panelConfig;
 
     if (left_panel) {
         var lp = new window.bundleEntries.panels.LeftPanel({
diff --git a/client/galaxy/scripts/onload/initQueue.js b/client/galaxy/scripts/onload/initQueue.js
index 7a32f59c91d..cc2caeebe79 100644
--- a/client/galaxy/scripts/onload/initQueue.js
+++ b/client/galaxy/scripts/onload/initQueue.js
@@ -23,12 +23,12 @@ const queue = new BehaviorSubject([]);
 export const initializations$ = queue.pipe(filter(list => list.length > 0));
 
 export const addInitialization = (...fns) => {
-    let nextInits = [...queue.getValue(), ...fns];
+    const nextInits = [...queue.getValue(), ...fns];
     queue.next(nextInits);
 };
 
 export const prependInitialization = (...fns) => {
-    let nextInits = [...fns, ...queue.getValue()];
+    const nextInits = [...fns, ...queue.getValue()];
     queue.next(nextInits);
 };
 
diff --git a/client/galaxy/scripts/onload/standardInit.js b/client/galaxy/scripts/onload/standardInit.js
index 028e68f121b..dc128718e06 100644
--- a/client/galaxy/scripts/onload/standardInit.js
+++ b/client/galaxy/scripts/onload/standardInit.js
@@ -37,7 +37,7 @@ export function standardInit(label = "Galaxy", appFactory = defaultAppFactory) {
     globalInits();
 
     // waits for configs to stop changing then instantiates Galaxy
-    let galaxy$ = config$.pipe(map(cfg => appFactory(cfg, label)));
+    const galaxy$ = config$.pipe(map(cfg => appFactory(cfg, label)));
 
     // once config, app and initialization observables have a value then run all
     // the initialization functions, this will keep running new initialization
diff --git a/client/galaxy/scripts/qunit/test-data/bootstrapped.js b/client/galaxy/scripts/qunit/test-data/bootstrapped.js
index 0d2c7c7b2b7..b31c561a744 100644
--- a/client/galaxy/scripts/qunit/test-data/bootstrapped.js
+++ b/client/galaxy/scripts/qunit/test-data/bootstrapped.js
@@ -9,7 +9,6 @@ export default {
         allow_library_path_paste: false,
         user_library_import_dir: null,
         terms_url: null,
-        ftp_upload_dir: null,
         library_import_dir: null,
         logo_url: null,
         enable_unique_workflow_defaults: false
diff --git a/client/galaxy/scripts/qunit/tests/masthead_tests.js b/client/galaxy/scripts/qunit/tests/masthead_tests.js
index 5718b9ab2ce..3b9763fa77c 100644
--- a/client/galaxy/scripts/qunit/tests/masthead_tests.js
+++ b/client/galaxy/scripts/qunit/tests/masthead_tests.js
@@ -24,7 +24,6 @@ QUnit.module("Masthead test", {
             logo_src: "../../../static/images/galaxyIcon_noText.png",
             is_admin_user: "is_admin_user",
             active_view: "analysis",
-            ftp_upload_dir: "ftp_upload_dir",
             ftp_upload_site: "ftp_upload_site",
             datatypes_disable_auto: true,
             allow_user_creation: true,
diff --git a/client/galaxy/scripts/qunit/tests/ui_tests.js b/client/galaxy/scripts/qunit/tests/ui_tests.js
index e60164f7986..5c200c0a477 100644
--- a/client/galaxy/scripts/qunit/tests/ui_tests.js
+++ b/client/galaxy/scripts/qunit/tests/ui_tests.js
@@ -734,10 +734,10 @@ QUnit.test("select-content", function(assert) {
             select.$(".ui-select:last").css("display") == (options.selectfields == 1 ? "block" : "none"),
             "Last select visibility"
         );
-        /*assert.ok(
+        assert.ok(
             (select.button_dialog.$el.css("display") != "none") === options.showdialog,
             "Data dialog button visible"
-        );*/
+        );
         _testSelect("first", options);
         _testSelect("last", options);
     };
diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
index c02570236ff..2ecfabd1c3d 100644
--- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
+++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
@@ -73,15 +73,6 @@ QUnit.module("Input terminal model test", {
             };
         }
         return this.input_terminal.canAccept(other).canAccept;
-    },
-    pja_change_datatype_node: function(output_name, newtype) {
-        var pja = {
-            action_type: "ChangeDatatypeAction",
-            output_name: output_name,
-            action_arguments: { newtype: newtype }
-        };
-        var otherNode = { post_job_actions: [pja] };
-        return otherNode;
     }
 });
 
@@ -130,7 +121,7 @@ QUnit.test("test destroy", function(assert) {
 });
 
 QUnit.test("can accept exact datatype", function(assert) {
-    var other = { node: {}, datatypes: ["txt"] }; // input also txt
+    var other = { node: {}, datatypes: ["txt"], force_datatype: null }; // input also txt
     assert.ok(this.test_accept(other));
 });
 
@@ -145,22 +136,12 @@ QUnit.test("cannot accept incorrect datatype", function(assert) {
 });
 
 QUnit.test("can accept incorrect datatype if converted with PJA", function(assert) {
-    var otherNode = this.pja_change_datatype_node("out1", "txt");
-    var other = { node: otherNode, datatypes: ["binary"], name: "out1" }; // Was binary but converted to txt
+    var other = { node: {}, datatypes: ["binary"], force_datatype: "txt", name: "out1" }; // Was binary but converted to txt
     assert.ok(this.test_accept(other));
 });
 
 QUnit.test("cannot accept incorrect datatype if converted with PJA to incompatible type", function(assert) {
-    var otherNode = this.pja_change_datatype_node("out1", "bam"); // bam's are not txt
-    var other = { node: otherNode, datatypes: ["binary"], name: "out1" };
-    assert.ok(!this.test_accept(other));
-});
-
-QUnit.test("cannot accept incorrect datatype if some other output converted with PJA to compatible type", function(
-    assert
-) {
-    var otherNode = this.pja_change_datatype_node("out2", "txt");
-    var other = { node: otherNode, datatypes: ["binary"], name: "out1" };
+    var other = { node: {}, datatypes: ["binary"], force_datatype: "bam", name: "out1" };
     assert.ok(!this.test_accept(other));
 });
 
diff --git a/client/galaxy/scripts/store/gridSearchStore.js b/client/galaxy/scripts/store/gridSearchStore.js
index e67ddaaf92d..c5fc2bb2c5b 100644
--- a/client/galaxy/scripts/store/gridSearchStore.js
+++ b/client/galaxy/scripts/store/gridSearchStore.js
@@ -17,12 +17,12 @@ export const gridSearchStore = {
     },
     actions: {
         toggleSearchTag({ state, commit }, { text }) {
-            let tags = new Set(state.searchTags);
+            const tags = new Set(state.searchTags);
             tags.has(text) ? tags.delete(text) : tags.add(text);
             commit("setSearchTags", tags);
         },
         removeSearchTag({ state, commit }, { text }) {
-            let tags = new Set(state.searchTags);
+            const tags = new Set(state.searchTags);
             tags.delete(text);
             commit("setSearchTags", tags);
         },
diff --git a/client/galaxy/scripts/store/index.js b/client/galaxy/scripts/store/index.js
index 3ab28141579..57f2183f151 100644
--- a/client/galaxy/scripts/store/index.js
+++ b/client/galaxy/scripts/store/index.js
@@ -4,14 +4,19 @@
 
 import Vue from "vue";
 import Vuex from "vuex";
+import createCache from "vuex-cache";
+
 import { gridSearchStore } from "./gridSearchStore";
 import { tagStore } from "./tagStore";
+import { jobMetricsStore } from "./jobMetricsStore";
 
 Vue.use(Vuex);
 
 export default new Vuex.Store({
+    plugins: [createCache()],
     modules: {
         gridSearch: gridSearchStore,
-        tags: tagStore
+        tags: tagStore,
+        jobMetrics: jobMetricsStore
     }
 });
diff --git a/client/galaxy/scripts/store/jobMetricsStore.js b/client/galaxy/scripts/store/jobMetricsStore.js
new file mode 100644
index 00000000000..cc3be4d399d
--- /dev/null
+++ b/client/galaxy/scripts/store/jobMetricsStore.js
@@ -0,0 +1,47 @@
+export const state = {
+    jobMetricsByHdaId: {},
+    jobMetricsByLddaId: {},
+    jobMetricsByJobId: {}
+};
+
+import Vue from "vue";
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+const getters = {
+    getJobMetricsByDatasetId: state => (datasetId, datasetType = "hda") => {
+        const jobMetricsObject = datasetType == "hda" ? state.jobMetricsByHdaId : state.jobMetricsByLddaId;
+        return jobMetricsObject[datasetId] || [];
+    },
+    getJobMetricsByJobId: state => jobId => {
+        return state.jobMetricsByJobId[jobId] || [];
+    }
+};
+
+const actions = {
+    fetchJobMetricsForDatasetId: async ({ commit }, { datasetId, datasetType }) => {
+        const { data } = await axios.get(`${getAppRoot()}api/datasets/${datasetId}/metrics?hda_ldda=${datasetType}`);
+        commit("saveJobMetricsForDatasetId", { datasetId, datasetType, jobMetrics: data });
+    },
+    fetchJobMetricsForJobId: async ({ commit }, jobId) => {
+        const { data } = await axios.get(`${getAppRoot()}api/jobs/${jobId}/metrics`);
+        commit("saveJobMetricsForJobId", { jobId, jobMetrics: data });
+    }
+};
+
+const mutations = {
+    saveJobMetricsForDatasetId: (state, { datasetId, datasetType, jobMetrics }) => {
+        const jobMetricsObject = datasetType == "hda" ? state.jobMetricsByHdaId : state.jobMetricsByLddaId;
+        Vue.set(jobMetricsObject, datasetId, jobMetrics);
+    },
+    saveJobMetricsForJobId: (state, { jobId, jobMetrics }) => {
+        Vue.set(state.jobMetricsByJobId, jobId, jobMetrics);
+    }
+};
+
+export const jobMetricsStore = {
+    state,
+    getters,
+    actions,
+    mutations
+};
diff --git a/client/galaxy/scripts/store/tagStore.js b/client/galaxy/scripts/store/tagStore.js
index 20dc8cee3c7..b04ec8fdff5 100644
--- a/client/galaxy/scripts/store/tagStore.js
+++ b/client/galaxy/scripts/store/tagStore.js
@@ -6,7 +6,7 @@ export const state = {
 export const getters = {
     getTagsById: state => key => {
         if (state.modelTagCache.has(key)) {
-            let tagSet = state.modelTagCache.get(key); //.sort();
+            const tagSet = state.modelTagCache.get(key); //.sort();
             return Array.from(tagSet);
         }
         return [];
diff --git a/client/galaxy/scripts/ui/filter-control.js b/client/galaxy/scripts/ui/filter-control.js
deleted file mode 100644
index 332cec800a5..00000000000
--- a/client/galaxy/scripts/ui/filter-control.js
+++ /dev/null
@@ -1,202 +0,0 @@
-import jQuery from "jquery";
-import _ from "underscore";
-
-var $ = jQuery;
-//==============================================================================
-/**
- *  Template function that produces a bootstrap dropdown to replace the
- *  vanilla HTML select input. Pass in an array of options and an initial selection:
- *  $( '.my-div' ).append( dropDownSelect( [ 'option1', 'option2' ], 'option2' );
- *
- *  When the user changes the selected option a 'change.dropdown-select' event will
- *  fire with both the jq event and the new selection text as arguments.
- *
- *  Get the currently selected choice using:
- *  var userChoice = $( '.my-div .dropdown-select .dropdown-select-selected' ).text();
- *
- */
-function dropDownSelect(options, selected) {
-    // replacement for vanilla select element using bootstrap dropdowns instead
-    selected = selected || (!_.isEmpty(options) ? options[0] : "");
-    var $select = $(
-        [
-            '<div class="dropdown-select btn-group">',
-            '<button type="button" class="btn btn-secondary">',
-            `<span class="dropdown-select-selected">${selected}</span>`,
-            "</button>",
-            "</div>"
-        ].join("\n")
-    );
-
-    // if there's only one option, do not style/create as buttons, dropdown - use simple span
-    // otherwise, a dropdown displaying the current selection
-    if (options && options.length > 1) {
-        $select
-            .find("button")
-            .addClass("dropdown-toggle")
-            .attr("data-toggle", "dropdown")
-            .append(' <span class="caret"></span>');
-        $select.append(
-            [
-                '<ul class="dropdown-menu" role="menu">',
-                _.map(options, option => ['<li><a href="javascript:void(0)">', option, "</a></li>"].join("")).join(
-                    "\n"
-                ),
-                "</ul>"
-            ].join("\n")
-        );
-    }
-
-    // trigger 'change.dropdown-select' when a new selection is made using the dropdown
-    function selectThis(event) {
-        var $this = $(this);
-        var $select = $this.parents(".dropdown-select");
-        var newSelection = $this.text();
-        $select.find(".dropdown-select-selected").text(newSelection);
-        $select.trigger("change.dropdown-select", newSelection);
-    }
-
-    $select.find("a").click(selectThis);
-    return $select;
-}
-
-//==============================================================================
-/**
- *  Creates a three part bootstrap button group (key, op, value) meant to
- *  allow the user control of filters (e.g. { key: 'name', op: 'contains', value: 'my_history' })
- *
- *  Each field uses a dropDownSelect (from ui.js) to allow selection
- *  (with the 'value' field appearing as an input when set to do so).
- *
- *  Any change or update in any of the fields will trigger a 'change.filter-control'
- *  event which will be passed an object containing those fields (as the example above).
- *
- *  Pass in an array of possible filter objects to control what the user can select.
- *  Each filter object should have:
- *      key : generally the attribute name on which to filter something
- *      ops : an array of 1 or more filter operations (e.g. [ 'is', '<', 'contains', '!=' ])
- *      values (optional) : an array of possible values for the filter (e.g. [ 'true', 'false' ])
- *  @example:
- *  $( '.my-div' ).filterControl({
- *      filters : [
- *          { key: 'name',    ops: [ 'is exactly', 'contains' ] }
- *          { key: 'deleted', ops: [ 'is' ], values: [ 'true', 'false' ] }
- *      ]
- *  });
- *  // after initialization, you can prog. get the current value using:
- *  $( '.my-div' ).filterControl( 'val' )
- *
- */
-function FilterControl(element, options) {
-    return this.init(element, options);
-}
-/** the data key that this object will be stored under in the DOM element */
-FilterControl.prototype.DATA_KEY = "filter-control";
-
-/** parses options, sets up instance vars, and does initial render */
-FilterControl.prototype.init = function _init(element, options) {
-    options = options || { filters: [] };
-    this.$element = $(element).addClass("filter-control btn-group");
-    this.options = jQuery.extend(true, {}, this.defaults, options);
-
-    this.currFilter = this.options.filters[0];
-    return this.render();
-};
-
-/** render (or re-render) the controls on the element */
-FilterControl.prototype.render = function _render() {
-    this.$element.empty().append([this._renderKeySelect(), this._renderOpSelect(), this._renderValueInput()]);
-    return this;
-};
-
-/** render the key dropDownSelect, bind a change event to it, and return it */
-FilterControl.prototype._renderKeySelect = function __renderKeySelect() {
-    var filterControl = this;
-    var keys = this.options.filters.map(filter => filter.key);
-    this.$keySelect = dropDownSelect(keys, this.currFilter.key)
-        .addClass("filter-control-key")
-        .on("change.dropdown-select", (event, selection) => {
-            filterControl.currFilter = _.findWhere(filterControl.options.filters, { key: selection });
-            // when the filter/key changes, re-render the control entirely
-            filterControl.render()._triggerChange();
-        });
-    return this.$keySelect;
-};
-
-/** render the op dropDownSelect, bind a change event to it, and return it */
-FilterControl.prototype._renderOpSelect = function __renderOpSelect() {
-    var filterControl = this;
-    var ops = this.currFilter.ops;
-    //TODO: search for currOp in avail. ops: use that for selected if there; otherwise: first op
-    this.$opSelect = dropDownSelect(ops, ops[0])
-        .addClass("filter-control-op")
-        .on("change.dropdown-select", (event, selection) => {
-            filterControl._triggerChange();
-        });
-    return this.$opSelect;
-};
-
-/** render the value control, bind a change event to it, and return it */
-FilterControl.prototype._renderValueInput = function __renderValueInput() {
-    var filterControl = this;
-    // if a values attribute is prov. on the filter - make this a dropdown; otherwise, use an input
-    if (this.currFilter.values) {
-        this.$valueSelect = dropDownSelect(this.currFilter.values, this.currFilter.values[0]).on(
-            "change.dropdown-select",
-            (event, selection) => {
-                filterControl._triggerChange();
-            }
-        );
-    } else {
-        //TODO: allow setting a value type (mainly for which html5 input to use: range, number, etc.)
-        this.$valueSelect = $("<input/>")
-            .addClass("form-control")
-            .on("change", (event, value) => {
-                filterControl._triggerChange();
-            });
-    }
-    this.$valueSelect.addClass("filter-control-value");
-    return this.$valueSelect;
-};
-
-/** return the current state/setting for the filter as a three key object: key, op, value */
-FilterControl.prototype.val = function _val() {
-    var key = this.$element.find(".filter-control-key .dropdown-select-selected").text();
-
-    var op = this.$element.find(".filter-control-op .dropdown-select-selected").text();
-
-    var // handle either a dropdown or plain input
-        $value = this.$element.find(".filter-control-value");
-
-    var value = $value.hasClass("dropdown-select") ? $value.find(".dropdown-select-selected").text() : $value.val();
-
-    return { key: key, op: op, value: value };
-};
-
-// single point of change for change event
-FilterControl.prototype._triggerChange = function __triggerChange() {
-    this.$element.trigger("change.filter-control", this.val());
-};
-
-// as jq plugin
-jQuery.fn.extend({
-    filterControl: function $filterControl(options) {
-        var nonOptionsArgs = jQuery.makeArray(arguments).slice(1);
-        return this.map(function() {
-            var $this = $(this);
-            var data = $this.data(FilterControl.prototype.DATA_KEY);
-
-            if (jQuery.type(options) === "object") {
-                data = new FilterControl($this, options);
-                $this.data(FilterControl.prototype.DATA_KEY, data);
-            }
-            if (data && jQuery.type(options) === "string") {
-                var fn = data[options];
-                if (jQuery.type(fn) === "function") {
-                    return fn.apply(data, nonOptionsArgs);
-                }
-            }
-            return this;
-        });
-    }
-});
diff --git a/client/galaxy/scripts/ui/popupmenu.js b/client/galaxy/scripts/ui/popupmenu.js
index 68b68d51c29..4b00f445105 100644
--- a/client/galaxy/scripts/ui/popupmenu.js
+++ b/client/galaxy/scripts/ui/popupmenu.js
@@ -29,27 +29,27 @@ export function make_popupmenu(button_element, initial_options) {
         // Need setTimeouts so clicks don't interfere with each other
         setTimeout(() => {
             // Dynamically generate the wrapper holding all the selectable options of the menu.
-            var menu_element = $(`<ul class='dropdown-menu' id='${button_element.attr("id")}-menu'></ul>`);
+            var menu_element = $(`<div class="dropdown-menu" id="${button_element.attr("id")}-menu"/>`);
             var options = button_element.data("menu_options");
             if (_.size(options) <= 0) {
-                $("<li>No Options.</li>").appendTo(menu_element);
+                $('<div class="dropdown-item">No Options.</div>').appendTo(menu_element);
             }
             $.each(options, (k, v) => {
                 if (v) {
                     // Action can be either an anonymous function and a mapped dict.
-                    var action = v.action || v;
+                    const action = v.action || v;
+                    const url = v.url || "javascript:void(0);";
                     menu_element.append(
-                        $("<li></li>").append(
-                            $("<a>")
-                                .attr("href", v.url)
-                                .html(k)
-                                .click(action)
-                        )
+                        $("<a>")
+                            .addClass("dropdown-item")
+                            .attr("href", url)
+                            .html(k)
+                            .click(action)
                     );
                 } else {
                     menu_element.append(
-                        $("<li></li>")
-                            .addClass("head")
+                        $("<div/>")
+                            .addClass("dropdown-item head")
                             .append($("<a href='#'></a>").html(k))
                     );
                 }
diff --git a/client/galaxy/scripts/ui/scroll-panel.js b/client/galaxy/scripts/ui/scroll-panel.js
index 9abac82e7ce..be11d18d5e8 100644
--- a/client/galaxy/scripts/ui/scroll-panel.js
+++ b/client/galaxy/scripts/ui/scroll-panel.js
@@ -43,24 +43,24 @@ $.ui.plugin.add("draggable", "scrollPanel", {
 
         // Move it
         if (panel_pos.left < p_max_x && mouse_x - close_dist < min_vis_x) {
-            let t = Math.min(nudge, p_max_x - panel_pos.left);
+            const t = Math.min(nudge, p_max_x - panel_pos.left);
             panel.css("left", panel_pos.left + t);
             moved = true;
             instance.offset.parent.left += t;
             ui.position.left -= t;
         }
         if (!moved && panel_pos.left > p_min_x && mouse_x + close_dist > max_vis_x) {
-            let t = Math.min(nudge, panel_pos.left - p_min_x);
+            const t = Math.min(nudge, panel_pos.left - p_min_x);
             panel.css("left", panel_pos.left - t);
             moved = true;
             instance.offset.parent.left -= t;
             ui.position.left += t;
         }
         if (!moved && panel_pos.top < p_max_y && mouse_y - close_dist < min_vis_y) {
-            let t = Math.min(nudge, p_max_y - panel_pos.top);
+            const t = Math.min(nudge, p_max_y - panel_pos.top);
             panel.css("top", panel_pos.top + t);
             // Firefox sometimes moves by less, so we need to check. Yuck.
-            let amount_moved = panel.position().top - panel_pos.top;
+            const amount_moved = panel.position().top - panel_pos.top;
             instance.offset.parent.top += amount_moved;
             ui.position.top -= amount_moved;
             moved = true;
@@ -69,7 +69,7 @@ $.ui.plugin.add("draggable", "scrollPanel", {
             var t = Math.min(nudge, panel_pos.top - p_min_x);
             panel.css("top", `${panel_pos.top - t}px`);
             // Firefox sometimes moves by less, so we need to check. Yuck.
-            let amount_moved = panel_pos.top - panel.position().top;
+            const amount_moved = panel_pos.top - panel.position().top;
             instance.offset.parent.top -= amount_moved;
             ui.position.top += amount_moved;
             moved = true;
diff --git a/client/galaxy/scripts/utils/color.js b/client/galaxy/scripts/utils/color.js
index 6dc89e51ab9..20ee5b6b772 100644
--- a/client/galaxy/scripts/utils/color.js
+++ b/client/galaxy/scripts/utils/color.js
@@ -57,15 +57,15 @@ export function hslToRgb(h, s, l) {
  * from a string key
  */
 export function keyedColorScheme(strKey) {
-    let hash = hashFnv32a(strKey);
-    let hue = Math.abs((hash >> 4) % 360);
-    let lightnessOffset = 75;
-    let lightness = lightnessOffset + (hash & 0xf);
+    const hash = hashFnv32a(strKey);
+    const hue = Math.abs((hash >> 4) % 360);
+    const lightnessOffset = 75;
+    const lightness = lightnessOffset + (hash & 0xf);
 
-    let primary = `hsl(${hue}, 100%, ${lightness}%)`;
-    let darker = `hsl(${hue}, 100%, ${lightness - 40}%)`;
-    let [r, g, b] = hslToRgb(hue, 1.0, lightness / 100);
-    let contrasting = contrastingColor(r, g, b);
+    const primary = `hsl(${hue}, 100%, ${lightness}%)`;
+    const darker = `hsl(${hue}, 100%, ${lightness - 40}%)`;
+    const [r, g, b] = hslToRgb(hue, 1.0, lightness / 100);
+    const contrasting = contrastingColor(r, g, b);
 
     return { primary, darker, contrasting };
 }
diff --git a/client/galaxy/scripts/utils/config.js b/client/galaxy/scripts/utils/config.js
index 0883c7261ba..2aba2263936 100644
--- a/client/galaxy/scripts/utils/config.js
+++ b/client/galaxy/scripts/utils/config.js
@@ -364,7 +364,7 @@ var ConfigSettingCollectionView = Backbone.View.extend({
     render_in_modal: function(title) {
         // Set up handlers for cancel, ok button and for handling esc key.
         var self = this;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         var cancel_fn = () => {
             Galaxy.modal.hide();
diff --git a/client/galaxy/scripts/utils/deferred.js b/client/galaxy/scripts/utils/deferred.js
index 04e93a10220..7b6e2656907 100644
--- a/client/galaxy/scripts/utils/deferred.js
+++ b/client/galaxy/scripts/utils/deferred.js
@@ -19,7 +19,7 @@ export default Backbone.Model.extend({
         var self = this;
         var id = Utils.uid();
         var has_deferred = callback.length > 0;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         // register process
         this.active[id] = true;
@@ -53,7 +53,7 @@ export default Backbone.Model.extend({
     /** Resets the promise queue. All currently queued but unexecuted callbacks/promises will be rejected.
      */
     reset: function() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         Galaxy.emit.debug("deferred::execute()", "Reset");
         for (var i in this.active) {
             this.active[i] = false;
diff --git a/client/galaxy/scripts/utils/genericConfig.js b/client/galaxy/scripts/utils/genericConfig.js
index c8348e144d7..057fdd13688 100644
--- a/client/galaxy/scripts/utils/genericConfig.js
+++ b/client/galaxy/scripts/utils/genericConfig.js
@@ -3,7 +3,7 @@
  */
 
 export function buildConfig(defaultConfigs = {}) {
-    let storage = Object.assign({}, defaultConfigs);
+    const storage = Object.assign({}, defaultConfigs);
 
     return new Proxy(storage, {
         get(target, propName) {
diff --git a/client/galaxy/scripts/utils/installMonitor.js b/client/galaxy/scripts/utils/installMonitor.js
index 218a997c0ab..146fda09384 100644
--- a/client/galaxy/scripts/utils/installMonitor.js
+++ b/client/galaxy/scripts/utils/installMonitor.js
@@ -26,9 +26,9 @@ export function installMonitor(globalProp) {
 }
 
 export function installObjectWatcher(globalProp, getter = null, setter = null) {
-    let label = `window.${globalProp}`;
-    let debug = isPropMonitored(globalProp);
-    let logger = debug ? console : mock(console);
+    const label = `window.${globalProp}`;
+    const debug = isPropMonitored(globalProp);
+    const logger = debug ? console : mock(console);
 
     // Replaces window.Thing with an object definition that forwards
     // gets and set values to window._monitorStorage
@@ -75,7 +75,7 @@ export function installObjectWatcher(globalProp, getter = null, setter = null) {
 // sets a flag in sessionStorage to install a monitor for the
 // indicated prop on the next page refresh
 export function toggleGlobalMonitor(prop, bShow = true) {
-    let toggleList = getToggles();
+    const toggleList = getToggles();
     if (bShow) {
         toggleList[prop] = true;
     } else {
@@ -89,20 +89,20 @@ export function toggleGlobalMonitor(prop, bShow = true) {
 
 // determines whether specified prop is toggled on or off by the user
 export function isPropMonitored(prop) {
-    let toggleList = getToggles();
+    const toggleList = getToggles();
     return toggleList[prop] == true;
 }
 
 // show list of monitor toggles
 export function showMonitorToggles() {
-    let toggleList = getToggles();
+    const toggleList = getToggles();
     console.log(toggleList);
 }
 
 // retrieve toggle list from the session storage
 function getToggles() {
-    let json = sessionStorage.getItem("global_monitors");
-    let existinglist = json ? JSON.parse(json) : {};
+    const json = sessionStorage.getItem("global_monitors");
+    const existinglist = json ? JSON.parse(json) : {};
     return existinglist;
 }
 
@@ -114,7 +114,7 @@ function setToggles(toggleList) {
 // Display properties available for monitoring at time of page reload
 // (you can add more during a page-session with installMonitor)
 export function monitorInit() {
-    let monitoredProps = Object.keys(getToggles());
+    const monitoredProps = Object.keys(getToggles());
 
     console.groupCollapsed("monitor init");
     console.log(
diff --git a/client/galaxy/scripts/utils/localization.js b/client/galaxy/scripts/utils/localization.js
index a6696b7c208..cf7269f662b 100644
--- a/client/galaxy/scripts/utils/localization.js
+++ b/client/galaxy/scripts/utils/localization.js
@@ -6,7 +6,7 @@ define(["i18n!nls/locale"], function(localeStrings) {
     if (localeStrings.hasOwnProperty("__root")) {
         //console.debug( 'amdi18n+webpack localization for ' + locale + ' loaded' );
 
-        let locale = sessionStorage.getItem("currentLocale");
+        const locale = sessionStorage.getItem("currentLocale");
 
         if (locale) {
             localeStrings =
diff --git a/client/galaxy/scripts/utils/mountVueComponent.js b/client/galaxy/scripts/utils/mountVueComponent.js
index ab13a882cb3..e46180ac541 100644
--- a/client/galaxy/scripts/utils/mountVueComponent.js
+++ b/client/galaxy/scripts/utils/mountVueComponent.js
@@ -9,6 +9,6 @@ import _l from "utils/localization";
 Vue.filter("localize", value => _l(value));
 
 export const mountVueComponent = ComponentDefinition => (propsData, el) => {
-    let component = Vue.extend(ComponentDefinition);
+    const component = Vue.extend(ComponentDefinition);
     return new component({ store, propsData, el });
 };
diff --git a/client/galaxy/scripts/utils/safeAssign.js b/client/galaxy/scripts/utils/safeAssign.js
new file mode 100644
index 00000000000..b10591e7fbf
--- /dev/null
+++ b/client/galaxy/scripts/utils/safeAssign.js
@@ -0,0 +1,11 @@
+// Object.assign, but props transferred must exist in target
+
+export function safeAssign(target, source = {}) {
+    if (!(source instanceof Object)) {
+        console.warn("safeAssign expected an object, instead got:", source);
+        source = {};
+    }
+    Object.keys(source)
+        .filter(prop => target.hasOwnProperty(prop))
+        .forEach(prop => (target[prop] = source[prop]));
+}
diff --git a/client/galaxy/scripts/utils/serverPath.js b/client/galaxy/scripts/utils/serverPath.js
index 862e35adaf1..c4233c11f31 100644
--- a/client/galaxy/scripts/utils/serverPath.js
+++ b/client/galaxy/scripts/utils/serverPath.js
@@ -1,4 +1,4 @@
 export function serverPath(rawUrl = window.location.href) {
-    let url = new URL(rawUrl);
+    const url = new URL(rawUrl);
     return url.pathname;
 }
diff --git a/client/galaxy/scripts/utils/uploadbox.js b/client/galaxy/scripts/utils/uploadbox.js
index ddbcd3cfe58..1e69b6b713e 100644
--- a/client/galaxy/scripts/utils/uploadbox.js
+++ b/client/galaxy/scripts/utils/uploadbox.js
@@ -197,13 +197,13 @@ import { getAppRoot } from "onload/loadConfig";
 
         // construct form data
         var form = new FormData();
-        for (let key in data.payload) {
+        for (const key in data.payload) {
             form.append(key, data.payload[key]);
         }
 
         // add files to submission
         var sizes = 0;
-        for (let key in data.files) {
+        for (const key in data.files) {
             var d = data.files[key];
             form.append(d.name, d.file, d.file.name);
             sizes += d.file.size;
@@ -256,7 +256,7 @@ import { getAppRoot } from "onload/loadConfig";
         );
 
         // drag/drop events
-        let element = el.get(0);
+        const element = el.get(0);
         element.addEventListener("drop", e => {
             opts.ondragleave(e);
             if (e.dataTransfer) {
@@ -377,7 +377,7 @@ import { getAppRoot } from "onload/loadConfig";
 
             // get an identifier from the queue
             var index = -1;
-            for (let key in queue) {
+            for (const key in queue) {
                 index = key;
                 break;
             }
diff --git a/client/galaxy/scripts/utils/utils.js b/client/galaxy/scripts/utils/utils.js
index fda27e2bf6d..f356a1ccc0e 100644
--- a/client/galaxy/scripts/utils/utils.js
+++ b/client/galaxy/scripts/utils/utils.js
@@ -340,7 +340,7 @@ export function getQueryString(key) {
 }
 
 export function setWindowTitle(title) {
-    let Galaxy = getGalaxyInstance();
+    const Galaxy = getGalaxyInstance();
     if (title) {
         window.document.title = `Galaxy ${Galaxy.config.brand ? ` | ${Galaxy.config.brand}` : ""} | ${_l(title)}`;
     } else {
diff --git a/client/galaxy/scripts/viz/circster.js b/client/galaxy/scripts/viz/circster.js
index 2ceb59d6516..432c37daca0 100644
--- a/client/galaxy/scripts/viz/circster.js
+++ b/client/galaxy/scripts/viz/circster.js
@@ -1172,7 +1172,7 @@ var Circster = Backbone.View.extend({
                     icon_class: "disk--arrow",
                     title: _l("Save"),
                     on_click: function() {
-                        let Galaxy = getGalaxyInstance();
+                        const Galaxy = getGalaxyInstance();
 
                         // show saving dialog box
                         Galaxy.modal.show({
diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js
index 9ab6dc122a3..66891e4b0f8 100644
--- a/client/galaxy/scripts/viz/trackster.js
+++ b/client/galaxy/scripts/viz/trackster.js
@@ -45,7 +45,7 @@ export class TracksterUI extends Backbone.Model {
      * Save visualization, returning a Deferred object for the remote call to save.
      */
     save_viz() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
 
         // show dialog
         Galaxy.modal.show({ title: "Saving...", body: "progress" });
@@ -347,7 +347,7 @@ export class TracksterUI extends Backbone.Model {
      * Handle unsaved changes in visualization.
      */
     handle_unsaved_changes(view) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         if (view.has_changes) {
             Galaxy.modal.show({
                 title: _l("Close visualization"),
@@ -416,7 +416,7 @@ export class TracksterUIView extends Backbone.View {
     }
 
     choose_existing_or_new() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var dbkey = query_string.get("dbkey");
         var listTracksParams = {};
 
@@ -452,7 +452,7 @@ export class TracksterUIView extends Backbone.View {
 
     // view
     view_in_saved(dataset_params) {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         var tracks_grid = new GridView({
             url_base: `${getAppRoot()}visualization/list_tracks`,
             embedded: true
@@ -501,7 +501,7 @@ export class TracksterUIView extends Backbone.View {
 
     // view
     view_new() {
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         // ajax
         $.ajax({
             url: `${getAppRoot()}api/genomes?chrom_info=True`,
diff --git a/client/galaxy/scripts/viz/trackster/filters.js b/client/galaxy/scripts/viz/trackster/filters.js
index a3e0e6c71f2..34309eeda8e 100644
--- a/client/galaxy/scripts/viz/trackster/filters.js
+++ b/client/galaxy/scripts/viz/trackster/filters.js
@@ -659,7 +659,7 @@ _.extend(FiltersManager.prototype, {
             // https://github.com/galaxyproject/galaxy/issues/7224
             // eslint-disable-next-line no-undef
             $.getJSON(run_tool_url, url_params, response => {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
                 if (response.error) {
                     // General error.
                     Galaxy.modal.show({
diff --git a/client/galaxy/scripts/viz/trackster/painters.js b/client/galaxy/scripts/viz/trackster/painters.js
index eda491e2a08..685d5ce715f 100644
--- a/client/galaxy/scripts/viz/trackster/painters.js
+++ b/client/galaxy/scripts/viz/trackster/painters.js
@@ -982,7 +982,7 @@ class ReadPainter extends FeaturePainter {
                         // Draw base if showing all (i.e. not showing differences) or there is a mismatch.
                         if ((cur_seq && !this.prefs.show_differences) || cig_op === "X") {
                             // Draw base.
-                            let c_start = Math.floor(Math.max(0, (start_pos + c - tile_low) * w_scale));
+                            const c_start = Math.floor(Math.max(0, (start_pos + c - tile_low) * w_scale));
                             ctx.fillStyle = this.base_color_fn(cur_seq[c]);
                             if (pack_mode && w_scale > char_width_px) {
                                 ctx.fillText(cur_seq[c], c_start, y_start + 9);
@@ -1057,7 +1057,7 @@ class ReadPainter extends FeaturePainter {
                                 }
                                 // Draw sequence.
                                 for (let c = 0, str_len = seq.length; c < str_len; c++) {
-                                    let c_start = Math.floor(Math.max(0, (seq_start + c - tile_low) * w_scale));
+                                    const c_start = Math.floor(Math.max(0, (seq_start + c - tile_low) * w_scale));
                                     ctx.fillText(seq[c], c_start - (s_end - s_start) / 2, y_start);
                                 }
                             } else {
diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js
index c93285b1684..7828331ae1a 100644
--- a/client/galaxy/scripts/viz/trackster/tracks.js
+++ b/client/galaxy/scripts/viz/trackster/tracks.js
@@ -783,11 +783,11 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
                 //
                 this.filters_manager.remove_all();
                 for (var filter_name in shared_filters) {
-                    let filters = shared_filters[filter_name];
+                    const filters = shared_filters[filter_name];
                     if (filters.length === num_feature_tracks) {
                         // Add new filter.
                         // FIXME: can filter.copy() be used?
-                        let new_filter = new filters_mod.NumberFilter({
+                        const new_filter = new filters_mod.NumberFilter({
                             name: filters[0].name,
                             index: filters[0].index
                         });
@@ -1000,6 +1000,9 @@ var TracksterView = Backbone.View.extend({
                 });
             });
 
+        // We break out of the parent container with nav (and potentially other
+        // things?) so we need to override any overflow settings here.
+        parent_element.css("overflow", "visible");
         // Navigation at top
         this.nav_container = $("<div/>")
             .addClass("trackster-nav-container")
@@ -1947,7 +1950,7 @@ var TracksterToolView = Backbone.View.extend({
      */
     run_on_dataset: function() {
         var tool = this.model;
-        let Galaxy = getGalaxyInstance();
+        const Galaxy = getGalaxyInstance();
         this.run(
             // URL params.
             {
@@ -2447,7 +2450,7 @@ extend(Track.prototype, Drawable.prototype, {
             title: _l("Tool parameter space visualization"),
             css_class: "arrow-split",
             on_click_fn: track => {
-                let Galaxy = getGalaxyInstance();
+                const Galaxy = getGalaxyInstance();
 
                 var html = `
                     <strong>Tool</strong>:${track.tool.get("name")}<br/>
@@ -2714,7 +2717,7 @@ extend(Track.prototype, Drawable.prototype, {
                         $("<a href='javascript:void(0);'></a>")
                             .text("View error")
                             .click(() => {
-                                let Galaxy = getGalaxyInstance();
+                                const Galaxy = getGalaxyInstance();
                                 Galaxy.modal.show({
                                     title: _l("Trackster Error"),
                                     body: `<pre>${result.message}</pre>`,
diff --git a/client/galaxy/scripts/viz/visualization.js b/client/galaxy/scripts/viz/visualization.js
index bac79766551..a439e8cae95 100644
--- a/client/galaxy/scripts/viz/visualization.js
+++ b/client/galaxy/scripts/viz/visualization.js
@@ -73,7 +73,7 @@ var select_datasets = (filters, success_fn) => {
     });
 
     // modal
-    let Galaxy = getGalaxyInstance();
+    const Galaxy = getGalaxyInstance();
     Galaxy.modal.show({
         title: _l("Select datasets for new tracks"),
         body: tabs.$el,
diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss
index 9fe96416cf5..cb5b7a3560c 100644
--- a/client/galaxy/style/scss/base.scss
+++ b/client/galaxy/style/scss/base.scss
@@ -36,6 +36,7 @@ $fa-font-path: "../../../node_modules/font-awesome/fonts/";
 @import "flex.scss";
 @import "charts.scss";
 @import "message.scss";
+@import "toolshed.scss";
 
 // Mixins
 @mixin user-select($select) {
@@ -139,7 +140,6 @@ body {
 }
 
 // Panels
-
 #left,
 #center,
 #right {
@@ -147,19 +147,22 @@ body {
     top: 0;
     height: 100%;
     overflow: hidden;
-    background: #fff;
+    background: white;
 }
 #left {
     left: 0px;
     width: $panel-width;
-    z-index: 200;
     border-right: $layout-border;
 }
+#right {
+    right: 0px;
+    width: $panel-width;
+    border-left: $layout-border;
+}
 #center {
     left: $panel-width;
     right: $panel-width;
     overflow: hidden;
-    z-index: 1;
     .center-container {
         position: absolute;
         width: 100%;
@@ -188,21 +191,6 @@ body {
     }
 }
 
-#right {
-    width: $panel-width;
-    right: 0px;
-    z-index: 200;
-    border-left: $layout-border;
-}
-
-#left,
-#right,
-.unified-panel {
-    background: $panel-bg-color;
-    display: flex;
-    flex-direction: column;
-}
-
 #left,
 #right,
 .unified-panel {
@@ -215,7 +203,6 @@ body {
     @extend .unselectable;
     @extend .mx-3;
     height: $panel_header_height;
-    z-index: 1000;
     font-size: 1rem;
     font-weight: bold;
     display: flex;
@@ -254,7 +241,6 @@ body {
     height: $panel_footer_height;
     line-height: $panel_footer_height;
     width: 100%;
-    z-index: 1000; // Above #dd-helper
     border-top: $layout-border;
     background: $panel-footer-bg-color;
     color: $panel-header-text-color;
@@ -284,42 +270,48 @@ body {
 
 // Needs to be outside panel to show when hidden
 .panel-collapse {
-    @extend .unified-panel-footer;
-    font-size: 4/3em;
     @extend .fa-icon;
-    &:before {
-        content: "\f053";
-    }
-    &.hidden:before {
-        content: "\f054";
-    }
-    z-index: 201;
+    $border-color: darken($panel-footer-bg-color, 20%);
+    font-size: 4/3em;
     cursor: pointer;
     display: block;
     position: fixed;
-    left: 0;
-    top: inherit;
-    bottom: 0;
-    padding: 0 5px;
     text-align: center;
     height: $panel_footer_height;
     line-height: $panel_footer_height;
-    width: $panel_footer_height - 5;
-    background: none;
-    border-right: $layout-border;
-    border-top: $layout-border;
+    width: $panel_footer_height;
     background: $panel-footer-bg-color;
+    border: solid $panel-footer-bg-color 1px;
+    z-index: 1;
     &.right {
-        left: inherit;
         right: 0;
-        border-right: none;
-        border-left: $layout_border;
-        &.right:before {
+        border-top-left-radius: $border-radius-base;
+        line-height: inherit;
+        &:before {
             content: "\f054";
         }
-        &.right.hidden:before {
+        &.hidden:before {
             content: "\f053";
         }
+        &.hidden {
+            border-top-color: $border-color;
+            border-left-color: $border-color;
+        }
+    }
+    &.left {
+        left: 0;
+        border-top-right-radius: $border-radius-base;
+        line-height: inherit;
+        &:before {
+            content: "\f053";
+        }
+        &.hidden:before {
+            content: "\f054";
+        }
+        &.hidden {
+            border-top-color: $border-color;
+            border-right-color: $border-color;
+        }
     }
 }
 
@@ -500,6 +492,7 @@ div.unified-panel-body-background {
         @extend .text-dark;
         font-size: 12px;
         text-decoration: none;
+        display: block;
     }
 }
 
@@ -684,7 +677,7 @@ div.form-row-input label {
 }
 
 #run-workflow {
-    @include float-right;
+    @extend .float-right;
     @extend .mt-3;
 }
 
@@ -1328,7 +1321,7 @@ div.popmenu-wrapper {
     top: 100%;
     z-index: 20000;
 
-    ul.dropdown-menu {
+    .dropdown-menu {
         // Since our menus are contained in a positioned div, need to override some styles
         display: block;
         position: relative;
@@ -1336,29 +1329,6 @@ div.popmenu-wrapper {
     }
 }
 
-// For all dropdowns, define some additional item types
-ul.dropdown-menu {
-    a {
-        text-decoration: none;
-    }
-    li.head > a {
-        // From nav-list nav-header
-        text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5);
-        font-size: 11px;
-        font-weight: bold;
-        line-height: $line-height-base;
-        color: $text-color;
-        text-transform: uppercase;
-    }
-    li.head > a:hover {
-        background: inherit;
-        border-color: transparent;
-    }
-    li > a {
-        @extend .dropdown-item;
-    }
-}
-
 .popup-arrow {
     cursor: pointer;
     text-decoration: none;
@@ -1918,7 +1888,8 @@ div.toolTitleNoSection {
 }
 
 /* Toolshed, reports custom styles from mako templates */
-body.toolshed, body.reports {
+body.toolshed,
+body.reports {
     margin: 0;
     padding: 0;
     overflow: hidden;
diff --git a/client/galaxy/style/scss/library.scss b/client/galaxy/style/scss/library.scss
index 7e7b99c807d..ca7b392c029 100644
--- a/client/galaxy/style/scss/library.scss
+++ b/client/galaxy/style/scss/library.scss
@@ -60,6 +60,10 @@
             }
         }
     }
+    tr.light {
+        font-weight: initial;
+        color: initial;
+    }
     tr.light td {
         background-color: white;
         color: black;
@@ -75,6 +79,12 @@
         background-color: #ebd4a4;
         color: white;
     }
+    tr.table-primary td {
+        color: $brand-light;
+    }
+    tr.table-primary td a {
+        color: $brand-white;
+    }
     a.dark {
         color: white;
     }
diff --git a/client/galaxy/style/scss/mixins.scss b/client/galaxy/style/scss/mixins.scss
index 6cdf41fd46f..81f7b907670 100644
--- a/client/galaxy/style/scss/mixins.scss
+++ b/client/galaxy/style/scss/mixins.scss
@@ -1,3 +1,7 @@
+$fa-font-path: "~font-awesome/fonts/";
+@import "~font-awesome/scss/font-awesome.scss";
+@import "~font-awesome/scss/_mixins";
+
 // Utility mixin expands to container edges
 @mixin fill() {
     position: relative;
@@ -29,3 +33,51 @@
         display: none;
     }
 }
+
+@mixin scrollMe() {
+    overflow-x: hidden;
+    overflow-y: scroll;
+    &::-webkit-scrollbar {
+        display: none;
+    }
+}
+
+// top selector fixed, bottom list scrolls
+@mixin scrollingListLayout($fixedTop, $listRegion) {
+    @include fill();
+
+    display: flex;
+    flex-direction: column;
+
+    #{$fixedTop} {
+        flex-grow: 0;
+    }
+
+    #{$listRegion} {
+        flex-grow: 1;
+        @include scrollMe();
+    }
+}
+
+// Removes browser formatting of lists
+
+@mixin list_reset() {
+    list-style: none;
+    padding: 0 0 0 0;
+    margin: 0 0 0 0;
+}
+
+// font awesome as a mixin
+// icon variables come from ~font-awesome/scss/_variables.scss
+
+@mixin fontawesome($icon) {
+    @include fa-icon();
+    &:before {
+        content: $icon;
+    }
+    span {
+        // Span for text readers
+        // <a><span>Label</span></a>
+        @include sr-only();
+    }
+}
diff --git a/client/galaxy/style/scss/overrides.scss b/client/galaxy/style/scss/overrides.scss
index f45f259ea75..456f65fc816 100644
--- a/client/galaxy/style/scss/overrides.scss
+++ b/client/galaxy/style/scss/overrides.scss
@@ -53,18 +53,8 @@ input[type="radio"] {
     max-width: 900px; // BS4 sets this to 500px now, so width not respected.
 }
 
-.pagination {
-    > .active > a {
-        background-color: #ebd9b2;
-        color: black;
-        &:hover {
-            color: black;
-            background-color: #ebd9b2;
-        }
-    }
-}
-
 // Scroll modal body.
+
 .modal-body {
     overflow: auto;
 }
@@ -95,3 +85,18 @@ pre.code {
     color: white;
     padding: 1em;
 }
+
+// increase visibility of links within alert boxes
+.alert-info, .alert-danger, .alert-warning, .alert-success {
+    a {
+        font-weight: bold;
+    }
+}
+
+// increase visibility of dropdown menu section headers
+.dropdown-header {
+    font-size: 1rem;
+    color: $brand-dark;
+    padding: .5rem 1.5rem .5rem 1rem;
+    font-weight: bold;
+}
diff --git a/client/galaxy/style/scss/theme/blue.scss b/client/galaxy/style/scss/theme/blue.scss
index 219a0f46afb..de520a37669 100644
--- a/client/galaxy/style/scss/theme/blue.scss
+++ b/client/galaxy/style/scss/theme/blue.scss
@@ -71,7 +71,7 @@ $font-family-sans-serif: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto,
     "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
 $font-family-monospace: Monaco, Menlo, Consolas, "Courier New", monospace;
 $font-family-base: $font-family-sans-serif;
-$font-size-base: 0.8rem; // default 1rem
+$font-size-base: 0.85rem; // default 1rem
 
 // Header font sizes
 $h1-font-size: $font-size-base * 2; // default 2.5
diff --git a/client/galaxy/style/scss/toolshed.scss b/client/galaxy/style/scss/toolshed.scss
new file mode 100644
index 00000000000..329a37b3261
--- /dev/null
+++ b/client/galaxy/style/scss/toolshed.scss
@@ -0,0 +1,21 @@
+@import "theme/blue.scss";
+.shed-style-container {
+    width: 95%;
+    margin: auto;
+    margin-top: 1em;
+    overflow: auto !important;
+    .header {
+        h2 {
+            float: left;
+        }
+        span {
+            float: right;
+        }
+    }
+}
+.ui-autocomplete {
+    background-color: #fff;
+    li.ui-menu-item {
+        list-style-type: none;
+    }
+}
diff --git a/client/galaxy/style/scss/ui.scss b/client/galaxy/style/scss/ui.scss
index 5d19dd67279..e0fc091a557 100644
--- a/client/galaxy/style/scss/ui.scss
+++ b/client/galaxy/style/scss/ui.scss
@@ -256,6 +256,8 @@ $ui-margin-horizontal-large: $margin-v * 2;
 .popover {
     max-width: 700px;
     .popover-header {
+        color: $brand-white;
+        background-color: $brand-primary;
         i {
             @extend .float-right;
             @extend .pl-4;
@@ -452,6 +454,12 @@ $ui-margin-horizontal-large: $margin-v * 2;
     }
 }
 
+.ui-select-content {
+    .btn-group {
+        @extend .d-flex;
+    }
+}
+
 .ui-dragover {
     border-radius: 3px;
     border: 2px solid $table-border-color;
diff --git a/client/package.json b/client/package.json
index 4aeb15dd09e..ac7e51c809e 100644
--- a/client/package.json
+++ b/client/package.json
@@ -15,7 +15,7 @@
     "@handsontable/vue": "^2.0.0-beta1",
     "@johmun/vue-tags-input": "^2.0.1",
     "@vue/test-utils": "1.0.0-beta.29",
-    "axios": "^0.18.0",
+    "axios": "^0.19.0",
     "backbone": "1.4.0",
     "bibtex-parse-js": "^0.0.24",
     "bootstrap": "4.3.1",
@@ -23,8 +23,10 @@
     "bootstrap-vue": "^2.0.0-rc.16",
     "d3": "3",
     "decode-uri-component": "^0.2.0",
+    "flush-promises": "^1.0.2",
     "font-awesome": "^4.7.0",
     "handsontable": "^2.0.0",
+    "imask": "^4.1.5",
     "imports-loader": "^0.8.0",
     "jquery": "2",
     "jquery-migrate": "~1.4",
@@ -45,7 +47,8 @@
     "vue": "^2.6.10",
     "vue-router": "^3.0.2",
     "vue-rx": "^6.1.0",
-    "vuex": "^3.1.0"
+    "vuex": "^3.1.0",
+    "vuex-cache": "^3.1.0"
   },
   "scripts": {
     "watch": "gulp && yarn run save-build-hash && yarn run webpack-watch",
diff --git a/client/webpack.config.js b/client/webpack.config.js
index 18973b9d67b..20a17781fd9 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -162,7 +162,10 @@ let buildconfig = {
                         loader: "sass-loader",
                         options: { 
                             sourceMap: true,
-                            includePaths: ["galaxy/style/scss"]
+                            includePaths: [
+                                "galaxy/style/scss", 
+                                path.resolve(__dirname, './node_modules') 
+                            ]
                         }
                     }
                 ]
diff --git a/client/yarn.lock b/client/yarn.lock
index 3f407c345fc..76424381eee 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -1717,13 +1717,13 @@ aws4@^1.8.0:
   resolved "https://registry.yarnpkg.com/aws4/-/aws4-1.8.0.tgz#f0e003d9ca9e7f59c7a508945d7b2ef9a04a542f"
   integrity sha512-ReZxvNHIOv88FlT7rxcXIIC0fPt4KZqZbOlivyWtXLt8ESx84zd3kMC6iK5jVeS2qt+g7ftS7ye4fi06X5rtRQ==
 
-axios@^0.18.0:
-  version "0.18.0"
-  resolved "https://registry.yarnpkg.com/axios/-/axios-0.18.0.tgz#32d53e4851efdc0a11993b6cd000789d70c05102"
-  integrity sha1-MtU+SFHv3AoRmTts0AB4nXDAUQI=
+axios@^0.19.0:
+  version "0.19.0"
+  resolved "https://registry.yarnpkg.com/axios/-/axios-0.19.0.tgz#8e09bff3d9122e133f7b8101c8fbdd00ed3d2ab8"
+  integrity sha512-1uvKqKQta3KBxIz14F2v06AEHZ/dIoeKfbTRkK1E5oqjDnuEerLmYTgJB5AiQZHJcljpg1TuRzdjDR06qNk0DQ==
   dependencies:
-    follow-redirects "^1.3.0"
-    is-buffer "^1.1.5"
+    follow-redirects "1.5.10"
+    is-buffer "^2.0.2"
 
 babel-code-frame@^6.26.0, babel-code-frame@^6.7.5:
   version "6.26.0"
@@ -5530,6 +5530,11 @@ flatted@^2.0.0:
   resolved "https://registry.yarnpkg.com/flatted/-/flatted-2.0.0.tgz#55122b6536ea496b4b44893ee2608141d10d9916"
   integrity sha512-R+H8IZclI8AAkSBRQJLVOsxwAoHd6WC40b4QTNWIjzAa6BXOBfQcM587MXDTVPeYaopFNWHUFLx7eNmHDSxMWg==
 
+flush-promises@^1.0.2:
+  version "1.0.2"
+  resolved "https://registry.yarnpkg.com/flush-promises/-/flush-promises-1.0.2.tgz#4948fd58f15281fed79cbafc86293d5bb09b2ced"
+  integrity sha512-G0sYfLQERwKz4+4iOZYQEZVpOt9zQrlItIxQAAYAWpfby3gbHrx0osCHz5RLl/XoXevXk0xoN4hDFky/VV9TrA==
+
 flush-write-stream@^1.0.0:
   version "1.0.3"
   resolved "https://registry.yarnpkg.com/flush-write-stream/-/flush-write-stream-1.0.3.tgz#c5d586ef38af6097650b49bc41b55fabb19f35bd"
@@ -5551,7 +5556,14 @@ fn-name@^2.0.0:
   resolved "https://registry.yarnpkg.com/fn-name/-/fn-name-2.0.1.tgz#5214d7537a4d06a4a301c0cc262feb84188002e7"
   integrity sha1-UhTXU3pNBqSjAcDMJi/rhBiAAuc=
 
-follow-redirects@^1.0.0, follow-redirects@^1.3.0:
+follow-redirects@1.5.10:
+  version "1.5.10"
+  resolved "https://registry.yarnpkg.com/follow-redirects/-/follow-redirects-1.5.10.tgz#7b7a9f9aea2fdff36786a94ff643ed07f4ff5e2a"
+  integrity sha512-0V5l4Cizzvqt5D44aTXbFZz+FtyXV1vrDN6qrelxtfYQKW0KO0W2T/hkE8xvGa/540LkZlkaUjO4ailYTFtHVQ==
+  dependencies:
+    debug "=3.1.0"
+
+follow-redirects@^1.0.0:
   version "1.5.9"
   resolved "https://registry.yarnpkg.com/follow-redirects/-/follow-redirects-1.5.9.tgz#c9ed9d748b814a39535716e531b9196a845d89c6"
   integrity sha512-Bh65EZI/RU8nx0wbYF9shkFZlqLP+6WT/5FnA3cE/djNSuKNHJEinGGZgu/cQEkeeb2GdFOgenAmn8qaqYke2w==
@@ -6480,6 +6492,11 @@ ignore@^4.0.6:
   resolved "https://registry.yarnpkg.com/ignore/-/ignore-4.0.6.tgz#750e3db5862087b4737ebac8207ffd1ef27b25fc"
   integrity sha512-cyFDKrqc/YdcWFniJhzI42+AzS+gNwmUzOSFcRCQYwySuBBBy/KjuxWLZ/FHEH6Moq1NizMOBWyTcv8O4OZIMg==
 
+imask@^4.1.5:
+  version "4.1.5"
+  resolved "https://registry.yarnpkg.com/imask/-/imask-4.1.5.tgz#9942993ece68b7b33d03e12781a7401b1207e52c"
+  integrity sha512-n9e3KkJxe6YZKueT02I8/tXpC0vzxmSzoBB5BPi6OPq0rp7qOZfXN5777Dkw6WEYRswlsxm+7pl7WocsG0LWyA==
+
 immer@1.10.0:
   version "1.10.0"
   resolved "https://registry.yarnpkg.com/immer/-/immer-1.10.0.tgz#bad67605ba9c810275d91e1c2a47d4582e98286d"
@@ -6743,7 +6760,7 @@ is-buffer@^1.1.5:
   resolved "https://registry.yarnpkg.com/is-buffer/-/is-buffer-1.1.6.tgz#efaa2ea9daa0d7ab2ea13a97b2b8ad51fefbe8be"
   integrity sha512-NcdALwpXkTm5Zvvbk7owOUSvVvBKDgKP5/ewfXEznmQFfs4ZRmanOeKBTjRVjka3QFoN6XJ+9F3USqfHqTaU5w==
 
-is-buffer@^2.0.0:
+is-buffer@^2.0.0, is-buffer@^2.0.2:
   version "2.0.3"
   resolved "https://registry.yarnpkg.com/is-buffer/-/is-buffer-2.0.3.tgz#4ecf3fcf749cbd1e472689e109ac66261a25e725"
   integrity sha512-U15Q7MXTuZlrbymiz95PJpZxu8IlipAp4dtS3wOdgPXx3mqBnslrWU14kxfHB+Py/+2PVKSr37dMAgM2A4uArw==
@@ -13057,6 +13074,11 @@ vue@^2.6.10, vue@^2.6.9:
   resolved "https://registry.yarnpkg.com/vue/-/vue-2.6.10.tgz#a72b1a42a4d82a721ea438d1b6bf55e66195c637"
   integrity sha512-ImThpeNU9HbdZL3utgMCq0oiMzAkt1mcgy3/E6zWC/G6AaQoeuFdsl9nDhTDU3X1R6FK7nsIUuRACVcjI+A2GQ==
 
+vuex-cache@^3.1.0:
+  version "3.1.0"
+  resolved "https://registry.yarnpkg.com/vuex-cache/-/vuex-cache-3.1.0.tgz#aad576cfb39b325cc7a43ea9a42414e356374c4b"
+  integrity sha512-XDzQ/jddmErZVquyHhbOHc6DPhVSt5bU8433Fzsai3XydU3cxyYTUd3PH2Ww5sesB9yu5f0wKk6MFIqgjSa3Yw==
+
 vuex@^3.1.0:
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/vuex/-/vuex-3.1.0.tgz#634b81515cf0cfe976bd1ffe9601755e51f843b9"
diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 21b4bdd2bbc..3613a6ee58c 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -102,6 +102,7 @@
     <datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
     <datatype extension="d3_hierarchy" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="true"/>
     <datatype extension="imgt.json" type="galaxy.datatypes.text:ImgtJson" mimetype="application/json" display_in_upload="True"/>
+    <datatype extension="geojson" type="galaxy.datatypes.text:GeoJson" mimetype="application/json" display_in_upload="True"/>
     <datatype extension="data_manager_json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
     <datatype extension="dbn" type="galaxy.datatypes.sequence:DotBracket" display_in_upload="true" description="Dot-Bracket format is a text-based format for storing both an RNA sequence and its corresponding 2D structure." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Dbn"/>
     <datatype extension="fai" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true" description="A Fasta Index File is a text file consisting of lines each with five TAB-delimited columns : Name, Length, offset, linebases, Linewidth" description_url="http://www.htslib.org/doc/faidx.html"/>
@@ -159,8 +160,10 @@
     <datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="h5ad" type="galaxy.datatypes.binary:Anndata" description="An HDF5-based anndata File" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
     <datatype extension="hivtrace" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
     <datatype extension="cool" type="galaxy.datatypes.binary:Cool" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="mcool" type="galaxy.datatypes.binary:MCool" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
     <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order).">
       <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
@@ -321,6 +324,7 @@
     </datatype>
     <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension.  You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/>
     <datatype extension="sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
+    <datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="true"/>
     <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.text:SnpSiftDbNSFP" display_in_upload="true"/>
     <datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true">
@@ -376,6 +380,8 @@
       <display file="igv/vcf.xml"/>
       <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>
     </datatype>
+    <datatype extension="kallisto.ec" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
+    <datatype extension="kallisto.idx" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
     <!-- Phylogenetic tree datatypes -->
     <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true"/>
     <datatype extension="newick" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
@@ -728,6 +734,13 @@
     <datatype extension="sbml" type="galaxy.datatypes.xml:Sbml" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="spalndbnp" type="galaxy.datatypes.spaln:SpalnNuclDb" display_in_upload="true" />
     <datatype extension="spalndba" type="galaxy.datatypes.spaln:SpalnProtDb" display_in_upload="true" />
+    <datatype extension="dada2_derep" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_dada" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_errorrates" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_mergepairs" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_sequencetable" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
+    <datatype extension="dada2_uniques" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
+    <datatype extension="ckpt" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />
   </registration>
   <sniffers>
     <!--
@@ -767,6 +780,7 @@
     <sniffer type="galaxy.datatypes.binary:GAFASQLite"/>
     <sniffer type="galaxy.datatypes.binary:SQlite"/>
     <sniffer type="galaxy.datatypes.binary:Cool"/>
+    <sniffer type="galaxy.datatypes.binary:MCool"/>
     <sniffer type="galaxy.datatypes.binary:Loom"/>
     <sniffer type="galaxy.datatypes.binary:Anndata"/>
     <sniffer type="galaxy.datatypes.binary:Biom2"/>
@@ -865,6 +879,7 @@
     <sniffer type="galaxy.datatypes.text:Ipynb"/>
     <sniffer type="galaxy.datatypes.text:Biom1"/>
     <sniffer type="galaxy.datatypes.text:ImgtJson"/>
+    <sniffer type="galaxy.datatypes.text:GeoJson"/>
     <sniffer type="galaxy.datatypes.text:Json"/>
     <sniffer type="galaxy.datatypes.genetics:GenotypeMatrix"/>
     <sniffer type="galaxy.datatypes.genetics:DataIn"/>
diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample
index 34032804c49..79ba81fb9d6 100644
--- a/config/galaxy.yml.sample
+++ b/config/galaxy.yml.sample
@@ -144,7 +144,7 @@ galaxy:
   # than 5 milliseconds.
   #slow_query_log_threshold: 0
 
-  # Enable's a per request sql debugging option. If this is set to true,
+  # Enables a per request sql debugging option. If this is set to true,
   # append ?sql_debug=1 to web request URLs to enable detailed logging
   # on the backend of SQL queries generated during that request. This is
   # useful for debugging slow endpoints during development.
@@ -163,6 +163,17 @@ galaxy:
   # not recommended for production use.
   #database_auto_migrate: false
 
+  # Wait for database to become available instead of failing
+  # immediately.
+  #database_wait: false
+
+  # Number of attempts before failing if database_wait is enabled.
+  #database_wait_attempts: 60
+
+  # Time to sleep between attempts if database_wait is enabled (in
+  # seconds).
+  #database_wait_sleep: 1.0
+
   # Where dataset files are stored. It must accessible at the same path
   # on any cluster nodes that will run Galaxy jobs, unless using Pulsar.
   #file_path: database/files
@@ -322,7 +333,7 @@ galaxy:
   # be used for job destinations with Docker enabled.
   #enable_beta_mulled_containers: false
 
-  # Container resolvers configuration (beta). Setup a file describing
+  # Container resolvers configuration (beta). Set up a file describing
   # container resolvers to use when discovering containers for Galaxy.
   # If this is set to None, the default containers loaded is determined
   # by enable_beta_mulled_containers.
@@ -621,7 +632,7 @@ galaxy:
 
   # Galaxy can display data at various external browsers.  These options
   # specify which browsers should be available.  URLs and builds
-  # available at these browsers are defined in the specifield files.  If
+  # available at these browsers are defined in the specified files.  If
   # use_remote_user = True, display application servers will be denied
   # access to Galaxy and so displaying datasets in these sites will
   # fail. display_servers contains a list of hostnames which should be
@@ -682,11 +693,10 @@ galaxy:
   # URL (with schema http/https) of the Galaxy instance as accessible
   # within your local network - if specified used as a default by pulsar
   # file staging and Jupyter Docker container for communicating back
-  # with Galaxy via the API.  If you are attempting to setup GIEs on Mac
-  # OS X with Docker for Mac - this should likely be the IP address of
-  # your machine on the virtualbox network (vboxnet0) setup for the
-  # Docker host VM. This can found by running ifconfig and using the IP
-  # address of the network vboxnet0.
+  # with Galaxy via the API.  If you are attempting to set up GIEs on
+  # Mac OS X with Docker Desktop for Mac and your Galaxy instance runs
+  # on port 8080 this should be 'http://host.docker.internal:8080'.  For
+  # more details see https://docs.docker.com/docker-for-mac/networking/
   #galaxy_infrastructure_url: http://localhost:8080
 
   # If the above URL cannot be determined ahead of time in dynamic
@@ -866,11 +876,11 @@ galaxy:
   # for IPC, set that here.
   #dynamic_proxy_session_map: database/session_map.sqlite
 
-  # Set the port and IP for the the dynamic proxy to bind to, this must
+  # Set the port and IP for the dynamic proxy to bind to, this must
   # match the external configuration if dynamic_proxy_manage is False.
   #dynamic_proxy_bind_port: 8800
 
-  # Set the port and IP for the the dynamic proxy to bind to, this must
+  # Set the port and IP for the dynamic proxy to bind to, this must
   # match the external configuration if dynamic_proxy_manage is False.
   #dynamic_proxy_bind_ip: 0.0.0.0
 
@@ -1515,6 +1525,17 @@ galaxy:
   # configuration file.
   #job_config_file: config/job_conf.xml
 
+  # Description of job running configuration, can be embedded into
+  # Galaxy configuration or loaded from an additional file with the
+  # job_config_file option.
+  #job_config: null
+
+  # Rather than specifying a dependency_resolvers_config_file, the
+  # definition of the resolvers to enable can be embedded into Galaxy's
+  # config with this option. This has no effect if a
+  # dependency_resolvers_config_file is used.
+  #dependency_resolvers: null
+
   # When jobs fail due to job runner problems, Galaxy can be configured
   # to retry these or reroute the jobs to new destinations. Very fine
   # control of this is available with resubmit declarations in
diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced
index 76661bb992d..e1e72044eb6 100644
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -51,7 +51,7 @@
           <param id="amqp_url">amqp://guest:guest@localhost:5672//</param>
           <!-- URL remote Pulsar apps should transfer files to this Galaxy
                instance to/from. This can be unspecified/empty if
-               galaxy_infrastructure_url is set in galaxy.ini.
+               galaxy_infrastructure_url is set in galaxy.yml.
           -->
           <param id="galaxy_url">http://localhost:8080</param>
           <!-- AMQP does not guarantee that a published message is received by
@@ -66,7 +66,7 @@
           <!-- <param id="persistence_directory">/path/to/dir</param> -->
           <!-- Number of seconds to wait for an acknowledgement before
                republishing a message. -->
-          <!-- <param id="amqp_republish_time">30</param> -->
+          <!-- <param id="amqp_ack_republish_time">30</param> -->
           <!-- Pulsar job manager to communicate with (see Pulsar
                docs for information on job managers). -->
           <!-- <param id="manager">_default_</param> -->
@@ -87,7 +87,7 @@
                higher value (in seconds) (or `None` to use blocking connections). -->
           <!-- <param id="amqp_consumer_timeout">None</param> -->
         </plugin>
-        <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner" shell="none">
+        <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner">
           <!-- Pulsar job runner with default parameters matching those
                of old LWR job runner. If your Pulsar server is running on a
                Windows machine for instance this runner should still be used.
@@ -141,7 +141,7 @@
                         server: 192.168.64.1
 
                  The path (nfs:path: in the example) set needs to be a parent directory of the directories used for
-                 variables “file_path� and “new_file_path� on the galaxy.ini files. Clearly, for this particular example
+                 variables “file_path� and “new_file_path� on the galaxy.yml files. Clearly, for this particular example
                  to work, there needs to be a NFS server serving that directory on that ip. Please make sure that you
                  use reasonable storage size for your set up (possibly larger that the 10Gi written).
                  An example of the volume claim should be (this needs to be followed more closely) (pv_claim.yaml):
@@ -303,7 +303,7 @@
 
                  This runner requires a shared file system where the directories of
                  `job_working_directory`, `file_path` and `new_file_path` settings defined on
-                 the `galaxy.ini` file are shared amongst the Mesos agents (i.e. nodes which
+                 the `galaxy.yml` file are shared amongst the Mesos agents (i.e. nodes which
                  actually run the jobs).
             -->
             <param id="chronos">`chronos_host`</param>
@@ -332,9 +332,9 @@
              For documentation on handler assignment methods, see the documentation under:
              https://docs.galaxyproject.org/en/latest/admin/scaling.html#job-handler-assignment-methods
 
-             The <handlers> container tag takes two optional attributes:
+             The <handlers> container tag takes three optional attributes:
 
-               <handlers assign_with="method" default="id_or_tag"/>
+               <handlers assign_with="method" max_grab="count" default="id_or_tag"/>
 
                - `assign_with` - How jobs should be assigned to handlers. The value can be a single method or a
                  comma-separated list that will be tried in order. The default depends on whether any handlers and a job
@@ -348,6 +348,11 @@
                    - `db-transaction-isolation` - Database Transaction Isolation
                    - `db-skip-locked` - Database SKIP LOCKED
 
+               - `max_grab` - Limit the number of jobs that a handler will self-assign per jobs-ready-to-run check loop
+                 iteration. This only applies for methods that cause handlers to self-assign multiple jobs at once
+                 (db-skip-locked, db-transaction-isolation) and the value is an integer > 0. Default is to grab as many
+                 jobs ready to run as possible.
+
                - `default` - An ID or tag of the handler(s) that should handle any jobs not assigned to a specific
                  handler (which is probably most of them). If unset, the default is any untagged handlers plus any
                  handlers in the `job-handlers` (no tag) pool.
@@ -415,7 +420,7 @@
 
                This configuration allows any docker instance to write to any Galaxy
                file - for greater isolation set outputs_to_working_directory in
-               galaxy.ini. This will cause $defaults to allow writing to much
+               galaxy.yml. This will cause $defaults to allow writing to much
                less. It will then expand as follows:
 
                $galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:rw,$default_file_path:ro
@@ -566,30 +571,32 @@
                such containers are defined (as in the example below), the first one matching
                the enabled container types for this destination will be used.
           -->
-          <!-- <param id="container_override">
+          <param id="container_override">
               <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:ubuntu-14.04</container>
               <container type="singularity" shell="/bin/sh" resolve_dependencies="false">/path/to/default/container</container>
-          </param> -->
-          <!-- <param id="container">
+          </param>
+          <param id="container">
               <container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:ubuntu-14.04</container>
               <container type="singularity" shell="/bin/sh" resolve_dependencies="false">/path/to/default/container</container>
-          </param> -->
+          </param>
         </destination>
         <destination id="pbs" runner="pbs" tags="mycluster"/>
         <destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs">
             <!-- Define parameters that are native to the job runner plugin. -->
             <param id="Resource_List">walltime=72:00:00</param>
         </destination>
-        <destination id="remote_cluster" runner="drmaa" tags="longjobs"/>
-        <destination id="java_cluster" runner="drmaa">
-          <!-- Allow users that are not mapped to any real users to run jobs
-               as a Galaxy (fallback). Default is False.
-          -->
-          <param id="allow_guests">True</param>
+        <destination id="remote_cluster" runner="drmaa" tags="longjobs">
           <!-- Set to False if cluster nodes don't shared Galaxy library,
                it will perform metadata calculation locally after the job finishes.
           -->
           <param id="embed_metadata_in_job">True</param>
+          <!-- If jobs are configured to run as the real user, this option allows
+               users that are not mapped to any real users to run jobs
+               as a Galaxy (fallback). Default is False.
+          -->
+          <param id="allow_guests">True</param>
+        </destination>
+        <destination id="java_cluster" runner="drmaa">
           <!-- set arbitrary environment variables at runtime. General
                dependencies for tools should be configured via
                tool_dependency_dir and package options and these
@@ -623,7 +630,7 @@
           <param id="tmp_dir">$(mktemp -d /mnt/scratch/fastest/gxyjobXXXXXXXXXXX)</param>
         </destination>
         <destination id="real_user_cluster" runner="drmaa">
-            <!-- Make sure to setup 3 real user parameters in galaxy.ini. -->
+            <!-- Make sure to setup 3 real user parameters in galaxy.yml. -->
         </destination>
         <destination id="dynamic" runner="dynamic">
             <!-- A destination that represents a method in the dynamic runner.
@@ -896,7 +903,7 @@
             <resubmit condition="unknown_error and attempt &lt;= 5" delay="attempt * 30" />
         </destination>
         <!-- Any tag param in this file can be set using an environment variable or using
-             values from galaxy.ini using the from_environ and from_config attributes
+             values from galaxy.yml using the from_environ and from_config attributes
              repectively. The text of the param will still be used if that environment variable
              or config value isn't set.
         -->
@@ -943,12 +950,12 @@
                 <param id="docker_image_default">my-tool</param>
                 <param id="docker_tag_default">latest</param>
             -->
-            <param id="max_pod_retrials">3</param>
+            <param id="max_pod_retries">3</param>
             <!-- Allows pods to retry up to this number of times, before marking the galaxy job failed. k8s is a state
                  setter essentially, so by default it will try to take a job submitted to successful completion. A job
                  submits pods, until the number of successes (1 in this use case) is achieved, assuming that whatever is
                  making the pods fail will be fixed (such as a stale disk or a dead node that it is being restarted).
-                 This option sets a limit of retrials, so that after that number of failed pods, the job is re-scaled to
+                 This option sets a limit of retries, so that after that number of failed pods, the job is re-scaled to
                  zero (no execution) and the stderr/stdout of the k8s job is reported in galaxy (and the galaxy job set
                  to failed).
 
@@ -1012,19 +1019,19 @@
              a tag, a handler or destination that matches that tag will be
              chosen at random.
          -->
-        <tool id="foo" handler="trackster_handler">
-            <param id="source">trackster</param>
+        <tool id="bwa" handler="handler0">
+        </tool>
+        <tool id="bowtie" handler="handler1">
         </tool>
         <tool id="bar" destination="dynamic"/>
         <!-- Next example defines resource group to insert into tool interface
              and pass to dynamic destination (as resource_params argument). -->
         <tool id="longbar" destination="dynamic" resources="all" />
+        <!-- Pick a handler randomly from those declaring this tag. -->
         <tool id="baz" handler="special_handlers" destination="bigmem"/>
-
-        <!-- Finally for Kubernetes runner, the following connects a particular tool to be executed with
-             the container of choice in Kubernetes.
-        -->
-        <tool id="my-tool" destination="my-tool-container"/>
+        <tool id="foo" handler="handler0">
+            <param id="source">trackster</param>
+        </tool>
     </tools>
     <limits>
         <!-- Certain limits can be defined. The 'concurrent_jobs' limits all
@@ -1066,11 +1073,11 @@
                 will be terminated by Galaxy.
          -->
         <limit type="walltime">24:00:00</limit>
-	<!-- total_walltime:
-		Total walltime that jobs may not exceed during a set period.
-		If total walltime of finished jobs exceeds this value, any
-		new jobs are paused.  `window` is a number in days,
-		representing the period.
+        <!-- total_walltime:
+                Total walltime that jobs may not exceed during a set period.
+                If total walltime of finished jobs exceeds this value, any
+                new jobs are paused.  `window` is a number in days,
+                representing the period.
          -->
         <limit type="total_walltime" window="30">24:00:00</limit>
         <!-- output_size:
diff --git a/config/object_store_conf.xml.sample b/config/object_store_conf.xml.sample
index 4b2c0b7879c..12dbf9aef5b 100644
--- a/config/object_store_conf.xml.sample
+++ b/config/object_store_conf.xml.sample
@@ -21,65 +21,80 @@
             <extra_dir type="job_work" path="database/job_working_directory3"/>
         </object_store>
 
-        <!--  Sample S3 Object Store
+        <!-- Sample S3 Object Store
+             The "size" attribute of <cache> is in gigabytes.
+        -->
+        <!--
         <object_store type="s3">
              <auth access_key="...." secret_key="....." />
              <bucket name="unique_bucket_name_all_lowercase" use_reduced_redundancy="False" />
-             <cache path="database/object_store_cache" size="1000" /> <!-- size is in gigabytes -->
+             <cache path="database/object_store_cache" size="1000" />
              <extra_dir type="job_work" path="database/job_working_directory_s3"/>
              <extra_dir type="temp" path="database/tmp_s3"/>
         </object_store>
         -->
 
-        <!--  Sample Swift Object Store
+        <!-- Sample Swift Object Store
+             The "size" attribute of <cache> is in gigabytes.
+        -->
+        <!--
         <object_store type="swift">
             <auth access_key="...." secret_key="....." />
             <bucket name="unique_bucket_name" use_reduced_redundancy="False" max_chunk_size="250"/>
             <connection host="" port="" is_secure="" conn_path="" multipart="True"/>
-            <cache path="database/object_store_cache" size="1000" />  <!-- size is in gigabytes -->
+            <cache path="database/object_store_cache" size="1000" />
             <extra_dir type="job_work" path="database/job_working_directory_swift"/>
             <extra_dir type="temp" path="database/tmp_swift"/>
         </object_store>
         -->
 
         <!-- Sample Azure Object Store
+             The "size" attribute of <cache> is in gigabytes.
+        -->
+        <!--
         <object_store type="azure_blob">
-            <auth account_name="..." account_key="...." />
+        <auth account_name="..." account_key="...." />
             <container name="unique_container_name" max_chunk_size="250"/>
-            <cache path="database/object_store_cache" size="100" /> <!-- size is in gigabytes -->
+            <cache path="database/object_store_cache" size="100" />
             <extra_dir type="job_work" path="database/job_working_directory_azure"/>
             <extra_dir type="temp" path="database/tmp_azure"/>
         </object_store>
         -->
 
-        <!-- Cloud ObjectStore: Amazon Simple Storage Service (S3) -->
+        <!-- Cloud ObjectStore: Amazon Simple Storage Service (S3)
+             The "size" attribute of <cache> is in gigabytes.
+        -->
         <!--
         <object_store type="cloud" provider="aws" order="0">
             <auth access_key="..." secret_key="..." />
             <bucket name="..." use_reduced_redundancy="False" />
-            <cache path="database/object_store_cache" size="100" /> <!-- size is in gigabytes -->
+            <cache path="database/object_store_cache" size="100" />
             <extra_dir type="job_work" path="database/job_working_directory_s3"/>
             <extra_dir type="temp" path="database/tmp_s3"/>
         </object_store>
         -->
 
-        <!-- Cloud ObjectStore: Microsoft Azure Blob Storage -->
+        <!-- Cloud ObjectStore: Microsoft Azure Blob Storage
+             The "size" attribute of <cache> is in gigabytes.
+        -->
         <!--
         <object_store type="cloud" provider="azure" order="0">
             <auth subscription_id="..." client_id="..." secret="..." tenant="..." />
             <bucket name="..." use_reduced_redundancy="False" />
-            <cache path="database/object_store_cache" size="100" /> <!-- size is in gigabytes -->
+            <cache path="database/object_store_cache" size="100" />
             <extra_dir type="job_work" path="database/job_working_directory_azure"/>
             <extra_dir type="temp" path="database/tmp_azure"/>
         </object_store>
         -->
 
-        <!-- Cloud ObjectStore: Google Compute Platform (GCP) -->
+        <!-- Cloud ObjectStore: Google Compute Platform (GCP)
+             The "size" attribute of <cache> is in gigabytes.
+        -->
         <!--
         <object_store type="cloud" provider="google" order="0">
             <auth credentials_file="..." />
             <bucket name="..." use_reduced_redundancy="False" />
-            <cache path="database/object_store_cache" size="1000" /> <!-- size is in gigabytes -->
+            <cache path="database/object_store_cache" size="1000" />
             <extra_dir type="job_work" path="database/job_working_directory_gcp"/>
             <extra_dir type="temp" path="database/tmp_gcp"/>
         </object_store>
diff --git a/config/oidc_backends_config.xml.sample b/config/oidc_backends_config.xml.sample
index b2317c45652..90b157b1632 100644
--- a/config/oidc_backends_config.xml.sample
+++ b/config/oidc_backends_config.xml.sample
@@ -100,4 +100,12 @@ Please mind `http` and `https`.
         <!-- (Optional) Override the default idp hint -->
         <!-- <idphint>cilogon</idphint> -->
     </provider>
+    <!-- Documentation: https://galaxyproject.org/authnz/config/oidc/idps/elixir-aai  -->
+    <provider name="Elixir">
+        <client_id>...</client_id>
+        <client_secret>...</client_secret>
+        <redirect_uri>http://localhost:8080/authnz/elixir/callback</redirect_uri>
+        <prompt>consent</prompt>
+    </provider>
+
 </OIDC>
diff --git a/config/plugins/interactive_environments/askomics/static/js/askomics.js b/config/plugins/interactive_environments/askomics/static/js/askomics.js
deleted file mode 100644
index ad674394807..00000000000
--- a/config/plugins/interactive_environments/askomics/static/js/askomics.js
+++ /dev/null
@@ -1,9 +0,0 @@
-var IES = window.IES;
-
-function load_askomics(url){
-    $( document ).ready(function() {
-        IES.test_ie_availability(url, function(){
-            IES.append_notebook(url);
-        });
-    });
-}
diff --git a/config/plugins/interactive_environments/askomics/static/js/main.js b/config/plugins/interactive_environments/askomics/static/js/main.js
new file mode 100644
index 00000000000..791dac16749
--- /dev/null
+++ b/config/plugins/interactive_environments/askomics/static/js/main.js
@@ -0,0 +1,9 @@
+var IES = window.IES;
+
+function load_askomics(url) {
+    $(document).ready(function() {
+        IES.test_ie_availability(url, function() {
+            IES.append_notebook(url);
+        });
+    });
+}
diff --git a/config/plugins/interactive_environments/askomics/templates/askomics.mako b/config/plugins/interactive_environments/askomics/templates/askomics.mako
index 29195f1baf5..e9dfb8441da 100644
--- a/config/plugins/interactive_environments/askomics/templates/askomics.mako
+++ b/config/plugins/interactive_environments/askomics/templates/askomics.mako
@@ -34,16 +34,13 @@ url = ie_request.url_template('${PROXY_URL}/login_api_gie?key=' + askomics_api_k
 <html>
 <head>
 ${ ie.load_default_js() }
+${ ie.load_default_app() }
 </head>
 <body>
 <script type="text/javascript">
 ${ ie.default_javascript_variables() }
 var url = '${ url }';
-${ ie.plugin_require_config() }
-requirejs(['galaxy.interactive_environments', 'plugin/askomics'], function(IES){
-    window.IES = IES;
-    load_askomics(url);
-});
+load_askomics(url);
 </script>
 <div id="main" width="100%" height="100%">
 </div>
diff --git a/config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js b/config/plugins/interactive_environments/bam_iobio/static/js/main.js
similarity index 53%
rename from config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
rename to config/plugins/interactive_environments/bam_iobio/static/js/main.js
index d706be38d26..b9e69702abf 100644
--- a/config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
+++ b/config/plugins/interactive_environments/bam_iobio/static/js/main.js
@@ -2,20 +2,20 @@
 var IES = window.IES;
 var toastr = window.toastr;
 
-function message_failed_auth(password){
-    toastr.info(
-        "Automatic authorization failed.",
-        "Please login manually",
-        {'closeButton': true, 'timeOut': 100000, 'tapToDismiss': false}
-    );
+function message_failed_auth(password) {
+    toastr.info("Automatic authorization failed.", "Please login manually", {
+        closeButton: true,
+        timeOut: 100000,
+        tapToDismiss: false
+    });
 }
 
-function message_failed_connection(){
-    toastr.error(
-        "Could not connect to BAM iobio. Please contact your administrator.",
-    "Security warning",
-        {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': true}
-    );
+function message_failed_connection() {
+    toastr.error("Could not connect to BAM iobio. Please contact your administrator.", "Security warning", {
+        closeButton: true,
+        timeOut: 20000,
+        tapToDismiss: true
+    });
 }
 
 /**
@@ -25,10 +25,10 @@ function message_failed_connection(){
  * @param {String} notebook_access_url: the URL embeded in the page and loaded
  *
  */
-function load_notebook(notebook_access_url){
+function load_notebook(notebook_access_url) {
     // Test notebook_login_url for accessibility, executing the login+load function whenever
     // we've successfully connected to the IE.
-    IES.test_ie_availability(notebook_access_url, function(){
+    IES.test_ie_availability(notebook_access_url, function() {
         _handle_notebook_loading(notebook_access_url);
     });
 }
@@ -36,6 +36,6 @@ function load_notebook(notebook_access_url){
 /**
  * Must be implemented by IEs
  */
-function _handle_notebook_loading(notebook_access_url){
+function _handle_notebook_loading(notebook_access_url) {
     IES.append_notebook(notebook_access_url);
 }
diff --git a/config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako b/config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
index 16115b2847a..4060fa9ff6a 100644
--- a/config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
+++ b/config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
@@ -24,6 +24,7 @@ root = h.url_for( '/' )
 <html>
 <head>
     ${ ie.load_default_js() }
+    ${ ie.load_default_app() }
 </head>
 <body>
 
@@ -31,12 +32,8 @@ root = h.url_for( '/' )
 
         ${ ie.default_javascript_variables() }
         var notebook_access_url = '${ notebook_access_url }';
-        ${ ie.plugin_require_config() }
 
-        requirejs(['galaxy.interactive_environments', 'plugin/bam_iobio'], function(IES){
-            window.IES = IES;
-            IES.display_spinner();
-        });
+        IES.display_spinner();
 
         toastr.info(
             "BAM io.bio is starting up!",
@@ -46,11 +43,8 @@ root = h.url_for( '/' )
 
         var startup = function(){
             // Load notebook
-            requirejs(['galaxy.interactive_environments', 'plugin/bam_iobio'], function(IES){
-                window.IES = IES;
-                IES.load_when_ready(ie_readiness_url, function(){
-                    load_notebook(notebook_access_url);
-                });
+            IES.load_when_ready(ie_readiness_url, function(){
+                load_notebook(notebook_access_url);
             });
 
         };
diff --git a/config/plugins/interactive_environments/cellxgene/config/allowed_images.yml.sample b/config/plugins/interactive_environments/cellxgene/config/allowed_images.yml.sample
index f3ec2cde2b8..2a4edc35be7 100644
--- a/config/plugins/interactive_environments/cellxgene/config/allowed_images.yml.sample
+++ b/config/plugins/interactive_environments/cellxgene/config/allowed_images.yml.sample
@@ -1,5 +1,5 @@
 ---
 -
-    image: quay.io/galaxy/cellxgene-galaxy-ie:2019.01.30
+    image: quay.io/galaxy/cellxgene-galaxy-ie:2019.05.13
     description: |
         An interactive data explorer for single-cell transcriptomics datasets
diff --git a/config/plugins/interactive_environments/cellxgene/docker/Dockerfile b/config/plugins/interactive_environments/cellxgene/docker/Dockerfile
index b172e4a0ec5..cd842996fb9 100644
--- a/config/plugins/interactive_environments/cellxgene/docker/Dockerfile
+++ b/config/plugins/interactive_environments/cellxgene/docker/Dockerfile
@@ -1,6 +1,10 @@
 FROM python:3.6.8-slim
+
+RUN apt-get update && apt-get install -y \
+    net-tools \
+ && rm -rf /var/lib/apt/lists/*
  
-RUN pip3 install cellxgene && rm -rf ~/.cache
+RUN pip3 install cellxgene galaxy-ie-helpers && rm -rf ~/.cache
 
 ADD ./run_cellxgene.sh /
 
diff --git a/config/plugins/interactive_environments/cellxgene/docker/run_cellxgene.sh b/config/plugins/interactive_environments/cellxgene/docker/run_cellxgene.sh
index 0759da7af8e..30fd71b2e05 100755
--- a/config/plugins/interactive_environments/cellxgene/docker/run_cellxgene.sh
+++ b/config/plugins/interactive_environments/cellxgene/docker/run_cellxgene.sh
@@ -1,3 +1,5 @@
 #!/bin/sh
 
-cellxgene launch --host 0.0.0.0 --port 80 /input/file.*
+get -i ${DATASET_HID} \
+    && mv /import/${DATASET_HID} /import/${DATASET_HID}.h5ad \
+    && cellxgene launch --host 0.0.0.0 --port 80 /import/${DATASET_HID}.h5ad
diff --git a/config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako b/config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako
index 3d91ae1c9b5..1965844f09c 100644
--- a/config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako
+++ b/config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako
@@ -2,12 +2,11 @@
 <%
     ie_request.load_deploy_config()
 
-    # Make the dataset available inside the container
-    data_file = ie_request.volume('/input/file.' + hda.ext, hda.file_name, mode='ro')
-
     ie_request.launch(
-       image = trans.request.params.get('image_tag', None),
-       volumes = [data_file]
+        image = trans.request.params.get('image_tag', None),
+        env_override={
+            'dataset_hid': hda.hid
+        }
     )
 
     url = ie_request.url_template('${PROXY_URL}')
@@ -21,14 +20,11 @@
 
     ${ ie.default_javascript_variables() }
     var url = '${ url }';
-    ${ ie.plugin_require_config() }
 
-    requirejs(['galaxy.interactive_environments'], function (IES) {
-        $( document ).ready(function() {
-            IES.keepAlive(url);
-            IES.test_ie_availability(url, function() {
-                IES.append_notebook(url);
-            });
+    $( document ).ready(function() {
+        IES.keepAlive(url);
+        IES.test_ie_availability(url, function() {
+            IES.append_notebook(url);
         });
     });
 
diff --git a/config/plugins/interactive_environments/common/templates/ie.mako b/config/plugins/interactive_environments/common/templates/ie.mako
index 63209322228..98fe7919c46 100644
--- a/config/plugins/interactive_environments/common/templates/ie.mako
+++ b/config/plugins/interactive_environments/common/templates/ie.mako
@@ -1,3 +1,10 @@
+<%def name="load_default_js()">
+${h.css( 'base' ) }
+${h.js('bundled/libs.chunk',
+       'bundled/base.chunk',
+       'bundled/generic.bundled')}
+</%def>
+
 <%def name="default_javascript_variables()">
 // Globals
 
@@ -10,28 +17,15 @@ ie_password = '${ ie_request.notebook_pw }';
 var galaxy_root = '${ ie_request.attr.root }';
 var app_root = '${ ie_request.attr.app_root }';
 var ie_readiness_url = '${ h.url_for("/interactive_environments/ready") }';
-</%def>
 
-
-<%def name="load_default_js()">
-${h.css( 'base' ) }
-${h.js( 'libs/jquery/jquery',
-        'libs/toastr',
-        'libs/require')}
-</%def>
-
-<%def name="plugin_require_config()">
-require.config({
-    baseUrl: app_root,
-    paths: {
-        "plugin" : app_root + "js",
-        "galaxy.interactive_environments": "${h.url_for('/static/scripts/galaxy.interactive_environments')}",
-    },
-    urlArgs: "v=${app.server_starttime}",
-});
+window.IES = bundleEntries.IES;
+window.toastr = bundleEntries.Toast;
 
 window.onbeforeunload = function() {
     return 'You are leaving your Interactive Environment.';
 };
+</%def>
 
+<%def name="load_default_app()">
+<script src="${'%sjs/main.js?v=%s' % (ie_request.attr.app_root, app.server_starttime)}" type="text/javascript"></script>
 </%def>
diff --git a/config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js b/config/plugins/interactive_environments/ethercalc/static/js/main.js
similarity index 60%
rename from config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
rename to config/plugins/interactive_environments/ethercalc/static/js/main.js
index bcf564666ae..a9727622ad7 100644
--- a/config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
+++ b/config/plugins/interactive_environments/ethercalc/static/js/main.js
@@ -2,8 +2,8 @@
 var IES = window.IES;
 var toastr = window.toastr;
 
-function load_notebook(url){
-    IES.test_ie_availability(url, function(){
+function load_notebook(url) {
+    IES.test_ie_availability(url, function() {
         IES.append_notebook(url);
     });
 }
diff --git a/config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako b/config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
index 5f2e83bd63a..a9c6a60b3e5 100644
--- a/config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
+++ b/config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
@@ -18,20 +18,17 @@ url = ie_request.url_template('${PROXY_URL}/ethercalc/')
 <html>
 <head>
 ${ ie.load_default_js() }
+${ ie.load_default_app() }
 </head>
 <body>
 <script type="text/javascript">
 ${ ie.default_javascript_variables() }
 var url = '${ url }';
-${ ie.plugin_require_config() }
 
 // Keep container running and load IE
-requirejs(['galaxy.interactive_environments', 'plugin/ethercalc'], function(IES){
-    window.IES = IES;
-    IES.keepAlive(url);
-    IES.load_when_ready(ie_readiness_url, function(){
-        load_notebook(url);
-    });
+IES.keepAlive(url);
+IES.load_when_ready(ie_readiness_url, function(){
+    load_notebook(url);
 });
 </script>
 <div id="main" width="100%" height="100%">
diff --git a/config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js b/config/plugins/interactive_environments/hicbrowser/static/js/main.js
similarity index 84%
rename from config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
rename to config/plugins/interactive_environments/hicbrowser/static/js/main.js
index a7803b7d16a..f0164119b9a 100644
--- a/config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
+++ b/config/plugins/interactive_environments/hicbrowser/static/js/main.js
@@ -3,12 +3,12 @@ var IES = window.IES;
 
 // Load an interactive environment (IE) from a remote URL
 // @param {String} hicexplorer_access_url: the URL embeded in the page and loaded
-function load_hicexplorer(hicexplorer_access_url){
+function load_hicexplorer(hicexplorer_access_url) {
     // When the page has completely loaded...
-    $( document ).ready(function() {
+    $(document).ready(function() {
         // Test if we can access the GIE, and if so, execute the function
         // to load the GIE for the user.
-        IES.test_ie_availability(hicexplorer_access_url, function(){
+        IES.test_ie_availability(hicexplorer_access_url, function() {
             IES.append_notebook(hicexplorer_access_url);
         });
     });
diff --git a/config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako b/config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
index cf69cc8f633..b4ad8329dab 100644
--- a/config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
+++ b/config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
@@ -29,19 +29,14 @@
 <html>
 <head>
     ${ ie.load_default_js() }
+    ${ ie.load_default_app() }
 </head>
 <body>
 <script type="text/javascript">
 
     ${ ie.default_javascript_variables() }
     var url = '${ url }';
-    ${ ie.plugin_require_config() }
-
-
-    requirejs(['galaxy.interactive_environments', 'plugin/hicbrowser'], function (IES) {
-        window.IES = IES;
-        load_hicexplorer(url);
-    });
+    load_hicexplorer(url);
 
 </script>
 <div id="main" width="100%" height="100%">
diff --git a/config/plugins/interactive_environments/jupyter/static/js/jupyter.js b/config/plugins/interactive_environments/jupyter/static/js/main.js
similarity index 60%
rename from config/plugins/interactive_environments/jupyter/static/js/jupyter.js
rename to config/plugins/interactive_environments/jupyter/static/js/main.js
index 3d386889dba..3d0ac5b7118 100644
--- a/config/plugins/interactive_environments/jupyter/static/js/jupyter.js
+++ b/config/plugins/interactive_environments/jupyter/static/js/main.js
@@ -2,23 +2,25 @@
 var IES = window.IES;
 var toastr = window.toastr;
 
-function message_failed_auth(password){
+function message_failed_auth(password) {
     toastr.info(
-        "Automatic authorization failed. You can manually login with:<br>" + password + "<br> <a href='https://github.com/bgruening/galaxy-ipython/wiki/Automatic-Authorization-Failed' target='_blank'>More details ...</a>",
+        "Automatic authorization failed. You can manually login with:<br>" +
+            password +
+            "<br> <a href='https://github.com/bgruening/galaxy-ipython/wiki/Automatic-Authorization-Failed' target='_blank'>More details ...</a>",
         "Please login manually",
-        {'closeButton': true, 'timeOut': 100000, 'tapToDismiss': false}
+        { closeButton: true, timeOut: 100000, tapToDismiss: false }
     );
 }
 
-function message_failed_connection(){
+function message_failed_connection() {
     toastr.error(
         "Could not connect to Jupyter Notebook. Please contact your administrator. <a href='https://github.com/bgruening/galaxy-ipython/wiki/Could-not-connect-to-IPython-Notebook' target='_blank'>More details ...</a>",
-    "Security warning",
-        {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': true}
+        "Security warning",
+        { closeButton: true, timeOut: 20000, tapToDismiss: true }
     );
 }
 
-function message_no_auth(){
+function message_no_auth() {
     // No longer a security issue, proxy validates Galaxy session token.
     /*
     toastr.warning(
@@ -29,7 +31,6 @@ function message_no_auth(){
     */
 }
 
-
 /**
  * Load an interactive environment (IE) from a remote URL
  * @param {String} password: password used to authenticate to the remote resource
@@ -37,68 +38,82 @@ function message_no_auth(){
  * @param {String} notebook_access_url: the URL embeded in the page and loaded
  *
  */
-function load_notebook(password, notebook_login_url, notebook_access_url){
+function load_notebook(password, notebook_login_url, notebook_access_url) {
     // Test notebook_login_url for accessibility, executing the login+load function whenever
     // we've successfully connected to the IE.
-    IES.test_ie_availability(notebook_login_url, function(){
+    IES.test_ie_availability(notebook_login_url, function() {
         _handle_notebook_loading(password, notebook_login_url, notebook_access_url);
         keep_alive();
     });
 }
 
-
-function keep_alive(){
+function keep_alive() {
     /**
-    * This is needed to keep the container alive. If the user leaves this site
-    * this function is not constantly pinging the container, the container will
-    * terminate itself.
-    */
+     * This is needed to keep the container alive. If the user leaves this site
+     * this function is not constantly pinging the container, the container will
+     * terminate itself.
+     */
     var warn_at = 4;
     var count_max = 60;
     // we sleep 15 seconds between requests and the default timeout for the Jupyter container is 120 seconds, so start
     // with a pretty high ajax timeout. sleep starts low because we want to get the warning up pretty quickly
     var spin_state = IES.make_spin_state("IE keepalive", 8000, 16000, 2000, 5000, 15000, 5000, false);
-    var success = function(){
+    var success = function() {
         console.log("IE keepalive request succeeded");
         toastr.clear();
-        if(spin_state.count >= warn_at){
+        if (spin_state.count >= warn_at) {
             toastr.clear();
-            toastr.success(
-                "Interactive environment connection restored",
-                {'closeButton': true, 'timeOut': 5000, 'extendedTimeOut': 2000, 'tapToDismiss': true}
-            );
+            toastr.success("Interactive environment connection restored", {
+                closeButton: true,
+                timeOut: 5000,
+                extendedTimeOut: 2000,
+                tapToDismiss: true
+            });
         }
         spin_state.count = 0;
         spin_state.timeout_count = 0;
         spin_state.error_count = 0;
-        return false;  // keep spinning
+        return false; // keep spinning
     };
-    var timeout_error = function(jqxhr, status, error){
-        console.log("IE keepalive request failed " + spin_state.count + " time(s) of " + count_max + " max: " + status + ": " + error);
-        if(spin_state.count == warn_at){
+    var timeout_error = function(jqxhr, status, error) {
+        console.log(
+            "IE keepalive request failed " +
+                spin_state.count +
+                " time(s) of " +
+                count_max +
+                " max: " +
+                status +
+                ": " +
+                error
+        );
+        if (spin_state.count == warn_at) {
             toastr.warning(
-                "Your browser has been unable to contact the interactive environment for "
-                + spin_state.count + " consecutive attempts, if you do not reestablish "
-                + "a connection, your IE container may be terminated.",
+                "Your browser has been unable to contact the interactive environment for " +
+                    spin_state.count +
+                    " consecutive attempts, if you do not reestablish " +
+                    "a connection, your IE container may be terminated.",
                 "Warning",
-                {'closeButton': true, 'timeOut': 0, 'extendedTimeOut': 0, 'tapToDismiss': false}
+                { closeButton: true, timeOut: 0, extendedTimeOut: 0, tapToDismiss: false }
             );
-            return false;  // keep spinning
-        }else if(spin_state.count >= count_max){
-            IES.spin_error("IE keepalive failure limit reached", "Lost connection to interactive environment, contact your administrator", false);
-            return true;  // stop spinning
+            return false; // keep spinning
+        } else if (spin_state.count >= count_max) {
+            IES.spin_error(
+                "IE keepalive failure limit reached",
+                "Lost connection to interactive environment, contact your administrator",
+                false
+            );
+            return true; // stop spinning
         }
     };
     console.log("IE keepalive worker starting");
     IES.spin(notebook_keepalive_url, false, success, timeout_error, timeout_error, spin_state);
 }
 
-
 /**
  * Must be implemented by IEs
  */
-function _handle_notebook_loading(password, notebook_login_url, notebook_access_url){
-    if ( ie_password_auth ) {
+function _handle_notebook_loading(password, notebook_login_url, notebook_access_url) {
+    if (ie_password_auth) {
         // Make an AJAX POST
         $.ajax({
             type: "POST",
@@ -106,29 +121,28 @@ function _handle_notebook_loading(password, notebook_login_url, notebook_access_
             url: notebook_login_url,
             // With our password
             data: {
-                'password': password
+                password: password
             },
             xhrFields: {
                 withCredentials: true
             },
             // If that is successful, load the notebook
-            success: function(){
+            success: function() {
                 IES.append_notebook(notebook_access_url);
             },
-            error: function(jqxhr, status, error){
-                if(ie_password_auth){
+            error: function(jqxhr, status, error) {
+                if (ie_password_auth) {
                     // Failure happens due to CORS
                     message_failed_auth(password);
                     IES.append_notebook(notebook_access_url);
-                }else{
+                } else {
                     message_failed_connection();
                     // Do we want to try and load the notebook anyway? Just in case?
                     IES.append_notebook(notebook_access_url);
                 }
             }
         });
-    }
-    else {
+    } else {
         // Not using password auth, just embed it to avoid content-origin issues.
         message_no_auth();
         IES.append_notebook(notebook_access_url);
diff --git a/config/plugins/interactive_environments/jupyter/templates/jupyter.mako b/config/plugins/interactive_environments/jupyter/templates/jupyter.mako
index fc8db1f3e5d..eb26eb34fc7 100644
--- a/config/plugins/interactive_environments/jupyter/templates/jupyter.mako
+++ b/config/plugins/interactive_environments/jupyter/templates/jupyter.mako
@@ -50,6 +50,7 @@ notebook_keepalive_url = ie_request.url_template('${PROXY_URL}/ipython/tree')
 <html>
 <head>
 ${ ie.load_default_js() }
+${ ie.load_default_app() }
 </head>
 <body>
 
@@ -58,16 +59,10 @@ ${ ie.default_javascript_variables() }
 var notebook_login_url = '${ notebook_login_url }';
 var notebook_access_url = '${ notebook_access_url }';
 var notebook_keepalive_url = '${ notebook_keepalive_url }';
-${ ie.plugin_require_config() }
 
 // Load notebook
-
-requirejs(['galaxy.interactive_environments', 'plugin/jupyter'], function(IES){
-    // This global is not awesome, get rid of it when possible (when IES are a part of the build process)
-    window.IES = IES;
-    IES.load_when_ready(ie_readiness_url, function(){
-        load_notebook(ie_password, notebook_login_url, notebook_access_url);
-    });
+IES.load_when_ready(ie_readiness_url, function(){
+    load_notebook(ie_password, notebook_login_url, notebook_access_url);
 });
 
 
diff --git a/config/plugins/interactive_environments/neo/static/js/neo.js b/config/plugins/interactive_environments/neo/static/js/main.js
similarity index 76%
rename from config/plugins/interactive_environments/neo/static/js/neo.js
rename to config/plugins/interactive_environments/neo/static/js/main.js
index 37244a7dd6e..06571d8328a 100644
--- a/config/plugins/interactive_environments/neo/static/js/neo.js
+++ b/config/plugins/interactive_environments/neo/static/js/main.js
@@ -3,10 +3,10 @@ var IES = window.IES;
 
 // Load an interactive environment (IE) from a remote URL
 // @param {String} notebook_access_url: the URL embeded in the page and loaded
-function load_notebook(notebook_access_url){
+function load_notebook(notebook_access_url) {
     // Test if we can access the GIE, and if so, execute the function
     // to load the GIE for the user.
-    IES.test_ie_availability(notebook_access_url, function(){
+    IES.test_ie_availability(notebook_access_url, function() {
         IES.append_notebook(notebook_access_url);
     });
 }
diff --git a/config/plugins/interactive_environments/neo/templates/neo.mako b/config/plugins/interactive_environments/neo/templates/neo.mako
index c1df7807375..24f3e968cd8 100644
--- a/config/plugins/interactive_environments/neo/templates/neo.mako
+++ b/config/plugins/interactive_environments/neo/templates/neo.mako
@@ -23,20 +23,14 @@
 <html>
 <head>
     ${ ie.load_default_js() }
+    ${ ie.load_default_app() }
 </head>
 <body>
 <script type="text/javascript">
-
-        ${ ie.default_javascript_variables() }
+    ${ ie.default_javascript_variables() }
     var url = '${ url }';
-        ${ ie.plugin_require_config() }
-
-
-    requirejs(['galaxy.interactive_environments', 'plugin/neo'], function (IES) {
-        window.IES = IES;
-        IES.load_when_ready(ie_readiness_url, function(){
-            load_notebook(url);
-        });
+    IES.load_when_ready(ie_readiness_url, function(){
+        load_notebook(url);
     });
 
 </script>
diff --git a/config/plugins/interactive_environments/phinch/static/js/main.js b/config/plugins/interactive_environments/phinch/static/js/main.js
new file mode 100644
index 00000000000..be12aeecca2
--- /dev/null
+++ b/config/plugins/interactive_environments/phinch/static/js/main.js
@@ -0,0 +1,54 @@
+// Globals to be rid of
+var IES = window.IES;
+var toastr = window.toastr;
+
+function load_notebook(url) {
+    IES.test_ie_availability(url, function() {
+        append_notebook(url);
+    });
+}
+
+function append_notebook(url) {
+    IES.clear_main_area();
+    $("#main").append(
+        '<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:auto;" scrolling="yes" src="' +
+            url +
+            '"></iframe>'
+    );
+}
+
+function keep_alive(notebook_access_url) {
+    /**
+     * This is needed to keep the container alive. If the user leaves this site
+     * this function is not constantly pinging the container, the container will
+     * terminate itself.
+     */
+
+    var request_count = 0;
+    var interval = window.setInterval(function() {
+        $.ajax({
+            url: notebook_access_url,
+            xhrFields: {
+                withCredentials: true
+            },
+            type: "GET",
+            timeout: 500,
+            success: function() {
+                console.log("Connected to IE, returning");
+            },
+            error: function(jqxhr, status, error) {
+                request_count++;
+                console.log("Request " + request_count);
+                if (request_count > 30) {
+                    window.clearInterval(interval);
+                    IES.clear_main_area();
+                    toastr.error("Could not connect to IE, contact your administrator", "Error", {
+                        closeButton: true,
+                        timeOut: 20000,
+                        tapToDismiss: false
+                    });
+                }
+            }
+        });
+    }, 10000);
+}
diff --git a/config/plugins/interactive_environments/phinch/static/js/phinch.js b/config/plugins/interactive_environments/phinch/static/js/phinch.js
deleted file mode 100644
index 1fea1fc08fc..00000000000
--- a/config/plugins/interactive_environments/phinch/static/js/phinch.js
+++ /dev/null
@@ -1,54 +0,0 @@
-// Globals to be rid of
-var IES = window.IES;
-var toastr = window.toastr;
-
-function load_notebook(url){
-    IES.test_ie_availability(url, function(){
-        append_notebook(url);
-    });
-}
-
-function append_notebook(url){
-    IES.clear_main_area();
-    $('#main').append(
-        '<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:auto;" scrolling="yes" src="'+ url +'"></iframe>'
-    );
-}
-
-
-function keep_alive(notebook_access_url){
-    /**
-    * This is needed to keep the container alive. If the user leaves this site
-    * this function is not constantly pinging the container, the container will
-    * terminate itself.
-    */
-
-    var request_count = 0;
-    var interval = window.setInterval(function(){
-        $.ajax({
-            url: notebook_access_url,
-            xhrFields: {
-                withCredentials: true
-            },
-            type: "GET",
-            timeout: 500,
-            success: function(){
-                console.log("Connected to IE, returning");
-            },
-            error: function(jqxhr, status, error){
-                request_count++;
-                console.log("Request " + request_count);
-                if(request_count > 30){
-                    window.clearInterval(interval);
-                    IES.clear_main_area();
-                    toastr.error(
-                        "Could not connect to IE, contact your administrator",
-                        "Error",
-                        {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': false}
-                    );
-                }
-            }
-        });
-    }, 10000);
-}
-
diff --git a/config/plugins/interactive_environments/phinch/templates/phinch.mako b/config/plugins/interactive_environments/phinch/templates/phinch.mako
index a98e1309cb3..fc84a905ae9 100644
--- a/config/plugins/interactive_environments/phinch/templates/phinch.mako
+++ b/config/plugins/interactive_environments/phinch/templates/phinch.mako
@@ -21,21 +21,18 @@ url = ie_request.url_template('${PROXY_URL}/phinch/')
 %>
 <html>
 <head>
-${ ie.load_default_js() }
+    ${ ie.load_default_js() }
+    ${ ie.load_default_app() }
 </head>
 <body>
 <script type="text/javascript">
 ${ ie.default_javascript_variables() }
 var url = '${ url }';
-${ ie.plugin_require_config() }
 
 // Keep container running and load notebook
-requirejs(['galaxy.interactive_environments', 'plugin/phinch'], function(IES){
-    window.IES = IES;
-    keep_alive(url);
-    IES.load_when_ready(ie_readiness_url, function(){
-        load_notebook(url);
-    });
+keep_alive(url);
+IES.load_when_ready(ie_readiness_url, function(){
+    load_notebook(url);
 });
 
 </script>
diff --git a/config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample b/config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
index a07739283d7..d9b061d93ce 100644
--- a/config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
+++ b/config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
@@ -6,7 +6,7 @@
 # appropriate `apt-get/pip install` statements.
 ---
 -
-    image: erasche/docker-rstudio-notebook:19.05
+    image: quay.io/erasche/docker-rstudio-notebook:19.05
     description: |
         This familiar R analysis software suite will let you explore your
         datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr,
diff --git a/config/plugins/interactive_environments/rstudio/static/js/main.js b/config/plugins/interactive_environments/rstudio/static/js/main.js
new file mode 100755
index 00000000000..bf4bcac3dfc
--- /dev/null
+++ b/config/plugins/interactive_environments/rstudio/static/js/main.js
@@ -0,0 +1,24 @@
+// Assumed globals we need to get rid of
+var IES = window.IES;
+var toastr = window.toastr;
+
+function message_failed_connection() {
+    toastr.error("Could not connect to RStudio. Please contact your administrator.", "Security warning", {
+        closeButton: true,
+        timeOut: 20000,
+        tapToDismiss: true
+    });
+}
+
+/**
+ * Load an interactive environment (IE) from a remote URL
+ * @param {String} notebook_access_url: the URL embeded in the page and loaded
+ *
+ */
+function load_notebook(notebook_access_url) {
+    // Test notebook_login_url for accessibility, executing the login+load function whenever
+    // we've successfully connected to the IE.
+    IES.test_ie_availability(notebook_access_url, function() {
+        IES.append_notebook(notebook_access_url);
+    });
+}
diff --git a/config/plugins/interactive_environments/rstudio/static/js/rstudio.js b/config/plugins/interactive_environments/rstudio/static/js/rstudio.js
deleted file mode 100755
index c8be493fd5c..00000000000
--- a/config/plugins/interactive_environments/rstudio/static/js/rstudio.js
+++ /dev/null
@@ -1,32 +0,0 @@
-// Assumed globals we need to get rid of
-var IES = window.IES;
-var toastr = window.toastr;
-
-function message_failed_connection(){
-    toastr.error(
-        "Could not connect to RStudio. Please contact your administrator.",
-        "Security warning",
-        {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': true}
-    );
-}
-
-
-/**
- * Load an interactive environment (IE) from a remote URL
- * @param {String} notebook_access_url: the URL embeded in the page and loaded
- *
- */
-function load_notebook(notebook_access_url){
-    // Test notebook_login_url for accessibility, executing the login+load function whenever
-    // we've successfully connected to the IE.
-    IES.test_ie_availability(notebook_access_url, function(){
-        $.ajax({
-            type: 'GET',
-            url: notebook_access_url,
-            success: function(response_text){
-                IES.append_notebook(notebook_access_url);
-            }
-        });
-
-    });
-}
diff --git a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako
index a9c0bf776db..fd181ac41cc 100755
--- a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako
+++ b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako
@@ -27,18 +27,15 @@ notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/')
 <html>
 <head>
 ${ ie.load_default_js() }
+${ ie.load_default_app() }
 </head>
 <body style="margin: 0px">
 
 <script type="text/javascript">
 ${ ie.default_javascript_variables() }
 var notebook_access_url = '${ notebook_access_url }';
-${ ie.plugin_require_config() }
-requirejs(['galaxy.interactive_environments', 'plugin/rstudio'], function(IES){
-    window.IES = IES;
-    IES.load_when_ready(ie_readiness_url, function(){
-        load_notebook(notebook_access_url);
-    });
+IES.load_when_ready(ie_readiness_url, function(){
+    load_notebook(notebook_access_url);
 });
 </script>
 <div id="main" width="100%" height="100%">
diff --git a/config/tool_conf.xml.sample b/config/tool_conf.xml.sample
index f77edc40d82..aeb42d29f3b 100644
--- a/config/tool_conf.xml.sample
+++ b/config/tool_conf.xml.sample
@@ -42,6 +42,9 @@
     <tool file="${model_tools_path}/build_list.xml" />
     <tool file="${model_tools_path}/extract_dataset.xml" />
   </section>
+  <section id="expression_tools" name="Expression Tools">
+    <tool file="expression_tools/parse_values_from_file.xml"/>
+  </section>
   <section id="liftOver" name="Lift-Over">
     <tool file="extract/liftOver_wrapper.xml" />
   </section>
diff --git a/config/tool_shed.yml.sample b/config/tool_shed.yml.sample
index 31c2fe7087f..59495ea0cd0 100644
--- a/config/tool_shed.yml.sample
+++ b/config/tool_shed.yml.sample
@@ -144,6 +144,9 @@ tool_shed:
   # For searching repositories at /api/repositories:
   #repo_owner_username_boost: 0.3
 
+  # For searching repositories at /api/repositories:
+  #categories_boost: 0.5
+
   # For searching tools at /api/tools
   #tool_name_boost: 1.2
 
diff --git a/create_db.sh b/create_db.sh
index 8c77eff858d..3c34dd6c3e5 100755
--- a/create_db.sh
+++ b/create_db.sh
@@ -1,9 +1,9 @@
 #!/bin/sh
 
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 . ./scripts/common_startup_functions.sh
 
 setup_python
 
-python ./scripts/create_db.py $@
+python ./scripts/create_db.py "$@"
diff --git a/doc/Makefile b/doc/Makefile
index 86166fce846..c4589e50479 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -42,8 +42,8 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 	@echo "  updaterst  to update Sphinx RST files for lib/ to reflect code structure changes"
 
-source/dev/schema.md: parse_gx_xsd.py schema_template.md ../lib/galaxy/tools/xsd/galaxy.xsd ## Build Github-flavored Markdown from Galaxy Tool XSD (expects lxml in environment)
-	python parse_gx_xsd.py schema_template.md ../lib/galaxy/tools/xsd/galaxy.xsd > $@
+source/dev/schema.md: parse_gx_xsd.py schema_template.md ../lib/galaxy/tool_util/xsd/galaxy.xsd ## Build Github-flavored Markdown from Galaxy Tool XSD (expects lxml in environment)
+	python parse_gx_xsd.py schema_template.md ../lib/galaxy/tool_util/xsd/galaxy.xsd > $@
 
 source/api/api.rst: source/lib/galaxy.webapps.galaxy.api.rst
 	printf "Galaxy API\n==========\n" > $@
diff --git a/doc/source/admin/conda_faq.rst b/doc/source/admin/conda_faq.rst
index a4fc5a0221c..96aeadea7c1 100644
--- a/doc/source/admin/conda_faq.rst
+++ b/doc/source/admin/conda_faq.rst
@@ -393,15 +393,31 @@ Gitter or IRC channel.
 17. How can I upgrade Conda?
 ****************************
 
-Many potential issues with Conda have been resolved with fixes in Conda itself. If
-you let Galaxy install Conda prior to the release of 17.01 you probably have version
-3.19.3. This can be updated to 4.2.13 with the following command:
+Many potential issues with Conda have been resolved with fixes in Conda itself.
+The Conda installed by Galaxy can be updated to e.g. version 4.6.14 with the
+following command:
 
 .. code-block:: bash
 
-   $ <tool_dependency_dir/_conda/bin/conda update -y conda==4.2.13
+   $ <tool_dependency_dir/_conda/bin/conda install conda==4.6.14
 
-The command can obviously be adapted to install any version of Conda.
+The command can obviously be adapted to install any version of Conda. If the
+above command fails with an error like:
+
+.. code-block:: bash
+
+   UnsatisfiableError: The following specifications were found to be in conflict:
+     - conda ==4.6.14 -> python >=3.6,<3.7.0a0
+     - python 3.5*
+   Use "conda info <package>" to see the dependencies for each package.
+
+Then you need to also update the ``python`` package installed in the base
+environment by appending to the ``conda install`` command above an appropriate
+specification, which for the example error above would be ``python==3.6``:
+
+.. code-block:: bash
+
+   $ <tool_dependency_dir/_conda/bin/conda install conda==4.6.14 python==3.6
 
 
 .. _Conda documentation: https://conda.io/docs/
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index ed0714f2d89..618defd1bf3 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -105,7 +105,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Enable's a per request sql debugging option. If this is set to
+    Enables a per request sql debugging option. If this is set to
     true, append ?sql_debug=1 to web request URLs to enable detailed
     logging on the backend of SQL queries generated during that
     request. This is useful for debugging slow endpoints during
@@ -142,6 +142,38 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~
+``database_wait``
+~~~~~~~~~~~~~~~~~
+
+:Description:
+    Wait for database to become available instead of failing
+    immediately.
+:Default: ``false``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+``database_wait_attempts``
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Number of attempts before failing if database_wait is enabled.
+:Default: ``60``
+:Type: int
+
+
+~~~~~~~~~~~~~~~~~~~~~~~
+``database_wait_sleep``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Time to sleep between attempts if database_wait is enabled (in
+    seconds).
+:Default: ``1.0``
+:Type: float
+
+
 ~~~~~~~~~~~~~
 ``file_path``
 ~~~~~~~~~~~~~
@@ -485,7 +517,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Container resolvers configuration (beta). Setup a file describing
+    Container resolvers configuration (beta). Set up a file describing
     container resolvers to use when discovering containers for Galaxy.
     If this is set to None, the default containers loaded is
     determined by enable_beta_mulled_containers.
@@ -1143,7 +1175,7 @@
 :Description:
     Galaxy can display data at various external browsers.  These
     options specify which browsers should be available.  URLs and
-    builds available at these browsers are defined in the specifield
+    builds available at these browsers are defined in the specified
     files.  If use_remote_user = True, display application servers
     will be denied access to Galaxy and so displaying datasets in
     these sites will fail. display_servers contains a list of
@@ -1269,11 +1301,11 @@
     URL (with schema http/https) of the Galaxy instance as accessible
     within your local network - if specified used as a default by
     pulsar file staging and Jupyter Docker container for communicating
-    back with Galaxy via the API.  If you are attempting to setup GIEs
-    on Mac OS X with Docker for Mac - this should likely be the IP
-    address of your machine on the virtualbox network (vboxnet0) setup
-    for the Docker host VM. This can found by running ifconfig and
-    using the IP address of the network vboxnet0.
+    back with Galaxy via the API.  If you are attempting to set up
+    GIEs on Mac OS X with Docker Desktop for Mac and your Galaxy
+    instance runs on port 8080 this should be
+    'http://host.docker.internal:8080'.  For more details see
+    https://docs.docker.com/docker-for-mac/networking/
 :Default: ``http://localhost:8080``
 :Type: str
 
@@ -1700,9 +1732,8 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Set the port and IP for the the dynamic proxy to bind to, this
-    must match the external configuration if dynamic_proxy_manage is
-    False.
+    Set the port and IP for the dynamic proxy to bind to, this must
+    match the external configuration if dynamic_proxy_manage is False.
 :Default: ``8800``
 :Type: int
 
@@ -1712,9 +1743,8 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Set the port and IP for the the dynamic proxy to bind to, this
-    must match the external configuration if dynamic_proxy_manage is
-    False.
+    Set the port and IP for the dynamic proxy to bind to, this must
+    match the external configuration if dynamic_proxy_manage is False.
 :Default: ``0.0.0.0``
 :Type: str
 
@@ -3144,6 +3174,31 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~
+``job_config``
+~~~~~~~~~~~~~~
+
+:Description:
+    Description of job running configuration, can be embedded into
+    Galaxy configuration or loaded from an additional file with the
+    job_config_file option.
+:Default: ``None``
+:Type: map
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~
+``dependency_resolvers``
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Rather than specifying a dependency_resolvers_config_file, the
+    definition of the resolvers to enable can be embedded into
+    Galaxy's config with this option. This has no effect if a
+    dependency_resolvers_config_file is used.
+:Default: ``None``
+:Type: seq
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``default_job_resubmission_condition``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/doc/source/admin/special_topics/interactive_environments.rst b/doc/source/admin/special_topics/interactive_environments.rst
index f075f041295..f7e7fce324c 100644
--- a/doc/source/admin/special_topics/interactive_environments.rst
+++ b/doc/source/admin/special_topics/interactive_environments.rst
@@ -36,17 +36,13 @@ and `Ansible Galaxy <https://galaxy.ansible.com/detail#/role/6056>`__.
 Setting up the Proxy
 ^^^^^^^^^^^^^^^^^^^^
 
-Currently the Galaxy proxy is a NodeJS+Sqlite3 proxy.
+The Galaxy IE Proxy is a NodeJS+Sqlite3 application.  The NodeJS that is
+installed by default into the Galaxy Virtualenv is suitable for an execution
+environment for the Galaxy IE Proxy.
 
-- Node has recently upgraded, and our proxy is pinned to an old version of
-  sqlite3. As such you'll currently need to have an older version of Node
-  available (0.10.X - 0.11.X vintage).
-- One can use `NVM <https://github.com/creationix/nvm>`__ to install and manage multiple versions of Node.
-- We're working on solutions in this space to provide a better deployment
-  mechanism here and fewer dependencies.
-- Please note that if you have NodeJS installed under Ubuntu, it often
-  installs to ``/usr/bin/nodejs``, whereas ``npm`` expects it to be
-  ``/usr/bin/node``. You will need to create that symlink yourself.
+- Note that if you have NodeJS installed under Ubuntu, it often installs to
+  ``/usr/bin/nodejs``, whereas ``npm`` expects it to be ``/usr/bin/node``. You
+  may need to create that symlink yourself.
 
 Once Node and npm are ready to go, you'll need to install the dependencies
 
diff --git a/doc/source/admin/special_topics/mulled_containers.rst b/doc/source/admin/special_topics/mulled_containers.rst
index 6cd0a281d36..271f97e8b73 100644
--- a/doc/source/admin/special_topics/mulled_containers.rst
+++ b/doc/source/admin/special_topics/mulled_containers.rst
@@ -4,10 +4,10 @@ Containers for Tool Dependencies
 
 Galaxy tools (also called wrappers) are able to use Conda packages
 (see more information in our `Galaxy Conda documentation`_) and Docker containers as dependency resolvers.
-The IUC_ recommends to use Conda packages as primary dependency resolver, mainly because Docker is not
+The IUC_ recommends to use Conda packages as the primary dependency resolver, mainly because Docker is not
 available on every (HPC-) system. Conda on the other hand can be installed by Galaxy and maintained
-entirely in user-space. Nevertheless, Docker (Containers in general) has some unique features and
-there are many use-cases in the Galaxy community which makes containerized systems very appealing.
+entirely in user-space. Nevertheless, Docker and containers in general have some unique features and
+there are many use-cases in the Galaxy community that make containerized tools very appealing.
 
 Since 2014 Galaxy supports running tools in Docker containers via a special `container annotation`_ inside of the 
 requirement field.
@@ -41,17 +41,16 @@ is not available already.
 Automatic build of Linux containers
 -----------------------------------
 
-We utilize [mulled](https://github.com/mulled/mulled) with [involucro](https://github.com/involucro/involucro)
-in an automatic way. This is for example used to convert all packages in bioconda_ into Linux Containers
-(Docker and rkt at the moment) and made available at the `BioContainers Quay.io account`_.
+We utilize mulled_ with involucro_ to automatically convert all packages in Bioconda_ into Linux containers images 
+(Docker and rkt at the moment) and make them available at the `BioContainers Quay.io account`_.
 
-We have developed small utilities around this technology stack which is currently included in galaxy-lib_.
+We have developed small utilities around this technology stack, which is currently included in galaxy-lib_.
 Here is a short introduction:
 
 Search for containers
 ^^^^^^^^^^^^^^^^^^^^^
 
-This will search for containers in the biocontainers organisation.
+This will search for containers in the biocontainers organization.
 
 .. code-block:: bash
 
@@ -72,40 +71,40 @@ The BioConda community is building a container for every package they create wit
 Building Docker containers for local Conda packages
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Conda packages can be tested with creating a busybox based container for this particular package in the following way.
+Conda packages can be tested with creating a *busybox* based container for this particular package in the following way.
 This also demonstrates how you can build a container locally and on-the-fly.
 
-  > we modified the samtools package to version 3.0 to make clear we are using a local version
+  > we modified the ``samtools`` package to version 3.0 to make it clear we are using a local version
 
-1) build your recipe
+1) Build your recipe
 
 .. code-block:: bash
    
    $ conda build recipes/samtools
 
-2) index your local builds
+2) Index your local builds
 
 .. code-block:: bash
    
    $ conda index /home/bag/miniconda2/conda-bld/linux-64/
 
 
-3) build a container for your local package
+3) Build a container for your local package
 
 .. code-block:: bash
    
    $ mulled-build build-and-test 'samtools=3.0--0' \
       --extra-channel file://home/bag/miniconda2/conda-bld/ --test 'samtools --help'
 
-The ``--0`` indicates the build version of the conda package. It is recommended to specify this number otherwise
+The ``--0`` indicates the build version of the conda package. It is recommended to specify this number, otherwise
 you will override already existing images. For Python Conda packages this extension might look like this ``--py35_1``.
 
-Build, test and push a conda-forge package to biocontainers
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Build, test, and push a conda-forge package to biocontainers
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
  > You need to have write access to the biocontainers repository
 
-You can build packages from other Conda channels as well, not only from BioConda. ``pandoc`` is available from the
+You can build packages from other Conda channels as well, not only from BioConda. ``pandoc`` tool is available from the
 conda-forge channel and conda-forge is also enabled by default in Galaxy. To build ``pandoc`` and push it to biocontainrs
 you could do something along these lines.
 
@@ -123,6 +122,8 @@ you could do something along these lines.
 .. _IUC: https://galaxyproject.org/iuc/
 .. _container annotation:  https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/catDocker.xml#L4
 .. _BioContainers: https://github.com/biocontainers
-.. _bioconda: https://github.com/bioconda/bioconda-recipes
+.. _mulled: https://github.com/mulled/mulled
+.. _involucro: https://github.com/involucro/involucro
+.. _Bioconda: https://bioconda.github.io/
 .. _BioContainers Quay.io account: https://quay.io/organization/biocontainers
 .. _galaxy-lib: https://github.com/galaxyproject/galaxy-lib
diff --git a/doc/source/dev/interactive_environments.rst b/doc/source/dev/interactive_environments.rst
index a9372fdc228..7f457228c7e 100644
--- a/doc/source/dev/interactive_environments.rst
+++ b/doc/source/dev/interactive_environments.rst
@@ -205,9 +205,10 @@ We'll continue appending to our ``helloworld.mako`` the HTML code that's actuall
 
     <html>
     <head>
-    <!-- Loads some necessary javascript libraries. Specifically jquery,
-         toastr, and requirejs -->
+    <!-- Loads core Galaxy javascript libraries for a 'generic' entrypoint. -->
     ${ ie.load_default_js() }
+    <!-- This will load code from static/main.js, often used to handle things like login  -->
+    ${ ie.load_default_app() }
     </head>
     <body>
 
@@ -217,18 +218,11 @@ We'll continue appending to our ``helloworld.mako`` the HTML code that's actuall
     var notebook_login_url = 'unused';
     var notebook_access_url = '${ notebook_access_url }';
 
-    // Load code with require.js
-    ${ ie.plugin_require_config() }
 
     // Load notebook
-    // This will load code from static/helloworld.js, often used to handle
-    // things like Login. The load_notebook function will eventually append
-    // an IFrame to the <div id="main" /> below.
-    requirejs(['galaxy.interactive_environments', 'plugin/helloworld'], function(IES){
-        window.IES = IES
-        IES.load_when_ready(ie_readiness_url, function(){
-            load_notebook(notebook_access_url);
-        });
+    // The load_notebook function will eventually append an IFrame to the <div id="main" /> below.
+    IES.load_when_ready(ie_readiness_url, function(){
+        load_notebook(notebook_access_url);
     });
     </script>
     <div id="main" width="100%" height="100%">
@@ -262,7 +256,7 @@ authentication of users, so you don't have to worry about it, and can just
 assume that only the correct user will have access to a given notebook.
 
 In the ``static/`` directory, we generally create a ``js/`` directory below that,
-and create a ``{gie}.js`` (so, ``static/js/helloworld.js``) file in there.
+and create a ``main.js`` file in there.
 That file will have a function, ``load_notebook`` which will check if the GIE is available,
 and when it is, display it to the user.
 
diff --git a/doc/source/releases/19.01_announce_user.rst b/doc/source/releases/19.01_announce_user.rst
index 7381c4d9049..d486d8bf735 100644
--- a/doc/source/releases/19.01_announce_user.rst
+++ b/doc/source/releases/19.01_announce_user.rst
@@ -41,13 +41,13 @@ There's a new discussion forum to replace Biostars. It is accessible under the '
    :alt: Galaxy's new help forum which replaces biostars
 
 
-New Visualisations
+New Visualizations
 ===========================================================
 
 `Aequatus visualisation plugin <https://docs.google.com/presentation/d/1_KdwjbIyjUhdb_huAzOuI34693mciw_vXDCGLctKs9A/edit#slide=id.p2>`__ has been released which allows visualisation of gene alignments and gene family aggregations.
 
 .. figure:: https://lh3.googleusercontent.com/wgNqZT2idSR4AkvUZ55ZQGXOfOPlAxFimO9795WvrQwP1ZMxxdYwNmRZErf-n5hZMGa1SulFry321vgHPoc11wsmJlmVPrmyxG8buV6P=s1600
-   :alt: The Aequatus visualisation allows analysing gene family alignments
+   :alt: The Aequatus visualization allows analyzing gene family alignments
 
 New Datatypes
 ===========================================================
diff --git a/doc/source/releases/19.05.rst b/doc/source/releases/19.05.rst
new file mode 100644
index 00000000000..160ab07a718
--- /dev/null
+++ b/doc/source/releases/19.05.rst
@@ -0,0 +1,726 @@
+
+.. to_doc
+
+19.05
+===============================
+
+.. announce_start
+
+Enhancements
+-------------------------------
+
+* Implement the ability to favorite tools.
+  `Pull Request 7209`_
+* Add data dialog option to tool form data selector.
+  `Pull Request 7553`_, `Pull Request 7460`_
+* Many workflow editor connection fixes and enhancements making
+  them more correct, accessible, and transparent
+  (with huge thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7466`_, `Pull Request 7435`_, `Pull Request 7972`_,
+  `Pull Request 7979`_, `Pull Request 7642`_, `Pull Request 7989`_,
+  `Pull Request 7254`_
+* Add a Galaxy IE for cellxgene.
+  `Pull Request 7268`_
+* Implement expression tools and non-data tool outputs
+  (with thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7556`_, `Pull Request 7796`_, `Pull Request 7797`_,
+  `Pull Request 7944`_
+* Add Galaxy cloud runner support
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 7226`_
+* More robust task messaging
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7548`_
+* Allow implicit conversion for input collection parameters
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7683`_
+* Allow import of "Format 2" workflows by default.
+  `Pull Request 7659`_
+* Decompose Galaxy into Python libraries in-tree.
+  `Pull Request 7524`_
+* Rewrite and generalize History import and export - dozens of fixes, support for collections,
+  Python library support, etc..
+  `Pull Request 7367`_, `Pull Request 7214`_, `Pull Request 7366`_,
+  `Pull Request 7369`_, `Pull Request 7370`_, `Pull Request 7358`_,
+  `Pull Request 7505`_, `Pull Request 7507`_, `Pull Request 7363`_,
+  `Pull Request 7193`_, `Pull Request 7192`_, `Pull Request 7537`_,
+  `Pull Request 7540`_, `Pull Request 7684`_, `Pull Request 7704`_
+* User facing release notes
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 7527`_
+* Implement dataset source and hash tracking.
+  `Pull Request 7487`_, `Pull Request 4659`_, `Pull Request 7549`_
+* Custos integration for AuthNZ
+  (thanks to `@machristie <https://github.com/machristie>`__).
+  `Pull Request 7195`_
+* Flush out API support for AuthNZ and CloudAuthz
+  `Pull Request 7598`_, `Pull Request 7609`_,
+  `Pull Request 7592`_, `Pull Request 7597`_,
+  `Pull Request 7639`_
+* Update to PSA 3.1 and support login with Globus identity.
+  `Pull Request 7463`_
+* Swap from 'slug.js' to 'slugify.js' - saving 10 MB in client bundles.
+  `Pull Request 7538`_
+* Update all client dependencies - including to Backbone 1.4, Bootstrap 4.2, Vue 2.6.
+  `Pull Request 7544`_, `Pull Request 7637`_
+* Allow admins to import dynamic JSON-based tools.
+  `Pull Request 7545`_
+* Implement environment modules mapping files
+  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
+  `Pull Request 7398`_
+* Allow tool testing of multiple files within a zip output
+  (thanks to `@thermokarst <https://github.com/thermokarst>`__).
+  `Pull Request 7400`_
+* Add datatype converters between tabular and CSV.
+  `Pull Request 7246`_
+* Add Azure and GCP support for ObjectStore Cloud backend.
+  `Pull Request 7272`_
+* Add a validator that ensure metadata value is on a range.
+  (thanks to `@fmareuil <https://github.com/fmareuil>`__).
+  `Pull Request 7288`_
+* Fix post job actions for "Database Operation" tools, implement ``change_datatype``
+  for collection output
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7480`_
+* Implement and enforce ESLint linting of the entire client code base.
+  `Pull Request 7202`_, `Pull Request 7860`_
+* Multiple enhancements to the LSF cli-plugin job runner - support
+  out of memory handling, project specification, and Spectrum LSF.
+  (thanks to `@pcm32 <https://github.com/pcm32>`__ and
+  `@selten <https://github.com/selten>`__).
+  `Pull Request 6866`_, `Pull Request 7581`_, `Pull Request 7486`_
+* Drop support for Python 3.4 and officially support Python 3.5 or greater.
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7291`_
+* Batch bulk hide and delete operations when multiple selected.
+  `Pull Request 5495`_
+* Implement client initialization pipeline.
+  `Pull Request 7117`_
+* Allow storing objects in the object store by UUID.
+  `Pull Request 7154`_, `Pull Request 7650`_
+* Replace login and registration mako templates with VueJS components.
+  `Pull Request 6621`_, `Pull Request 7047`_, `Pull Request 7329`_,
+  `Pull Request 7442`_, `Pull Request 7756`_, `Pull Request 7347`_
+* Track messages generated tool stdio tags in the database instead of just appending them
+  to tool standard error. Structured UI in reporting also.
+  (with help from `@bernt-matthias <https://github.com/bernt-matthias>`__)
+  `Pull Request 7095`_
+* Track job script stdout and stderr separately from the tool's stdout and stderr in the database.
+  `Pull Request 7095`_
+* Support loading/using tools that are not in the install database
+  (with help from `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7316`_, `Pull Request 8021`_
+* Git providers error reporting plugins
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 7485`_
+* Rename ``_future_expose_api`` to ``expose_api`` and ``expose_api`` to ``legacy_expose_api``
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7743`_
+* Add ``mtx`` datatype
+  (thanks to `@bebatut <https://github.com/bebatut>`__ and
+  `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7569`_, `Pull Request 7702`_, `Pull Request 7717`_
+* Add ``geojson`` datatype
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 7773`_
+* Add shapefile (``shp``) datatype
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 7819`_
+* Add ``imgt.json`` datatype for IMGT immune system libraries
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 7587`_
+* Add microarrays data types ``gpr`` and ``gal``
+  (thanks to `@bensellak <https://github.com/bensellak>`__).
+  `Pull Request 7457`_
+* Add ``spaln`` database type
+  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
+  `Pull Request 7718`_
+* Redefine ``cel`` datatype
+  (thanks to `@bensellak <https://github.com/bensellak>`__).
+  `Pull Request 7514`_
+* Run most tests formerly ran on Travis on CircleCI
+  (with help from `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7424`_, `Pull Request 7573`_, `Pull Request 7451`_,
+  `Pull Request 7207`_, `Pull Request 7539`_, `Pull Request 7574`_
+* Toolshed API enhancements.
+  `Pull Request 6652`_
+* Kubernetes job runner integration test and enhancements
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6958`_
+* Implement sniffing of datatypes for library datasets.
+  `Pull Request 7379`_
+* Rewrite tool output metadata collection - now portable and more correct, tested,
+  and documented.
+  `Pull Request 7470`_, `Pull Request 7459`_, `Pull Request 7156`_
+  `Pull Request 7483`_, `Pull Request 7158`_, `Pull Request 7213`_,
+  `Pull Request 7694`_, `Pull Request 7596`_, `Pull Request 7186`_,
+  `Pull Request 7471`_
+* Add ``python`` to ``Count1`` tool requirements
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7185`_
+* Fixes and enhancements for the grouping1 tool - including not removing empty cells
+  at the begin/start of lines
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__ and
+  `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7205`_, `Pull Request 7844`_
+* Workflow editor accessibility fixes.
+  `Pull Request 7750`_
+* Python dependency updates and documentation fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7215`_, `Pull Request 7247`_, `Pull Request 7285`_,
+  `Pull Request 7740`_
+* Remove requirement pin on specific Sphinx version
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7365`_
+* Drop conditional pygmentz requirement (autoinstalled as necessary), minor
+  formatting in conditional-reqs
+  `Pull Request 7219`_
+* Fix spacing between checkbox and buttons in history sharing view.
+  `Pull Request 7222`_
+* Use regular font-size and styling in uploader.
+  `Pull Request 7232`_
+* Remove underline from history datasets.
+  `Pull Request 7235`_
+* Add headless testing option for Selenium tests.
+  `Pull Request 7287`_
+* Build tool XML schema docs using ``sphinx_markdown_tables``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7313`_
+* Refactor dataset controller to reuse input validation checks between get/set.
+  `Pull Request 7322`_
+* Add web server documentation notes about ``Range`` support
+  (thanks to `@pvanheus <https://github.com/pvanheus>`__ and
+  `@nsoranzo <https://github.com/nsoranzo>`_).
+  `Pull Request 7323`_, `Pull Request 7334`_
+* Fall back to binary comparison if BAM conversion fails during tool tests
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 7342`_
+* Update ``area`` issue/PR labels
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7344`_
+* Remove deprecated ``collect_outputs_from`` configuration option.
+  `Pull Request 7144`_
+* Remove ``ToolsController._rerun_tool()`` API method
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7345`_
+* Refactor ``item_attrs.py`` for reuse without mixin inheritance.
+  `Pull Request 7346`_
+* Add ``--force_path_paste`` argument to tool test verify script.
+  `Pull Request 7356`_
+* Separate client node version requirement into individual dotfile for reuse.
+  `Pull Request 7357`_
+* Improve tool testing for counting datasets in paired collections
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 7359`_
+* Do not default to ``DEV_WHEELS=1`` if no ``git`` is found
+  (thanks to `@ic4f <https://github.com/ic4f>`__).
+  `Pull Request 7371`_
+* Restore gray scale difference between panel vs portlet background color for
+  contrast.
+  `Pull Request 7387`_
+* Specify exceptions more precisely in user API controller.
+  `Pull Request 7397`_
+* Automatically set ``cookie_path`` using ``url_for()``.
+  `Pull Request 7404`_
+* Allow configuration location of user preferences extra configuration
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 7428`_
+* Add hover styling to target tool in tool panel
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 7437`_
+* Update Docker testing image
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7439`_, `Pull Request 7187`_
+* Remove unused code
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7445`_
+* Note `cannot import name _remove_dead_weakref` error and solution
+  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
+  `Pull Request 7461`_
+* Add option to pass in individual globs to client unit test watcher
+  `Pull Request 7477`_
+* Update of tours overview according to `#5860
+  <https://github.com/galaxyproject/galaxy/issues/5860>`__
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 7478`_
+* Add new metadata and data table tool validators
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 7500`_
+* Updated documentation in ``admin/scaling.md`` for Systemd
+  (thanks to `@ooobik <https://github.com/ooobik>`__).
+  `Pull Request 7515`_
+* Replace backbone tagging views with VueJs components.
+  `Pull Request 7516`_
+* Eliminate import dependency of datatypes on galaxy.web (``url_for``).
+  `Pull Request 7521`_
+* Static plugin staging as a part of client build instead of startup.
+  `Pull Request 7532`_
+* Implement dockerized variant of ``update.sh`` for project Python dependencies.
+  `Pull Request 7546`_
+* Refactor XSD output elements to share common output attributes.
+  `Pull Request 7555`_
+* Improve linking between job conf handler assignment and documentation
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 7558`_
+* Refactor ``galaxy.web.security`` into ``galaxy.security.idencoding``.
+  `Pull Request 7560`_
+* Move the 'create new history' out of the history context menu
+  `Pull Request 7565`_, `Pull Request 7606`_
+* Improve workflow cog menu user interface.
+  `Pull Request 7594`_, `Pull Request 7858`_
+* Make ``galaxy.model.dataset_collections`` more usable outside manager context.
+  `Pull Request 7595`_
+* Webpack bundle overhaul and initial dynamic loading.
+  `Pull Request 7605`_
+* Don't un-hide mapped-over outputs when job fails
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7630`_
+* Continue gracefully in set_meta if unable to count number of dataset lines.
+  `Pull Request 7641`_
+* Implement functional dict-ifiable tool outputs and error detection.
+  `Pull Request 7651`_
+* Refactor ``IntegrationTestCase`` to allow integration test functions.
+  `Pull Request 7657`_
+* Drop .pyc files before attempting to migrate
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7677`_
+* Add docs to OIDC backends configuration file.
+  `Pull Request 7691`_
+* Update ``CITATION`` to latest Galaxy update paper
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7698`_
+* Update pull request procedures to exempt notes, changelogs, and
+  packages from mandatory review.
+  `Pull Request 7706`_
+* Update procedures to relax the vote requirement for fixing bugs in releases
+  `Pull Request 7707`_
+* Improve error message if GFF file is missing attribute col
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7708`_
+* Add hostname to task message queues
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7712`_
+* OIDC login buttons based on configuration
+  (thanks to `@machristie <https://github.com/machristie>`__).
+  `Pull Request 7720`_
+* Enable the selection of library datasets in the tool form
+  `Pull Request 7746`_
+* Replace ``enable_beta_export_format2_default`` with
+  ``default_workflow_export_format``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7748`_
+* Report a couple common errors in dataset/job report.
+  `Pull Request 7755`_
+* Add singularity to valid types, allow customization of test history name
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7760`_
+* Update parameter_input type when changing parameter type
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7780`_
+* Don't clean up jobs when running tests if `$GALAXY_TEST_NO_CLEANUP` is set
+  `Pull Request 7798`_
+* Add option to wait for the database to become available
+  (thanks to `@ic4f <https://github.com/ic4f>`__).
+  `Pull Request 7827`_
+* Remove recursion from ``expand_nested_tokens()``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7834`_
+* Allow composite upload if all non-optional files are selected
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7872`_
+* Cleanup integration test configuration code.
+  `Pull Request 7874`_
+* Add "Reset" button to composite upload interface
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7875`_
+* Add local namespaced resolver to default container resolvers
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7896`_
+* Use node-watch instead of fs.watch to watch for db changes
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7967`_
+* Remove reset handler from ruler input element.
+  `Pull Request 6321`_
+* Declutter the history 'cog' menu.
+  `Pull Request 6437`_
+* Remove deprecated OpenID features.
+  `Pull Request 7028`_, `Pull Request 7395`_
+* Restores OpenID post authentication protocols.
+  `Pull Request 7676`_
+* Replace custom UI colors with equivalent theme colors, consolidate color
+  handling.
+  `Pull Request 7203`_
+* Modernize library toolbar client code.
+  `Pull Request 7234`_
+* Large refactoring of model migrations
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7621`_, `Pull Request 7248`_,
+  `Pull Request 7737`_, `Pull Request 7695`_
+* Implement a general purpose tagging component in the Galaxy client code.
+  `Pull Request 7270`_
+* Define doctype method on XMLParser target
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7303`_
+* Refactor ``galaxy.util.handlers`` -> ``galaxy.web.stack.handlers``.
+  `Pull Request 7339`_
+* Move ``create_history_template`` out of ``galaxy.util``.
+  `Pull Request 7522`_
+* Refactor ``galaxy.web.form_builder`` into ``galaxy.util.form_builder``.
+  `Pull Request 7529`_
+* Drop unused install keyword and load TS workflows with utf-8 encoding
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7423`_
+* Remove biostar integrations.
+  (with help from `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7443`_, `Pull Request 7510`_
+* Refactor TagManager (back) to TagHandler.
+  `Pull Request 7530`_
+* Refactor ``output_collect.py`` toward a database session-less modality.
+  `Pull Request 7541`_
+* Drop D3 from publicly provided libs
+  `Pull Request 7542`_
+* Fix dependency cycle between ``galaxy.security`` and ``galaxy.model``.
+  `Pull Request 7554`_
+* Refactor ``galaxy.dataset_collections`` into ``galaxy.model.dataset_collections``.
+  `Pull Request 7588`_
+* Toastr debowerization and refactoring.
+  `Pull Request 7640`_
+* Tweak ``popup-menu.js`` error handling.
+  `Pull Request 7643`_
+* Update Conda version that new Galaxies will install
+  `Pull Request 8048`_
+
+Fixes
+-------------------------------
+
+* Explicitly specify system user under which Kubernetes jobs should run.
+  `Pull Request 8103`_
+* Ensure Kubernetes job querries filter the same namespace as defined in the
+  job destination.
+  `Pull Request 8092`_
+* Fix client styleguide asset handling.
+  `Pull Request 7664`_
+* Handle subworkflows in view workflow mako
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7276`_
+* Fix removing tags from a dataset previously only the first tag could be removed
+  (thanks to `@gtrack <https://github.com/gtrack>`__).
+  `Pull Request 7674`_, `Pull Request 7680`_
+* Fix displaying and editing SelectTagParameters in workflow editor
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7534`_
+* Fix workflow output rectification.
+  `Pull Request 7101`_
+* Interactive Environment Fixes
+  `Pull Request 7917`_
+* Make job script actually return tool exit code
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 7147`_
+* Fix client galaxy object instance access in visualizations.
+  `Pull Request 7198`_
+* Assorted component bugfixes.
+  `Pull Request 7200`_
+* Update IE proxy dependencies.
+  `Pull Request 7208`_
+* Cleanup code for univa job runner
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 7210`_
+* Verify and update .venv's node version.
+  `Pull Request 7220`_
+* Update ``use_interactive`` default in docs
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7221`_
+* Fix hotdata method access.
+  `Pull Request 7256`_
+* Fix saving imported subworkflows
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7262`_
+* Fix "occured" typo everywhere
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7266`_
+* Fix flakey history import metadata test
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7279`_
+* Do not skip the client build in dockerized selenium tests
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7280`_
+* Fixes for the cluster documentation
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7281`_
+* Fix ``ObjectNotFound`` exception when exporting an history
+  (thanks to `@abretaud <https://github.com/abretaud>`__).
+  `Pull Request 7286`_
+* Do not remove tools from other installed revisions when uninstalling TS
+  repo
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7300`_
+* Remove unused keyword in resend email helper.
+  `Pull Request 7315`_
+* Fix popupmenu creation.
+  `Pull Request 7318`_
+* Fix trackster toolbox filter for logged-in users
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7319`_
+* Remove overlapping tooltip from dropdown button in library toolbar.
+  `Pull Request 7321`_
+* UI fixes for libraries.
+  `Pull Request 7337`_
+* Fix ``test_import_metadata_regeneration`` API test
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7340`_
+* Possible fix for fasta file never getting filesize
+  (thanks to `@Slugger70 <https://github.com/Slugger70>`__).
+  `Pull Request 7374`_
+* Fix upload button style.
+  `Pull Request 7381`_
+* Fix link doc syntax
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 7388`_
+* Update application documentation
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7391`_
+* Fix pie chart and portlet height in flexboxes.
+  `Pull Request 7396`_
+* Fix ``LocalShellRunner``
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7438`_
+* Use a lock on cleanup, expire_tool and cache_tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7446`_
+* Fix loading workflows with steps without default label
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7448`_
+* Remove broken configuration option tool_submission_burst
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7449`_
+* Restore ``get_filename`` to ``galaxy.tools.verify:verify()``
+  `Pull Request 7452`_
+* Fix documentation for statsd and uwsgi
+  (thanks to `@abretaud <https://github.com/abretaud>`__).
+  `Pull Request 7453`_
+* Fix hidden parameter use in workflows
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7458`_
+* Fix syntax of XSD tool schema.
+  `Pull Request 7462`_
+* Fix workflow building typo
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7472`_
+* Correct ``virtualenv`` download with no ``wget``/``curl``
+  (thanks to `@hmenager <https://github.com/hmenager>`__).
+  `Pull Request 7476`_
+* Use a relative ``output.publicPath`` to avoid 404 errors when serving with a url
+  prefix
+  (thanks to `@abretaud <https://github.com/abretaud>`__).
+  `Pull Request 7481`_
+* Restrict loading of JSON files on the server via the workflow API to Galaxy
+  admins
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7499`_
+* Fix warning message formatting in sharing controller
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7504`_
+* Make sure ``temp_output_dir`` path is absolute
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7517`_
+* Create directory before copying file there
+  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
+  `Pull Request 7519`_
+* Fix routing when serving Galaxy at a prefix.
+  `Pull Request 7523`_
+* Small object store fixes.
+  `Pull Request 7536`_
+* Fix entering workflow parameter in workflow run form
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7543`_
+* Extend reload test case logging
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7547`_
+* Correct db-self handler assignment method
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 7561`_
+* Fix database config doctests when env vars are in use for dburi
+  `Pull Request 7562`_
+* Fix help warnings style.
+  `Pull Request 7566`_
+* Fix to run ``bootstrap_history.py`` inside Galaxy's virtualenv
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7584`_
+* Update cloud imports to adhere with cloudbridge interface changes.
+  `Pull Request 7586`_
+* Fix RStudio GIE
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 7590`_, `Pull Request 7925`_
+* Fix styleguide.
+  `Pull Request 7602`_
+* Fix history options menu href navigation
+  `Pull Request 7612`_
+* Minor cli and metadata fixes
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7614`_
+* Improve string escaping and changeset validation on toolshed.
+  `Pull Request 7616`_
+* Delay workflow step execution for discovered & mapped-over input
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7633`_
+* Fix float to int casting
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7634`_
+* Adjust ``test_run_with_numeric_input_connection`` to extra line
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7645`_
+* Fix incorrect LDDAs being used as collection members.
+  `Pull Request 7646`_
+* Fix GenomeSpace tools.
+  `Pull Request 7647`_, `Pull Request 7697`_
+* Bugfix for input selection with tag representation in ``ui-select-default``.
+  `Pull Request 7658`_
+* Drop now unused import endpoint from workflow controller.
+  `Pull Request 7660`_
+* Fix for ``trans.redirect`` not setting cookies/headers.
+  `Pull Request 7663`_
+* Fix shutdown for Pulsar MQ Runner.
+  `Pull Request 7667`_
+* Fix "Run workflow" jumps when clicking
+  (thanks to `@gtrack <https://github.com/gtrack>`__).
+  `Pull Request 7675`_
+* Detect errors using exit code for sort tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7679`_
+* Fix ``format_source`` for implicit conversion inputs and ``fasta.gz`` upload
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7682`_
+* Plugin static staging fix.
+  `Pull Request 7689`_
+* Fix side panel styling, adjust appearance in reports.
+  `Pull Request 7690`_
+* Patch for metadata setting of minimal BIOM1 files
+  (thanks to `@bebatut <https://github.com/bebatut>`__).
+  `Pull Request 7696`_
+* Only check for exit code on actual sort command
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7699`_
+* Update ``pytest-posgresql`` to 1.4.0, which removes a hard dependency on
+  ``psycopg2``
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7703`_
+* Fix runner param validation in the DRMAA runner.
+  `Pull Request 7709`_
+* Restrict workflow invocation index to current user
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7711`_
+* Copy ``tools_by_id`` before collecting dependency status
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7713`_
+* Fix uWSGI startup with separate ini file under Python 3
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7716`_
+* Fix (re)starting Galaxy using paste, ``GALAXY_RUN_ALL=1`` and ``--wait``
+  under macOS
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7722`_
+* Fix check on links in ``CompressedFile.safemembers()``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7723`_
+* Unpause dependent jobs when resuming jobs
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7724`_
+* Commented-out cloudbridge requirement for the cloud/send tool.
+  `Pull Request 7727`_
+* Fix comments
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7738`_
+* Upgrade to latest Pulsar release for various remote job running fixes.
+  `Pull Request 7744`_, `Pull Request 7865`_
+* Fix automatic user registration.
+  `Pull Request 7749`_
+* Sanitize HTML in messages using ``galaxy.util.sanitize_html``.
+  `Pull Request 7751`_
+* Fix Kubernetes integration tests for Docker on Mac.
+  `Pull Request 7754`_
+* Fix BootstrapVue component specification in Citations.
+  `Pull Request 7778`_
+* Symlink two more images that are accessed via non-webpack'd applications.
+  `Pull Request 7779`_
+* Make ``url_get`` return unicode
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7782`_
+* Disable flexible spreading of radio buttons by default.
+  `Pull Request 7788`_
+* Fix default value handling of color parameter.
+  `Pull Request 7475`_
+* Fix various Python deprecations
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7800`_
+* Return HTTP 400 for `GET /api/datasets/nonexistent_id`
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7806`_
+* Encode email messages using UTF-8
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7812`_
+* Fix nested macro/token expansion on Python 3
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7823`_
+* Possible fix for WSGI process issue `#7758
+  <https://github.com/galaxyproject/galaxy/issues/7758>`__
+  (thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
+  `Pull Request 7824`_
+* Fix ``InputValueWrapper`` gt/ge/lt/le comparisons
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7826`_
+* Fix trackster issue with constraining (``overflow:non-visible``) containers.
+  `Pull Request 7845`_
+* Improve upload accessibility.
+  `Pull Request 7848`_
+* Adjust appearance of user creation form in admin panel.
+  `Pull Request 7851`_
+* Use just the env name when checking ``CONDA_DEFAULT_ENV``
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7853`_
+* Fix workflow extraction for jobs whose JobToDatasetOutputAssociation
+  references a discovered dataset
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7855`_
+* Fix flag for library dataset option in data selector.
+  `Pull Request 7859`_
+* Fix bug preventing handler runner plugin handling.
+  `Pull Request 7870`_
+* Fix click targeting for quota usage details
+  `Pull Request 7877`_
+* Allow typing e in float param field.
+  `Pull Request 7880`_
+* Update Cheetah dependency, fixes ``AssertionError``
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7887`_
+* Fix application of history default permissions to anonymous histories
+  carried over upon login.
+  `Pull Request 7904`_
+* Fix multi-history copying of collections.
+  `Pull Request 7906`_
+* Remove GFF headers during conversion and test fix
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7916`_
+* Fix community tags showing JSON file.
+  `Pull Request 7923`_
+* Fix upload of gzipped VCF files
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7933`_
+* Fix documentation building
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7934`_
+* Listen to history changes in tool form until job has been submitted.
+  `Pull Request 7943`_
+* Fixed wrong example for ``amqp_ack_republish_time`` in
+  ``job_conf.xml.sample_advanced``
+  (thanks to `@AndreasSko <https://github.com/AndreasSko>`__).
+  `Pull Request 7983`_
+* Backport various upload encoding fixes from `#7995 <https://github.com/galaxyproject/galaxy/issues/7995>`__
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 8000`_, `Pull Request 8004`_
+* Disable create user button while request is being processed
+  `Pull Request 8029`_
+* Fix multipanel history search
+  `Pull Request 8085`_
+
+.. include:: 19.05_prs.rst
+
diff --git a/doc/source/releases/19.05_announce.rst b/doc/source/releases/19.05_announce.rst
index feb23a84dc9..557133feea8 100644
--- a/doc/source/releases/19.05_announce.rst
+++ b/doc/source/releases/19.05_announce.rst
@@ -3,8 +3,60 @@
 May 2019 Galaxy Release (v 19.05)
 ===========================================================
 
+.. include:: _header.rst
 
-Schedule
+Highlights
 ===========================================================
- * Planned Freeze Date: 2019-05-06
- * Planned Release Date: 2019-05-27
+
+**User Facing Release Notes**
+  Galaxy releases now include "user facing" release notes, you are reading
+  the traditional release notes which have always been relatively admin and developer
+  oriented but will likely be even more so now. Features such as favoriting tools,
+  improved workflow editor feedback, and an exciting new cellxgene GIE may have
+  been featured in these release notes in the past but are now featured in the
+  user release notes instead. A huge thanks to `@erasche <https://github.com/erasche>`__
+  for getting the ball rolling on this initiative.
+
+  Check out the `19.05 user release notes <https://docs.galaxyproject.org/en/release_19.05/releases/19.05_announce_user.html>`__.
+
+**Login and Registration Rewrite**
+  The march toward replacing templated backend generated HTML with modern, reactive
+  components accelerated in Galaxy 19.05. Galaxy's login, logout, and registration pages
+  were replaced with VueJS components. Support for OIDC login options was added and
+  certain deprecated OpenID login options were removed. This release contains many other
+  client code enhancements including a new client initialization pipeline, ESLint based
+  linting, and greatly optimized initial dynamic loading of bundles.
+
+**Improvements to Workflow Expressivity**
+  In 19.01, non-data connections were added to the workflow editor in the form of
+  explicit, typed, non-data inputs to workflows. This idea has been generalized in 19.05
+  and tool can now produce non-data outputs and a new class of tools called "Expression"
+  tools has been added to make this especially easy. The Format 2 workflow format is now
+  importable by default and admin-only extensions even allow embedding tool definitions
+  directly into workflows. Many thanks to `@mvdbeek <https://github.com/mvdbeek>`__ for
+  pushing this effort.
+
+Get Galaxy
+==========
+
+The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
+
+To get a new Galaxy repository run:
+  .. code-block:: shell
+
+      $ git clone -b release_19.05 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git fetch origin && git checkout release_19.05 && git pull --ff-only origin release_19.05
+
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
+
+Release Notes
+===========================================================
+
+.. include:: 19.05.rst
+   :start-after: announce_start
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/19.05_announce_user.rst b/doc/source/releases/19.05_announce_user.rst
new file mode 100644
index 00000000000..dc4dfa1c960
--- /dev/null
+++ b/doc/source/releases/19.05_announce_user.rst
@@ -0,0 +1,97 @@
+
+===========================================================
+May 2019 Galaxy Release (v 19.05)
+===========================================================
+
+.. include:: _header.rst
+
+Highlights
+===========================================================
+
+**Tool Favorites**
+
+
+Tools can now be marked as favorites, and then they'll be easily accessible from the star button in your tool panel.
+
+.. figure:: images/19.05-favs.gif
+   :alt: Adding a favorite tool.
+
+**Workflow Editor Connection Feedback**
+
+The editor now provides feedback on why connections are invalid, so you aren't left wondering why two tools won't connect. For complex data pipelines this should greatly simplify your life!
+
+.. figure:: images/19.05-wf-hints.gif
+   :alt: Workflow editor connections provide feedback on why they won't connect.
+
+**Data Dialog for Tool Form**
+
+There is a new way to select datasets when running tools! It is a very simple method to select any number of files from both your History and Data Libraries.
+
+.. figure:: images/19.05-inputs.gif
+   :alt: Data dialog for selecting dataset in the tool form.
+
+Additionally the selector implements a highly requested feature, the ability to run tools on arbitrary datasets from a collection
+
+.. figure:: images/19.05-input-collection.gif
+   :alt: Selecting datasets from within a collection.
+
+**History Export/Import Reworked**
+
+These features used to be clumsy in the past but do not despair since in this release they got a revamp and their reliability skyrocketed! Moving historic object across Galaxies should now be easier than ever. Rocketfuel included.
+
+New Visualizations
+===========================================================
+
+.. visualizations
+
+`@jxtx <https://github.com/jxtx>`__ has implemented a Galaxy Interactive
+Environment for `cellxgene <https://github.com/chanzuckerberg/cellxgene>`__, an
+interactive explorer for single-cell transcriptomics data. `Pull Request 7268`_
+
+.. figure:: https://user-images.githubusercontent.com/79973/51766184-f5faea80-20a7-11e9-86c8-a3127d501076.gif
+   :alt: cellxgene demo
+
+
+New Datatypes
+===========================================================
+
+* Add the single-cell datatype ``mtx``
+  (thanks to `@bebatut <https://github.com/bebatut>`__ and
+  `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 7569`_, `Pull Request 7702`_, `Pull Request 7717`_
+* Add ``geojson`` and shapefile (``shp``) datatypes for better GIS data support
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 7773`_, `Pull Request 7819`_
+* Add ``imgt.json`` datatype for IMGT immune system libraries
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 7587`_
+* Add microarrays data types ``gpr`` and ``gal``
+  (thanks to `@bensellak <https://github.com/bensellak>`__).
+  `Pull Request 7457`_
+* Add ``spaln`` (space-efficient spliced alignment) database type
+  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
+  `Pull Request 7718`_
+* Redefine ``cel`` datatype
+  (thanks to `@bensellak <https://github.com/bensellak>`__).
+  `Pull Request 7514`_
+
+Builtin Tool Updates
+===========================================================
+
+.. tools
+
+* Update grouping tool to not remove empty cells at the begin/start of lines
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 7205`_
+* Add general purpose expression tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 7796`_
+
+Release Notes
+===========================================================
+
+Please see the `full release notes <19.05_announce.html>`_ for more details.
+
+.. include:: 19.05_prs.rst
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/19.05_prs.rst b/doc/source/releases/19.05_prs.rst
new file mode 100644
index 00000000000..4498056e1a8
--- /dev/null
+++ b/doc/source/releases/19.05_prs.rst
@@ -0,0 +1,372 @@
+
+.. github_links
+.. _Pull Request 8103: https://github.com/galaxyproject/galaxy/pull/8103
+.. _Pull Request 8092: https://github.com/galaxyproject/galaxy/pull/8092
+.. _Pull Request 4659: https://github.com/galaxyproject/galaxy/pull/4659
+.. _Pull Request 5495: https://github.com/galaxyproject/galaxy/pull/5495
+.. _Pull Request 6321: https://github.com/galaxyproject/galaxy/pull/6321
+.. _Pull Request 6437: https://github.com/galaxyproject/galaxy/pull/6437
+.. _Pull Request 6621: https://github.com/galaxyproject/galaxy/pull/6621
+.. _Pull Request 6652: https://github.com/galaxyproject/galaxy/pull/6652
+.. _Pull Request 6866: https://github.com/galaxyproject/galaxy/pull/6866
+.. _Pull Request 6958: https://github.com/galaxyproject/galaxy/pull/6958
+.. _Pull Request 7028: https://github.com/galaxyproject/galaxy/pull/7028
+.. _Pull Request 7047: https://github.com/galaxyproject/galaxy/pull/7047
+.. _Pull Request 7095: https://github.com/galaxyproject/galaxy/pull/7095
+.. _Pull Request 7101: https://github.com/galaxyproject/galaxy/pull/7101
+.. _Pull Request 7117: https://github.com/galaxyproject/galaxy/pull/7117
+.. _Pull Request 7144: https://github.com/galaxyproject/galaxy/pull/7144
+.. _Pull Request 7147: https://github.com/galaxyproject/galaxy/pull/7147
+.. _Pull Request 7154: https://github.com/galaxyproject/galaxy/pull/7154
+.. _Pull Request 7156: https://github.com/galaxyproject/galaxy/pull/7156
+.. _Pull Request 7158: https://github.com/galaxyproject/galaxy/pull/7158
+.. _Pull Request 7177: https://github.com/galaxyproject/galaxy/pull/7177
+.. _Pull Request 7185: https://github.com/galaxyproject/galaxy/pull/7185
+.. _Pull Request 7186: https://github.com/galaxyproject/galaxy/pull/7186
+.. _Pull Request 7187: https://github.com/galaxyproject/galaxy/pull/7187
+.. _Pull Request 7192: https://github.com/galaxyproject/galaxy/pull/7192
+.. _Pull Request 7193: https://github.com/galaxyproject/galaxy/pull/7193
+.. _Pull Request 7195: https://github.com/galaxyproject/galaxy/pull/7195
+.. _Pull Request 7198: https://github.com/galaxyproject/galaxy/pull/7198
+.. _Pull Request 7200: https://github.com/galaxyproject/galaxy/pull/7200
+.. _Pull Request 7202: https://github.com/galaxyproject/galaxy/pull/7202
+.. _Pull Request 7203: https://github.com/galaxyproject/galaxy/pull/7203
+.. _Pull Request 7205: https://github.com/galaxyproject/galaxy/pull/7205
+.. _Pull Request 7207: https://github.com/galaxyproject/galaxy/pull/7207
+.. _Pull Request 7208: https://github.com/galaxyproject/galaxy/pull/7208
+.. _Pull Request 7209: https://github.com/galaxyproject/galaxy/pull/7209
+.. _Pull Request 7210: https://github.com/galaxyproject/galaxy/pull/7210
+.. _Pull Request 7213: https://github.com/galaxyproject/galaxy/pull/7213
+.. _Pull Request 7214: https://github.com/galaxyproject/galaxy/pull/7214
+.. _Pull Request 7215: https://github.com/galaxyproject/galaxy/pull/7215
+.. _Pull Request 7219: https://github.com/galaxyproject/galaxy/pull/7219
+.. _Pull Request 7220: https://github.com/galaxyproject/galaxy/pull/7220
+.. _Pull Request 7221: https://github.com/galaxyproject/galaxy/pull/7221
+.. _Pull Request 7222: https://github.com/galaxyproject/galaxy/pull/7222
+.. _Pull Request 7226: https://github.com/galaxyproject/galaxy/pull/7226
+.. _Pull Request 7232: https://github.com/galaxyproject/galaxy/pull/7232
+.. _Pull Request 7234: https://github.com/galaxyproject/galaxy/pull/7234
+.. _Pull Request 7235: https://github.com/galaxyproject/galaxy/pull/7235
+.. _Pull Request 7246: https://github.com/galaxyproject/galaxy/pull/7246
+.. _Pull Request 7247: https://github.com/galaxyproject/galaxy/pull/7247
+.. _Pull Request 7248: https://github.com/galaxyproject/galaxy/pull/7248
+.. _Pull Request 7254: https://github.com/galaxyproject/galaxy/pull/7254
+.. _Pull Request 7255: https://github.com/galaxyproject/galaxy/pull/7255
+.. _Pull Request 7256: https://github.com/galaxyproject/galaxy/pull/7256
+.. _Pull Request 7262: https://github.com/galaxyproject/galaxy/pull/7262
+.. _Pull Request 7266: https://github.com/galaxyproject/galaxy/pull/7266
+.. _Pull Request 7268: https://github.com/galaxyproject/galaxy/pull/7268
+.. _Pull Request 7270: https://github.com/galaxyproject/galaxy/pull/7270
+.. _Pull Request 7272: https://github.com/galaxyproject/galaxy/pull/7272
+.. _Pull Request 7276: https://github.com/galaxyproject/galaxy/pull/7276
+.. _Pull Request 7279: https://github.com/galaxyproject/galaxy/pull/7279
+.. _Pull Request 7280: https://github.com/galaxyproject/galaxy/pull/7280
+.. _Pull Request 7281: https://github.com/galaxyproject/galaxy/pull/7281
+.. _Pull Request 7285: https://github.com/galaxyproject/galaxy/pull/7285
+.. _Pull Request 7286: https://github.com/galaxyproject/galaxy/pull/7286
+.. _Pull Request 7287: https://github.com/galaxyproject/galaxy/pull/7287
+.. _Pull Request 7288: https://github.com/galaxyproject/galaxy/pull/7288
+.. _Pull Request 7291: https://github.com/galaxyproject/galaxy/pull/7291
+.. _Pull Request 7300: https://github.com/galaxyproject/galaxy/pull/7300
+.. _Pull Request 7303: https://github.com/galaxyproject/galaxy/pull/7303
+.. _Pull Request 7313: https://github.com/galaxyproject/galaxy/pull/7313
+.. _Pull Request 7315: https://github.com/galaxyproject/galaxy/pull/7315
+.. _Pull Request 7316: https://github.com/galaxyproject/galaxy/pull/7316
+.. _Pull Request 7318: https://github.com/galaxyproject/galaxy/pull/7318
+.. _Pull Request 7319: https://github.com/galaxyproject/galaxy/pull/7319
+.. _Pull Request 7321: https://github.com/galaxyproject/galaxy/pull/7321
+.. _Pull Request 7322: https://github.com/galaxyproject/galaxy/pull/7322
+.. _Pull Request 7323: https://github.com/galaxyproject/galaxy/pull/7323
+.. _Pull Request 7329: https://github.com/galaxyproject/galaxy/pull/7329
+.. _Pull Request 7334: https://github.com/galaxyproject/galaxy/pull/7334
+.. _Pull Request 7337: https://github.com/galaxyproject/galaxy/pull/7337
+.. _Pull Request 7339: https://github.com/galaxyproject/galaxy/pull/7339
+.. _Pull Request 7340: https://github.com/galaxyproject/galaxy/pull/7340
+.. _Pull Request 7342: https://github.com/galaxyproject/galaxy/pull/7342
+.. _Pull Request 7344: https://github.com/galaxyproject/galaxy/pull/7344
+.. _Pull Request 7345: https://github.com/galaxyproject/galaxy/pull/7345
+.. _Pull Request 7346: https://github.com/galaxyproject/galaxy/pull/7346
+.. _Pull Request 7347: https://github.com/galaxyproject/galaxy/pull/7347
+.. _Pull Request 7350: https://github.com/galaxyproject/galaxy/pull/7350
+.. _Pull Request 7356: https://github.com/galaxyproject/galaxy/pull/7356
+.. _Pull Request 7357: https://github.com/galaxyproject/galaxy/pull/7357
+.. _Pull Request 7358: https://github.com/galaxyproject/galaxy/pull/7358
+.. _Pull Request 7359: https://github.com/galaxyproject/galaxy/pull/7359
+.. _Pull Request 7363: https://github.com/galaxyproject/galaxy/pull/7363
+.. _Pull Request 7365: https://github.com/galaxyproject/galaxy/pull/7365
+.. _Pull Request 7366: https://github.com/galaxyproject/galaxy/pull/7366
+.. _Pull Request 7367: https://github.com/galaxyproject/galaxy/pull/7367
+.. _Pull Request 7369: https://github.com/galaxyproject/galaxy/pull/7369
+.. _Pull Request 7370: https://github.com/galaxyproject/galaxy/pull/7370
+.. _Pull Request 7371: https://github.com/galaxyproject/galaxy/pull/7371
+.. _Pull Request 7374: https://github.com/galaxyproject/galaxy/pull/7374
+.. _Pull Request 7379: https://github.com/galaxyproject/galaxy/pull/7379
+.. _Pull Request 7381: https://github.com/galaxyproject/galaxy/pull/7381
+.. _Pull Request 7387: https://github.com/galaxyproject/galaxy/pull/7387
+.. _Pull Request 7388: https://github.com/galaxyproject/galaxy/pull/7388
+.. _Pull Request 7391: https://github.com/galaxyproject/galaxy/pull/7391
+.. _Pull Request 7395: https://github.com/galaxyproject/galaxy/pull/7395
+.. _Pull Request 7396: https://github.com/galaxyproject/galaxy/pull/7396
+.. _Pull Request 7397: https://github.com/galaxyproject/galaxy/pull/7397
+.. _Pull Request 7398: https://github.com/galaxyproject/galaxy/pull/7398
+.. _Pull Request 7400: https://github.com/galaxyproject/galaxy/pull/7400
+.. _Pull Request 7404: https://github.com/galaxyproject/galaxy/pull/7404
+.. _Pull Request 7423: https://github.com/galaxyproject/galaxy/pull/7423
+.. _Pull Request 7424: https://github.com/galaxyproject/galaxy/pull/7424
+.. _Pull Request 7428: https://github.com/galaxyproject/galaxy/pull/7428
+.. _Pull Request 7435: https://github.com/galaxyproject/galaxy/pull/7435
+.. _Pull Request 7437: https://github.com/galaxyproject/galaxy/pull/7437
+.. _Pull Request 7438: https://github.com/galaxyproject/galaxy/pull/7438
+.. _Pull Request 7439: https://github.com/galaxyproject/galaxy/pull/7439
+.. _Pull Request 7442: https://github.com/galaxyproject/galaxy/pull/7442
+.. _Pull Request 7443: https://github.com/galaxyproject/galaxy/pull/7443
+.. _Pull Request 7445: https://github.com/galaxyproject/galaxy/pull/7445
+.. _Pull Request 7446: https://github.com/galaxyproject/galaxy/pull/7446
+.. _Pull Request 7448: https://github.com/galaxyproject/galaxy/pull/7448
+.. _Pull Request 7449: https://github.com/galaxyproject/galaxy/pull/7449
+.. _Pull Request 7451: https://github.com/galaxyproject/galaxy/pull/7451
+.. _Pull Request 7452: https://github.com/galaxyproject/galaxy/pull/7452
+.. _Pull Request 7453: https://github.com/galaxyproject/galaxy/pull/7453
+.. _Pull Request 7457: https://github.com/galaxyproject/galaxy/pull/7457
+.. _Pull Request 7458: https://github.com/galaxyproject/galaxy/pull/7458
+.. _Pull Request 7459: https://github.com/galaxyproject/galaxy/pull/7459
+.. _Pull Request 7460: https://github.com/galaxyproject/galaxy/pull/7460
+.. _Pull Request 7461: https://github.com/galaxyproject/galaxy/pull/7461
+.. _Pull Request 7462: https://github.com/galaxyproject/galaxy/pull/7462
+.. _Pull Request 7463: https://github.com/galaxyproject/galaxy/pull/7463
+.. _Pull Request 7466: https://github.com/galaxyproject/galaxy/pull/7466
+.. _Pull Request 7470: https://github.com/galaxyproject/galaxy/pull/7470
+.. _Pull Request 7471: https://github.com/galaxyproject/galaxy/pull/7471
+.. _Pull Request 7472: https://github.com/galaxyproject/galaxy/pull/7472
+.. _Pull Request 7475: https://github.com/galaxyproject/galaxy/pull/7475
+.. _Pull Request 7476: https://github.com/galaxyproject/galaxy/pull/7476
+.. _Pull Request 7477: https://github.com/galaxyproject/galaxy/pull/7477
+.. _Pull Request 7478: https://github.com/galaxyproject/galaxy/pull/7478
+.. _Pull Request 7480: https://github.com/galaxyproject/galaxy/pull/7480
+.. _Pull Request 7481: https://github.com/galaxyproject/galaxy/pull/7481
+.. _Pull Request 7483: https://github.com/galaxyproject/galaxy/pull/7483
+.. _Pull Request 7485: https://github.com/galaxyproject/galaxy/pull/7485
+.. _Pull Request 7486: https://github.com/galaxyproject/galaxy/pull/7486
+.. _Pull Request 7487: https://github.com/galaxyproject/galaxy/pull/7487
+.. _Pull Request 7499: https://github.com/galaxyproject/galaxy/pull/7499
+.. _Pull Request 7500: https://github.com/galaxyproject/galaxy/pull/7500
+.. _Pull Request 7504: https://github.com/galaxyproject/galaxy/pull/7504
+.. _Pull Request 7505: https://github.com/galaxyproject/galaxy/pull/7505
+.. _Pull Request 7507: https://github.com/galaxyproject/galaxy/pull/7507
+.. _Pull Request 7510: https://github.com/galaxyproject/galaxy/pull/7510
+.. _Pull Request 7514: https://github.com/galaxyproject/galaxy/pull/7514
+.. _Pull Request 7515: https://github.com/galaxyproject/galaxy/pull/7515
+.. _Pull Request 7516: https://github.com/galaxyproject/galaxy/pull/7516
+.. _Pull Request 7517: https://github.com/galaxyproject/galaxy/pull/7517
+.. _Pull Request 7518: https://github.com/galaxyproject/galaxy/pull/7518
+.. _Pull Request 7519: https://github.com/galaxyproject/galaxy/pull/7519
+.. _Pull Request 7521: https://github.com/galaxyproject/galaxy/pull/7521
+.. _Pull Request 7522: https://github.com/galaxyproject/galaxy/pull/7522
+.. _Pull Request 7523: https://github.com/galaxyproject/galaxy/pull/7523
+.. _Pull Request 7524: https://github.com/galaxyproject/galaxy/pull/7524
+.. _Pull Request 7527: https://github.com/galaxyproject/galaxy/pull/7527
+.. _Pull Request 7529: https://github.com/galaxyproject/galaxy/pull/7529
+.. _Pull Request 7530: https://github.com/galaxyproject/galaxy/pull/7530
+.. _Pull Request 7532: https://github.com/galaxyproject/galaxy/pull/7532
+.. _Pull Request 7534: https://github.com/galaxyproject/galaxy/pull/7534
+.. _Pull Request 7536: https://github.com/galaxyproject/galaxy/pull/7536
+.. _Pull Request 7537: https://github.com/galaxyproject/galaxy/pull/7537
+.. _Pull Request 7538: https://github.com/galaxyproject/galaxy/pull/7538
+.. _Pull Request 7539: https://github.com/galaxyproject/galaxy/pull/7539
+.. _Pull Request 7540: https://github.com/galaxyproject/galaxy/pull/7540
+.. _Pull Request 7541: https://github.com/galaxyproject/galaxy/pull/7541
+.. _Pull Request 7542: https://github.com/galaxyproject/galaxy/pull/7542
+.. _Pull Request 7543: https://github.com/galaxyproject/galaxy/pull/7543
+.. _Pull Request 7544: https://github.com/galaxyproject/galaxy/pull/7544
+.. _Pull Request 7545: https://github.com/galaxyproject/galaxy/pull/7545
+.. _Pull Request 7546: https://github.com/galaxyproject/galaxy/pull/7546
+.. _Pull Request 7547: https://github.com/galaxyproject/galaxy/pull/7547
+.. _Pull Request 7548: https://github.com/galaxyproject/galaxy/pull/7548
+.. _Pull Request 7549: https://github.com/galaxyproject/galaxy/pull/7549
+.. _Pull Request 7553: https://github.com/galaxyproject/galaxy/pull/7553
+.. _Pull Request 7554: https://github.com/galaxyproject/galaxy/pull/7554
+.. _Pull Request 7555: https://github.com/galaxyproject/galaxy/pull/7555
+.. _Pull Request 7556: https://github.com/galaxyproject/galaxy/pull/7556
+.. _Pull Request 7558: https://github.com/galaxyproject/galaxy/pull/7558
+.. _Pull Request 7560: https://github.com/galaxyproject/galaxy/pull/7560
+.. _Pull Request 7561: https://github.com/galaxyproject/galaxy/pull/7561
+.. _Pull Request 7562: https://github.com/galaxyproject/galaxy/pull/7562
+.. _Pull Request 7565: https://github.com/galaxyproject/galaxy/pull/7565
+.. _Pull Request 7566: https://github.com/galaxyproject/galaxy/pull/7566
+.. _Pull Request 7569: https://github.com/galaxyproject/galaxy/pull/7569
+.. _Pull Request 7570: https://github.com/galaxyproject/galaxy/pull/7570
+.. _Pull Request 7571: https://github.com/galaxyproject/galaxy/pull/7571
+.. _Pull Request 7572: https://github.com/galaxyproject/galaxy/pull/7572
+.. _Pull Request 7573: https://github.com/galaxyproject/galaxy/pull/7573
+.. _Pull Request 7574: https://github.com/galaxyproject/galaxy/pull/7574
+.. _Pull Request 7575: https://github.com/galaxyproject/galaxy/pull/7575
+.. _Pull Request 7581: https://github.com/galaxyproject/galaxy/pull/7581
+.. _Pull Request 7584: https://github.com/galaxyproject/galaxy/pull/7584
+.. _Pull Request 7586: https://github.com/galaxyproject/galaxy/pull/7586
+.. _Pull Request 7587: https://github.com/galaxyproject/galaxy/pull/7587
+.. _Pull Request 7588: https://github.com/galaxyproject/galaxy/pull/7588
+.. _Pull Request 7589: https://github.com/galaxyproject/galaxy/pull/7589
+.. _Pull Request 7590: https://github.com/galaxyproject/galaxy/pull/7590
+.. _Pull Request 7592: https://github.com/galaxyproject/galaxy/pull/7592
+.. _Pull Request 7594: https://github.com/galaxyproject/galaxy/pull/7594
+.. _Pull Request 7595: https://github.com/galaxyproject/galaxy/pull/7595
+.. _Pull Request 7596: https://github.com/galaxyproject/galaxy/pull/7596
+.. _Pull Request 7597: https://github.com/galaxyproject/galaxy/pull/7597
+.. _Pull Request 7598: https://github.com/galaxyproject/galaxy/pull/7598
+.. _Pull Request 7601: https://github.com/galaxyproject/galaxy/pull/7601
+.. _Pull Request 7602: https://github.com/galaxyproject/galaxy/pull/7602
+.. _Pull Request 7605: https://github.com/galaxyproject/galaxy/pull/7605
+.. _Pull Request 7606: https://github.com/galaxyproject/galaxy/pull/7606
+.. _Pull Request 7609: https://github.com/galaxyproject/galaxy/pull/7609
+.. _Pull Request 7612: https://github.com/galaxyproject/galaxy/pull/7612
+.. _Pull Request 7614: https://github.com/galaxyproject/galaxy/pull/7614
+.. _Pull Request 7616: https://github.com/galaxyproject/galaxy/pull/7616
+.. _Pull Request 7621: https://github.com/galaxyproject/galaxy/pull/7621
+.. _Pull Request 7630: https://github.com/galaxyproject/galaxy/pull/7630
+.. _Pull Request 7633: https://github.com/galaxyproject/galaxy/pull/7633
+.. _Pull Request 7634: https://github.com/galaxyproject/galaxy/pull/7634
+.. _Pull Request 7637: https://github.com/galaxyproject/galaxy/pull/7637
+.. _Pull Request 7639: https://github.com/galaxyproject/galaxy/pull/7639
+.. _Pull Request 7640: https://github.com/galaxyproject/galaxy/pull/7640
+.. _Pull Request 7641: https://github.com/galaxyproject/galaxy/pull/7641
+.. _Pull Request 7642: https://github.com/galaxyproject/galaxy/pull/7642
+.. _Pull Request 7643: https://github.com/galaxyproject/galaxy/pull/7643
+.. _Pull Request 7645: https://github.com/galaxyproject/galaxy/pull/7645
+.. _Pull Request 7646: https://github.com/galaxyproject/galaxy/pull/7646
+.. _Pull Request 7647: https://github.com/galaxyproject/galaxy/pull/7647
+.. _Pull Request 7650: https://github.com/galaxyproject/galaxy/pull/7650
+.. _Pull Request 7651: https://github.com/galaxyproject/galaxy/pull/7651
+.. _Pull Request 7652: https://github.com/galaxyproject/galaxy/pull/7652
+.. _Pull Request 7655: https://github.com/galaxyproject/galaxy/pull/7655
+.. _Pull Request 7656: https://github.com/galaxyproject/galaxy/pull/7656
+.. _Pull Request 7657: https://github.com/galaxyproject/galaxy/pull/7657
+.. _Pull Request 7658: https://github.com/galaxyproject/galaxy/pull/7658
+.. _Pull Request 7659: https://github.com/galaxyproject/galaxy/pull/7659
+.. _Pull Request 7660: https://github.com/galaxyproject/galaxy/pull/7660
+.. _Pull Request 7663: https://github.com/galaxyproject/galaxy/pull/7663
+.. _Pull Request 7664: https://github.com/galaxyproject/galaxy/pull/7664
+.. _Pull Request 7666: https://github.com/galaxyproject/galaxy/pull/7666
+.. _Pull Request 7667: https://github.com/galaxyproject/galaxy/pull/7667
+.. _Pull Request 7674: https://github.com/galaxyproject/galaxy/pull/7674
+.. _Pull Request 7675: https://github.com/galaxyproject/galaxy/pull/7675
+.. _Pull Request 7676: https://github.com/galaxyproject/galaxy/pull/7676
+.. _Pull Request 7677: https://github.com/galaxyproject/galaxy/pull/7677
+.. _Pull Request 7678: https://github.com/galaxyproject/galaxy/pull/7678
+.. _Pull Request 7679: https://github.com/galaxyproject/galaxy/pull/7679
+.. _Pull Request 7680: https://github.com/galaxyproject/galaxy/pull/7680
+.. _Pull Request 7681: https://github.com/galaxyproject/galaxy/pull/7681
+.. _Pull Request 7682: https://github.com/galaxyproject/galaxy/pull/7682
+.. _Pull Request 7683: https://github.com/galaxyproject/galaxy/pull/7683
+.. _Pull Request 7684: https://github.com/galaxyproject/galaxy/pull/7684
+.. _Pull Request 7689: https://github.com/galaxyproject/galaxy/pull/7689
+.. _Pull Request 7690: https://github.com/galaxyproject/galaxy/pull/7690
+.. _Pull Request 7691: https://github.com/galaxyproject/galaxy/pull/7691
+.. _Pull Request 7693: https://github.com/galaxyproject/galaxy/pull/7693
+.. _Pull Request 7694: https://github.com/galaxyproject/galaxy/pull/7694
+.. _Pull Request 7695: https://github.com/galaxyproject/galaxy/pull/7695
+.. _Pull Request 7696: https://github.com/galaxyproject/galaxy/pull/7696
+.. _Pull Request 7697: https://github.com/galaxyproject/galaxy/pull/7697
+.. _Pull Request 7698: https://github.com/galaxyproject/galaxy/pull/7698
+.. _Pull Request 7699: https://github.com/galaxyproject/galaxy/pull/7699
+.. _Pull Request 7702: https://github.com/galaxyproject/galaxy/pull/7702
+.. _Pull Request 7703: https://github.com/galaxyproject/galaxy/pull/7703
+.. _Pull Request 7704: https://github.com/galaxyproject/galaxy/pull/7704
+.. _Pull Request 7706: https://github.com/galaxyproject/galaxy/pull/7706
+.. _Pull Request 7707: https://github.com/galaxyproject/galaxy/pull/7707
+.. _Pull Request 7708: https://github.com/galaxyproject/galaxy/pull/7708
+.. _Pull Request 7709: https://github.com/galaxyproject/galaxy/pull/7709
+.. _Pull Request 7711: https://github.com/galaxyproject/galaxy/pull/7711
+.. _Pull Request 7712: https://github.com/galaxyproject/galaxy/pull/7712
+.. _Pull Request 7713: https://github.com/galaxyproject/galaxy/pull/7713
+.. _Pull Request 7716: https://github.com/galaxyproject/galaxy/pull/7716
+.. _Pull Request 7717: https://github.com/galaxyproject/galaxy/pull/7717
+.. _Pull Request 7718: https://github.com/galaxyproject/galaxy/pull/7718
+.. _Pull Request 7719: https://github.com/galaxyproject/galaxy/pull/7719
+.. _Pull Request 7720: https://github.com/galaxyproject/galaxy/pull/7720
+.. _Pull Request 7722: https://github.com/galaxyproject/galaxy/pull/7722
+.. _Pull Request 7723: https://github.com/galaxyproject/galaxy/pull/7723
+.. _Pull Request 7724: https://github.com/galaxyproject/galaxy/pull/7724
+.. _Pull Request 7727: https://github.com/galaxyproject/galaxy/pull/7727
+.. _Pull Request 7737: https://github.com/galaxyproject/galaxy/pull/7737
+.. _Pull Request 7738: https://github.com/galaxyproject/galaxy/pull/7738
+.. _Pull Request 7740: https://github.com/galaxyproject/galaxy/pull/7740
+.. _Pull Request 7743: https://github.com/galaxyproject/galaxy/pull/7743
+.. _Pull Request 7744: https://github.com/galaxyproject/galaxy/pull/7744
+.. _Pull Request 7746: https://github.com/galaxyproject/galaxy/pull/7746
+.. _Pull Request 7748: https://github.com/galaxyproject/galaxy/pull/7748
+.. _Pull Request 7749: https://github.com/galaxyproject/galaxy/pull/7749
+.. _Pull Request 7750: https://github.com/galaxyproject/galaxy/pull/7750
+.. _Pull Request 7751: https://github.com/galaxyproject/galaxy/pull/7751
+.. _Pull Request 7754: https://github.com/galaxyproject/galaxy/pull/7754
+.. _Pull Request 7755: https://github.com/galaxyproject/galaxy/pull/7755
+.. _Pull Request 7756: https://github.com/galaxyproject/galaxy/pull/7756
+.. _Pull Request 7760: https://github.com/galaxyproject/galaxy/pull/7760
+.. _Pull Request 7773: https://github.com/galaxyproject/galaxy/pull/7773
+.. _Pull Request 7777: https://github.com/galaxyproject/galaxy/pull/7777
+.. _Pull Request 7778: https://github.com/galaxyproject/galaxy/pull/7778
+.. _Pull Request 7779: https://github.com/galaxyproject/galaxy/pull/7779
+.. _Pull Request 7780: https://github.com/galaxyproject/galaxy/pull/7780
+.. _Pull Request 7782: https://github.com/galaxyproject/galaxy/pull/7782
+.. _Pull Request 7785: https://github.com/galaxyproject/galaxy/pull/7785
+.. _Pull Request 7788: https://github.com/galaxyproject/galaxy/pull/7788
+.. _Pull Request 7789: https://github.com/galaxyproject/galaxy/pull/7789
+.. _Pull Request 7796: https://github.com/galaxyproject/galaxy/pull/7796
+.. _Pull Request 7797: https://github.com/galaxyproject/galaxy/pull/7797
+.. _Pull Request 7798: https://github.com/galaxyproject/galaxy/pull/7798
+.. _Pull Request 7800: https://github.com/galaxyproject/galaxy/pull/7800
+.. _Pull Request 7806: https://github.com/galaxyproject/galaxy/pull/7806
+.. _Pull Request 7812: https://github.com/galaxyproject/galaxy/pull/7812
+.. _Pull Request 7815: https://github.com/galaxyproject/galaxy/pull/7815
+.. _Pull Request 7819: https://github.com/galaxyproject/galaxy/pull/7819
+.. _Pull Request 7823: https://github.com/galaxyproject/galaxy/pull/7823
+.. _Pull Request 7824: https://github.com/galaxyproject/galaxy/pull/7824
+.. _Pull Request 7826: https://github.com/galaxyproject/galaxy/pull/7826
+.. _Pull Request 7827: https://github.com/galaxyproject/galaxy/pull/7827
+.. _Pull Request 7834: https://github.com/galaxyproject/galaxy/pull/7834
+.. _Pull Request 7839: https://github.com/galaxyproject/galaxy/pull/7839
+.. _Pull Request 7840: https://github.com/galaxyproject/galaxy/pull/7840
+.. _Pull Request 7844: https://github.com/galaxyproject/galaxy/pull/7844
+.. _Pull Request 7845: https://github.com/galaxyproject/galaxy/pull/7845
+.. _Pull Request 7848: https://github.com/galaxyproject/galaxy/pull/7848
+.. _Pull Request 7851: https://github.com/galaxyproject/galaxy/pull/7851
+.. _Pull Request 7853: https://github.com/galaxyproject/galaxy/pull/7853
+.. _Pull Request 7855: https://github.com/galaxyproject/galaxy/pull/7855
+.. _Pull Request 7856: https://github.com/galaxyproject/galaxy/pull/7856
+.. _Pull Request 7858: https://github.com/galaxyproject/galaxy/pull/7858
+.. _Pull Request 7859: https://github.com/galaxyproject/galaxy/pull/7859
+.. _Pull Request 7860: https://github.com/galaxyproject/galaxy/pull/7860
+.. _Pull Request 7864: https://github.com/galaxyproject/galaxy/pull/7864
+.. _Pull Request 7865: https://github.com/galaxyproject/galaxy/pull/7865
+.. _Pull Request 7866: https://github.com/galaxyproject/galaxy/pull/7866
+.. _Pull Request 7870: https://github.com/galaxyproject/galaxy/pull/7870
+.. _Pull Request 7872: https://github.com/galaxyproject/galaxy/pull/7872
+.. _Pull Request 7874: https://github.com/galaxyproject/galaxy/pull/7874
+.. _Pull Request 7875: https://github.com/galaxyproject/galaxy/pull/7875
+.. _Pull Request 7877: https://github.com/galaxyproject/galaxy/pull/7877
+.. _Pull Request 7880: https://github.com/galaxyproject/galaxy/pull/7880
+.. _Pull Request 7887: https://github.com/galaxyproject/galaxy/pull/7887
+.. _Pull Request 7896: https://github.com/galaxyproject/galaxy/pull/7896
+.. _Pull Request 7904: https://github.com/galaxyproject/galaxy/pull/7904
+.. _Pull Request 7906: https://github.com/galaxyproject/galaxy/pull/7906
+.. _Pull Request 7916: https://github.com/galaxyproject/galaxy/pull/7916
+.. _Pull Request 7917: https://github.com/galaxyproject/galaxy/pull/7917
+.. _Pull Request 7923: https://github.com/galaxyproject/galaxy/pull/7923
+.. _Pull Request 7925: https://github.com/galaxyproject/galaxy/pull/7925
+.. _Pull Request 7933: https://github.com/galaxyproject/galaxy/pull/7933
+.. _Pull Request 7934: https://github.com/galaxyproject/galaxy/pull/7934
+.. _Pull Request 7943: https://github.com/galaxyproject/galaxy/pull/7943
+.. _Pull Request 7944: https://github.com/galaxyproject/galaxy/pull/7944
+.. _Pull Request 7954: https://github.com/galaxyproject/galaxy/pull/7954
+.. _Pull Request 7956: https://github.com/galaxyproject/galaxy/pull/7956
+.. _Pull Request 7967: https://github.com/galaxyproject/galaxy/pull/7967
+.. _Pull Request 7969: https://github.com/galaxyproject/galaxy/pull/7969
+.. _Pull Request 7972: https://github.com/galaxyproject/galaxy/pull/7972
+.. _Pull Request 7979: https://github.com/galaxyproject/galaxy/pull/7979
+.. _Pull Request 7983: https://github.com/galaxyproject/galaxy/pull/7983
+.. _Pull Request 7989: https://github.com/galaxyproject/galaxy/pull/7989
+.. _Pull Request 8000: https://github.com/galaxyproject/galaxy/pull/8000
+.. _Pull Request 8004: https://github.com/galaxyproject/galaxy/pull/8004
+.. _Pull Request 8021: https://github.com/galaxyproject/galaxy/pull/8021
+.. _Pull Request 8029: https://github.com/galaxyproject/galaxy/pull/8029
+.. _Pull Request 8048: https://github.com/galaxyproject/galaxy/pull/8048
+.. _Pull Request 8085: https://github.com/galaxyproject/galaxy/pull/8085
diff --git a/doc/source/releases/19.09_announce.rst b/doc/source/releases/19.09_announce.rst
new file mode 100644
index 00000000000..7a051006b08
--- /dev/null
+++ b/doc/source/releases/19.09_announce.rst
@@ -0,0 +1,10 @@
+
+===========================================================
+September 2019 Galaxy Release (v 19.09)
+===========================================================
+
+
+Schedule
+===========================================================
+ * Planned Freeze Date: 2019-09-02
+ * Planned Release Date: 2019-09-23
diff --git a/doc/source/releases/images/19.05-favs.gif b/doc/source/releases/images/19.05-favs.gif
new file mode 100644
index 00000000000..b0b4218da3d
Binary files /dev/null and b/doc/source/releases/images/19.05-favs.gif differ
diff --git a/doc/source/releases/images/19.05-input-collection.gif b/doc/source/releases/images/19.05-input-collection.gif
new file mode 100644
index 00000000000..08073613628
Binary files /dev/null and b/doc/source/releases/images/19.05-input-collection.gif differ
diff --git a/doc/source/releases/images/19.05-inputs.gif b/doc/source/releases/images/19.05-inputs.gif
new file mode 100644
index 00000000000..3c4122e5162
Binary files /dev/null and b/doc/source/releases/images/19.05-inputs.gif differ
diff --git a/doc/source/releases/images/19.05-wf-hints.gif b/doc/source/releases/images/19.05-wf-hints.gif
new file mode 100644
index 00000000000..69fa3e69778
Binary files /dev/null and b/doc/source/releases/images/19.05-wf-hints.gif differ
diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst
index 1a59eb20ee8..edc8647c307 100644
--- a/doc/source/releases/index.rst
+++ b/doc/source/releases/index.rst
@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   19.05_announce
    19.01_announce
    18.09_announce
    18.05_announce
diff --git a/extract_dataset_parts.sh b/extract_dataset_parts.sh
index f17ced8bcd5..7591b4a5ae3 100755
--- a/extract_dataset_parts.sh
+++ b/extract_dataset_parts.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 . ./scripts/common_startup_functions.sh
 
@@ -9,5 +9,5 @@ setup_python
 for file in $1/split_info*.json
 do
     # echo processing $file
-    python ./scripts/extract_dataset_part.py $file
+    python ./scripts/extract_dataset_part.py "$file"
 done
diff --git a/lib/galaxy/actions/library.py b/lib/galaxy/actions/library.py
index 38a1211817e..a9c5170819d 100644
--- a/lib/galaxy/actions/library.py
+++ b/lib/galaxy/actions/library.py
@@ -164,7 +164,7 @@ class LibraryActions(object):
                 if os.path.isfile(path):
                     files.append(path)
         except Exception as e:
-            message = "Unable to get file list for configured %s, error: %s" % (import_dir_desc, str(e))
+            message = "Unable to get file list for configured %s, error: %s" % (import_dir_desc, util.unicodify(e))
             response_code = 500
             return None, response_code, message
         if not files:
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 98a6114762c..03d56cac84b 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -10,22 +10,22 @@ import galaxy.model.security
 import galaxy.queues
 import galaxy.quota
 import galaxy.security
-from galaxy import config, jobs
+from galaxy import config, job_metrics, jobs
 from galaxy.containers import build_container_interfaces
-from galaxy.jobs import metrics as job_metrics
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.folders import FolderManager
 from galaxy.managers.histories import HistoryManager
 from galaxy.managers.libraries import LibraryManager
 from galaxy.managers.tools import DynamicToolManager
+from galaxy.model.database_heartbeat import DatabaseHeartbeat
 from galaxy.model.tags import GalaxyTagHandler
 from galaxy.queue_worker import GalaxyQueueWorker
+from galaxy.tool_util.deps.views import DependencyResolversView
 from galaxy.tools.cache import (
     ToolCache,
     ToolShedRepositoryCache
 )
 from galaxy.tools.data_manager.manager import DataManagers
-from galaxy.tools.deps.views import DependencyResolversView
 from galaxy.tools.error_reports import ErrorReports
 from galaxy.tools.special_tools import load_lib_tools
 from galaxy.tools.verify import test_data
@@ -39,8 +39,7 @@ from galaxy.visualization.genomes import Genomes
 from galaxy.visualization.plugins.registry import VisualizationsRegistry
 from galaxy.web import url_for
 from galaxy.web.proxy import ProxyManager
-from galaxy.web.stack import application_stack_instance
-from galaxy.web.stack.database_heartbeat import DatabaseHeartbeat
+from galaxy.web_stack import application_stack_instance
 from galaxy.webapps.galaxy.config_watchers import ConfigWatchers
 from galaxy.webhooks import WebhooksRegistry
 from tool_shed.galaxy_install import (
diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index cad76855d36..139990ec542 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -122,15 +122,14 @@ class CustosAuthnz(IdentityProvider):
             trans.sa_session.flush()
             return True, "", disconnect_redirect_url
         except Exception as e:
-            return False, "Failed to disconnect provider {}: {}".format(provider, str(e)), None
+            return False, "Failed to disconnect provider {}: {}".format(provider, util.unicodify(e)), None
 
     def _create_oauth2_session(self, state=None, scope=None):
         client_id = self.config['client_id']
         redirect_uri = self.config['redirect_uri']
         if (redirect_uri.startswith('http://localhost')
                 and os.environ.get("OAUTHLIB_INSECURE_TRANSPORT", None) != "1"):
-            log.warn("Setting OAUTHLIB_INSECURE_TRANSPORT to '1' to "
-                     "allow plain HTTP (non-SSL) callback")
+            log.warning("Setting OAUTHLIB_INSECURE_TRANSPORT to '1' to allow plain HTTP (non-SSL) callback")
             os.environ['OAUTHLIB_INSECURE_TRANSPORT'] = "1"
         session = OAuth2Session(client_id,
                              scope=scope,
diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index 7a8bb69cabd..be5e2269730 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -17,6 +17,7 @@ from cloudauthz.exceptions import (
 
 from galaxy import exceptions
 from galaxy import model
+from galaxy.util import unicodify
 from .custos_authnz import CustosAuthnz
 from .psa_authnz import (
     BACKENDS_NAME,
@@ -133,7 +134,7 @@ class AuthnzManager(object):
     def _unify_provider_name(self, provider):
         if provider.lower() in self.oidc_backends_config:
             return provider.lower()
-        for k, v in BACKENDS_NAME.iteritems():
+        for k, v in BACKENDS_NAME.items():
             if v == provider:
                 return k.lower()
         return None
@@ -147,7 +148,7 @@ class AuthnzManager(object):
                 return True, "", identity_provider_class(unified_provider_name, self.oidc_config, self.oidc_backends_config[unified_provider_name])
             except Exception as e:
                 log.exception('An error occurred when loading {}'.format(identity_provider_class.__name__))
-                return False, str(e), None
+                return False, unicodify(e), None
         else:
             msg = 'The requested identity provider, `{}`, is not a recognized/expected provider.'.format(provider)
             log.debug(msg)
@@ -193,7 +194,7 @@ class AuthnzManager(object):
         if qres.user_id != trans.user.id:
             msg = "The request authentication with ID `{}` is not accessible to user with ID " \
                   "`{}`.".format(trans.security.encode_id(authn_id), trans.security.encode_id(trans.user.id))
-            log.warn(msg)
+            log.warning(msg)
             raise exceptions.ItemAccessibilityException(msg)
 
     @staticmethod
@@ -220,7 +221,7 @@ class AuthnzManager(object):
         if user_id != qres.user_id:
             msg = "The request authorization configuration (with ID:`{}`) is not accessible for user with " \
                   "ID:`{}`.".format(qres.id, user_id)
-            log.warn(msg)
+            log.warning(msg)
             raise exceptions.ItemAccessibilityException(msg)
         return qres
 
diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py
index 881313e9f22..fef95925abb 100644
--- a/lib/galaxy/authnz/psa_authnz.py
+++ b/lib/galaxy/authnz/psa_authnz.py
@@ -19,12 +19,14 @@ DEFAULTS = {
 
 BACKENDS = {
     'google': 'social_core.backends.google_openidconnect.GoogleOpenIdConnect',
-    "globus": "social_core.backends.globus.GlobusOpenIdConnect"
+    "globus": "social_core.backends.globus.GlobusOpenIdConnect",
+    'elixir': 'social_core.backends.elixir.ElixirOpenIdConnect'
 }
 
 BACKENDS_NAME = {
     'google': 'google-openidconnect',
-    "globus": "globus"
+    "globus": "globus",
+    'elixir': 'elixir'
 }
 
 AUTH_PIPELINE = (
@@ -84,7 +86,7 @@ DISCONNECT_PIPELINE = (
 class PSAAuthnz(IdentityProvider):
     def __init__(self, provider, oidc_config, oidc_backend_config):
         self.config = {'provider': provider.lower()}
-        for key, value in oidc_config.iteritems():
+        for key, value in oidc_config.items():
             self.config[setting_name(key)] = value
 
         self.config[setting_name('USER_MODEL')] = 'models.User'
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 01aa911168f..ca2f1eaa510 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -25,15 +25,20 @@ from six.moves import configparser
 
 from galaxy.containers import parse_containers_config
 from galaxy.exceptions import ConfigurationError
-from galaxy.tools.deps.container_resolvers.mulled import DEFAULT_CHANNELS
-from galaxy.util import ExecutionTimer
-from galaxy.util import listify
-from galaxy.util import string_as_bool
-from galaxy.util import unicodify
+from galaxy.tool_util.deps.container_resolvers.mulled import DEFAULT_CHANNELS
+from galaxy.util import (
+    ExecutionTimer,
+    listify,
+    string_as_bool,
+    unicodify,
+)
 from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.util.logging import LOGLV_TRACE
 from galaxy.web.formatting import expand_pretty_datetime_format
-from galaxy.web.stack import get_stack_facts, register_postfork_function
+from galaxy.web_stack import (
+    get_stack_facts,
+    register_postfork_function
+)
 from .version import VERSION_MAJOR
 
 log = logging.getLogger(__name__)
@@ -50,7 +55,7 @@ PATH_DEFAULTS = dict(
     error_report_file=['config/error_report.yml', 'config/error_report.yml.sample'],
     oidc_config_file=['config/oidc_config.yml', 'config/oidc_config.yml.sample'],
     oidc_backends_config_file=['config/oidc_backends_config.yml', 'config/oidc_backends_config.yml.sample'],
-    dependency_resolvers_config_file=['config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml'],
+    dependency_resolvers_config_file=['config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml', None],
     job_resource_params_file=['config/job_resource_params_conf.xml', 'job_resource_params_conf.xml'],
     workflow_resource_params_file=['config/workflow_resource_params_conf.xml', 'workflow_resource_params_conf.xml'],
     migrated_tools_config=['migrated_tools_conf.xml', 'config/migrated_tools_conf.xml'],
@@ -106,7 +111,7 @@ LOGGING_CONFIG_DEFAULT = {
     },
     'filters': {
         'stack': {
-            '()': 'galaxy.web.stack.application_stack_log_filter',
+            '()': 'galaxy.web_stack.application_stack_log_filter',
         },
     },
     'handlers': {
@@ -120,7 +125,7 @@ LOGGING_CONFIG_DEFAULT = {
     },
     'formatters': {
         'stack': {
-            '()': 'galaxy.web.stack.application_stack_log_formatter',
+            '()': 'galaxy.web_stack.application_stack_log_formatter',
         },
     },
 }
@@ -142,6 +147,9 @@ def find_path(kwargs, var, root):
         path = kwargs.get(var)
     else:
         for default in defaults:
+            if default is None:
+                # if None is the final default - just return that.
+                return None
             if os.path.exists(resolve_path(default, root)):
                 path = default
                 break
@@ -194,6 +202,13 @@ class Configuration(object):
         self.install_database_connection = kwargs.get("install_database_connection", None)
         self.install_database_engine_options = get_database_engine_options(kwargs, model_prefix="install_")
 
+        # Wait for database to become available instead of failing
+        self.database_wait = string_as_bool(kwargs.get("database_wait", "False"))
+        # Attempts before failing
+        self.database_wait_attempts = int(kwargs.get("database_wait_attempts", 60))
+        # Sleep period between attepmts (seconds)
+        self.database_wait_sleep = float(kwargs.get("database_wait_sleep", 1))
+
         # Where dataset files are stored
         self.file_path = resolve_path(kwargs.get("file_path", "database/files"), self.root)
         # new_file_path and legacy_home_dir can be overridden per destination in job_conf.
@@ -495,6 +510,7 @@ class Configuration(object):
         self.use_cached_dependency_manager = use_cached_dependency_manager
         self.tool_dependency_cache_dir = tool_dependency_cache_dir
         self.precache_dependencies = precache_dependencies
+        self.dependency_resolvers = kwargs.get("dependency_resolvers")
         # Deployers may either specify a complete list of mapping files or get the default for free and just
         # specify a local mapping file to adapt and extend the default one.
         if "conda_mapping_files" in kwargs:
@@ -502,7 +518,7 @@ class Configuration(object):
         else:
             self.conda_mapping_files = [
                 self.local_conda_mapping_file,
-                os.path.join(self.root, "lib", "galaxy", "tools", "deps", "resolvers", "default_conda_mapping.yml"),
+                os.path.join(self.root, "lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml"),
             ]
 
         self.enable_beta_mulled_containers = string_as_bool(kwargs.get('enable_beta_mulled_containers', 'False'))
@@ -827,7 +843,7 @@ class Configuration(object):
             try:
                 os.makedirs(path)
             except Exception as e:
-                raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, e))
+                raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
 
     def check(self):
         paths_to_check = [self.root, self.tool_path, self.tool_data_path, self.template_path]
@@ -837,7 +853,7 @@ class Configuration(object):
                 try:
                     os.makedirs(path)
                 except Exception as e:
-                    raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, e))
+                    raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
         # Create the directories that it makes sense to create
         for path in (self.new_file_path, self.template_cache, self.ftp_upload_dir,
                      self.library_import_dir, self.user_library_import_dir,
@@ -923,7 +939,10 @@ def parse_dependency_options(kwargs, root, dependency_resolvers_config_file):
         precache_dependencies = string_as_bool(kwargs.get("precache_dependencies", 'True'))
     else:
         tool_dependency_dir = None
-        use_tool_dependencies = os.path.exists(dependency_resolvers_config_file)
+        if dependency_resolvers_config_file is None:
+            use_tool_dependencies = bool(kwargs.get("dependency_resolvers", None))
+        else:
+            use_tool_dependencies = os.path.exists(dependency_resolvers_config_file)
         tool_dependency_cache_dir = None
         precache_dependencies = False
         use_cached_dependency_manager = False
@@ -1042,8 +1061,8 @@ class ConfiguresGalaxyMixin(object):
     def _configure_toolbox(self):
         from galaxy import tools
         from galaxy.managers.citations import CitationsManager
-        from galaxy.tools.deps import containers
-        from galaxy.tools.deps.dependencies import AppInfo
+        from galaxy.tool_util.deps import containers
+        from galaxy.tool_util.deps.dependencies import AppInfo
         import galaxy.tools.search
 
         self.citations_manager = CitationsManager(self)
@@ -1150,6 +1169,9 @@ class ConfiguresGalaxyMixin(object):
         combined_install_database = not(install_db_url and install_db_url != db_url)
         install_db_url = install_db_url or db_url
 
+        if self.config.database_wait:
+            self._wait_for_database(db_url)
+
         if getattr(self.config, "max_metadata_value_size", None):
             from galaxy.model import custom_types
             custom_types.MAX_METADATA_VALUE_SIZE = self.config.max_metadata_value_size
@@ -1192,3 +1214,15 @@ class ConfiguresGalaxyMixin(object):
     def _configure_signal_handlers(self, handlers):
         for sig, handler in handlers.items():
             signal.signal(sig, handler)
+
+    def _wait_for_database(self, url):
+        from sqlalchemy_utils import database_exists
+        attempts = self.config.database_wait_attempts
+        pause = self.config.database_wait_sleep
+        for i in range(1, attempts):
+            try:
+                database_exists(url)
+                break
+            except Exception:
+                log.info("Waiting for database: attempt %d of %d" % (i, attempts))
+                time.sleep(pause)
diff --git a/lib/galaxy/containers/docker_model.py b/lib/galaxy/containers/docker_model.py
index 23e41f5b5f5..f112f85bf38 100644
--- a/lib/galaxy/containers/docker_model.py
+++ b/lib/galaxy/containers/docker_model.py
@@ -16,7 +16,10 @@ from galaxy.containers import (
     ContainerPort,
     ContainerVolume
 )
-from galaxy.util import pretty_print_time_interval
+from galaxy.util import (
+    pretty_print_time_interval,
+    unicodify,
+)
 
 
 CPUS_LABEL = '_galaxy_cpus'
@@ -133,9 +136,9 @@ class DockerContainer(Container):
         rval = []
         try:
             port_mappings = self.inspect['NetworkSettings']['Ports']
-        except KeyError as exc:
+        except KeyError:
             log.warning("Failed to get ports for container %s from `docker inspect` output at "
-                        "['NetworkSettings']['Ports']: %s: %s", self.id, exc.__class__.__name__, str(exc))
+                        "['NetworkSettings']['Ports']: %s: %s", self.id, exc_info=True)
             return None
         for port_name in port_mappings:
             for binding in port_mappings[port_name]:
@@ -217,9 +220,9 @@ class DockerService(Container):
         rval = []
         try:
             port_mappings = self.inspect['Endpoint']['Ports']
-        except (IndexError, KeyError) as exc:
+        except (IndexError, KeyError):
             log.warning("Failed to get ports for container %s from `docker service inspect` output at "
-                        "['Endpoint']['Ports']: %s: %s", self.id, exc.__class__.__name__, str(exc))
+                        "['Endpoint']['Ports']: %s: %s", self.id, exc_info=True)
             return None
         for binding in port_mappings:
             rval.append(ContainerPort(
@@ -283,7 +286,7 @@ class DockerService(Container):
                     except ValueError:
                         self._env[env_str] = None
             except KeyError as exc:
-                log.debug('Cannot retrieve container environment: KeyError: %s', str(exc))
+                log.debug('Cannot retrieve container environment: KeyError: %s', unicodify(exc))
         return self._env
 
     @property
diff --git a/lib/galaxy/containers/docker_swarm.py b/lib/galaxy/containers/docker_swarm.py
index 27e21c5d607..a6a3a9d1fe4 100644
--- a/lib/galaxy/containers/docker_swarm.py
+++ b/lib/galaxy/containers/docker_swarm.py
@@ -33,6 +33,7 @@ from galaxy.containers.docker_model import (
     IMAGE_CONSTRAINT
 )
 from galaxy.exceptions import ContainerRunError
+from galaxy.util import unicodify
 from galaxy.util.json import safe_dumps_formatted
 
 log = logging.getLogger(__name__)
@@ -124,7 +125,7 @@ class DockerSwarmInterface(DockerInterface):
                 subprocess.check_call(['python', SWARM_MANAGER_PATH, '--containers-config-file',
                                       self.containers_config_file, '--swarm', self.key])
             except subprocess.CalledProcessError as exc:
-                log.error('Failed to launch swarm manager: %s', str(exc))
+                log.error('Failed to launch swarm manager: %s', unicodify(exc))
 
     def _get_image(self, image):
         """Get the image string, either from the argument, or from the
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index f80639f954c..e161c1f844d 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -699,7 +699,7 @@ class Bcf(BaseBcf):
             subprocess.check_call(cmd)
             shutil.move(dataset_symlink + '.csi', index_file.file_name)
         except Exception as e:
-            raise Exception('Error setting BCF metadata: %s' % (str(e)))
+            raise Exception('Error setting BCF metadata: %s' % util.unicodify(e))
         finally:
             # Remove temp file and symlink
             os.remove(dataset_symlink)
@@ -1107,6 +1107,66 @@ class Cool(H5):
             return "Cool (HDF5) file (%s)." % (nice_size(dataset.get_size()))
 
 
+class MCool(H5):
+    """
+    Class describing the multi-resolution cool format (https://github.com/mirnylab/cooler)
+    """
+
+    file_ext = "mcool"
+
+    def sniff(self, filename):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('matrix.mcool')
+        >>> MCool().sniff(fname)
+        True
+        >>> fname = get_test_fname('matrix.cool')
+        >>> MCool().sniff(fname)
+        False
+        >>> fname = get_test_fname('test.mz5')
+        >>> MCool().sniff(fname)
+        False
+        >>> fname = get_test_fname('wiggle.wig')
+        >>> MCool().sniff(fname)
+        False
+        >>> fname = get_test_fname('biom2_sparse_otu_table_hdf5.biom2')
+        >>> MCool().sniff(fname)
+        False
+        """
+
+        MAGIC = "HDF5::Cooler"
+        URL = "https://github.com/mirnylab/cooler"
+
+        if super(MCool, self).sniff(filename):
+            keys0 = ['resolutions']
+            with h5py.File(filename, 'r') as handle:
+                if not all(name in handle.keys() for name in keys0):
+                    return False
+                res0 = list(handle['resolutions'].keys())[0]
+                keys = ['chroms', 'bins', 'pixels', 'indexes']
+                fmt = handle['resolutions'][res0].attrs.get('format', None)
+                url = handle['resolutions'][res0].attrs.get('format-url', None)
+                if fmt == MAGIC or url == URL:
+                    if not all(name in handle['resolutions'][res0].keys() for name in keys):
+                        return False
+                    return True
+        return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = "Multi-resolution Cool (HDF5) file for storing genomic interaction data."
+            dataset.blurb = nice_size(dataset.get_size())
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except Exception:
+            return "MCool (HDF5) file (%s)." % (nice_size(dataset.get_size()))
+
+
 class Scf(Binary):
     """Class describing an scf binary sequence file"""
     edam_format = "format_1632"
@@ -1595,7 +1655,7 @@ class GAFASQLite(SQlite):
                 raise Exception('Multiple versions found in meta table')
             dataset.metadata.gafa_schema_version = results[0][0]
         except Exception as e:
-            log.warn("%s, set_meta Exception: %s", self, e)
+            log.warning("%s, set_meta Exception: %s", self, e)
 
     def sniff(self, filename):
         if super(GAFASQLite, self).sniff(filename):
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
index 91fdc12b55e..ac965e105ae 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
@@ -11,6 +11,7 @@ import sys
 
 import bx.wiggle
 
+from galaxy.util import unicodify
 from galaxy.util.ucsc import (
     UCSCLimitException,
     UCSCOutWrapper
@@ -19,7 +20,7 @@ from galaxy.util.ucsc import (
 
 def stop_err(msg):
     sys.stderr.write(msg)
-    sys.exit()
+    sys.exit(1)
 
 
 def main():
@@ -40,7 +41,7 @@ def main():
         # Wiggle data was truncated, at the very least need to warn the user.
         print('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
     except ValueError as e:
-        stop_err(str(e))
+        stop_err(unicodify(e))
     finally:
         in_file.close()
         out_file.close()
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 8cdd9fcf91c..ab34acc299f 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -8,11 +8,11 @@ import shutil
 import string
 import tempfile
 import zipfile
-from cgi import escape
 from inspect import isclass
 
 import six
 import webob.exc
+from markupsafe import escape
 
 from galaxy import util
 from galaxy.datatypes.metadata import MetadataElement  # import directly to maintain ease of use in Datatype class definitions
@@ -210,7 +210,7 @@ class Data(object):
             out.append('</table>')
             out = "".join(out)
         except Exception as exc:
-            out = "Can't create peek %s" % str(exc)
+            out = "Can't create peek: %s" % unicodify(exc)
         return out
 
     def _archive_main_file(self, archive, display_name, data_filename):
@@ -910,7 +910,7 @@ class Text(Data):
                     part_file.write(a_line)
                     lines_remaining -= 1
         except Exception as e:
-            log.error('Unable to split files: %s' % str(e))
+            log.error('Unable to split files: %s', unicodify(e))
             raise
         finally:
             f.close()
@@ -1030,8 +1030,14 @@ def get_file_peek(file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipc
     :param is_multi_byte: deprecated
     :type  is_multi_byte: bool
 
-    >>> fname = get_test_fname('4.bed')
-    >>> assert get_file_peek(fname, LINE_COUNT=1) == u'chr22\\t30128507\\t31828507\\tuc003bnx.1_cds_2_0_chr22_29227_f\\t0\\t+\\n'
+    >>> def assert_peek_is(file_name, expected, *args, **kwd):
+    ...     path = get_test_fname(file_name)
+    ...     peek = get_file_peek(path, *args, **kwd)
+    ...     assert peek == expected, "%s != %s" % (peek, expected)
+    >>> assert_peek_is('0_nonewline', u'0')
+    >>> assert_peek_is('0.txt', u'0\\n')
+    >>> assert_peek_is('4.bed', u'chr22\\t30128507\\t31828507\\tuc003bnx.1_cds_2_0_chr22_29227_f\\t0\\t+\\n', LINE_COUNT=1)
+    >>> assert_peek_is('1.bed', u'chr1\\t147962192\\t147962580\\tCCDS989.1_cds_0_0_chr1_147962193_r\\t0\\t-\\nchr1\\t147984545\\t147984630\\tCCDS990.1_cds_0_0_chr1_147984546_f\\t0\\t+\\n', LINE_COUNT=2)
     """
     # Set size for file.readline() to a negative number to force it to
     # read until either a newline or EOF.  Needed for datasets with very
@@ -1042,20 +1048,27 @@ def get_file_peek(file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipc
         skipchars = []
     lines = []
     count = 0
+
+    last_line_break = False
     with compression_utils.get_fileobj(file_name, "U") as temp:
         while count < LINE_COUNT:
             try:
                 line = temp.readline(WIDTH)
             except UnicodeDecodeError:
                 return "binary file"
-            if not line_wrap:
-                if line.endswith('\n'):
-                    line = line[:-1]
-                else:
-                    while True:
-                        i = temp.read(1)
-                        if not i or i == '\n':
-                            break
+            if line == "":
+                break
+            last_line_break = False
+            if line.endswith('\n'):
+                line = line[:-1]
+                last_line_break = True
+            elif not line_wrap:
+                while True:
+                    i = temp.read(1)
+                    if i == '\n':
+                        last_line_break = True
+                    if not i or i == '\n':
+                        break
             skip_line = False
             for skipchar in skipchars:
                 if line.startswith(skipchar):
@@ -1064,4 +1077,4 @@ def get_file_peek(file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipc
             if not skip_line:
                 lines.append(line)
                 count += 1
-    return '\n'.join(lines)
+    return '\n'.join(lines) + ('\n' if last_line_break else '')
diff --git a/lib/galaxy/datatypes/display_applications/util.py b/lib/galaxy/datatypes/display_applications/util.py
index 81f2f3818ef..6af23bf5b94 100644
--- a/lib/galaxy/datatypes/display_applications/util.py
+++ b/lib/galaxy/datatypes/display_applications/util.py
@@ -1,6 +1,4 @@
-from Crypto.Cipher import Blowfish
-
-from galaxy.util import smart_str
+from galaxy.security.idencoding import IdEncodingHelper
 
 
 def encode_dataset_user(trans, dataset, user):
@@ -10,11 +8,8 @@ def encode_dataset_user(trans, dataset, user):
     if user is None:
         user_hash = 'None'
     else:
-        user_hash = str(user.id)
-        # Pad to a multiple of 8 with leading "!"
-        user_hash = ("!" * (8 - len(user_hash) % 8)) + user_hash
-        cipher = Blowfish.new(smart_str(dataset.create_time), mode=Blowfish.MODE_ECB)
-        user_hash = cipher.encrypt(user_hash).encode('hex')
+        security = IdEncodingHelper(id_secret=dataset.create_time)
+        user_hash = security.encode_id(user.id)
     return dataset_hash, user_hash
 
 
@@ -27,8 +22,8 @@ def decode_dataset_user(trans, dataset_hash, user_hash):
     if user_hash in [None, 'None']:
         user = None
     else:
-        cipher = Blowfish.new(smart_str(dataset.create_time), mode=Blowfish.MODE_ECB)
-        user_id = cipher.decrypt(user_hash.decode('hex')).lstrip("!")
-        user = trans.sa_session.query(trans.app.model.User).get(int(user_id))
+        security = IdEncodingHelper(id_secret=dataset.create_time)
+        user_id = security.decode_id(user_hash)
+        user = trans.sa_session.query(trans.app.model.User).get(user_id)
         assert user, "A Bad user id was passed to decode_dataset_user"
     return dataset, user
diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 3af65de2e35..efcf82e2e1d 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -15,8 +15,8 @@ import logging
 import os
 import re
 import sys
-from cgi import escape
 
+from markupsafe import escape
 from six.moves.urllib.parse import quote_plus
 
 from galaxy.datatypes import metadata
@@ -25,7 +25,10 @@ from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import build_sniff_from_prefix
 from galaxy.datatypes.tabular import Tabular
 from galaxy.datatypes.text import Html
-from galaxy.util import nice_size
+from galaxy.util import (
+    nice_size,
+    unicodify,
+)
 
 gal_Log = logging.getLogger(__name__)
 verbose = False
@@ -835,7 +838,7 @@ class RexpBase(Html):
             out.append('</table>')
             out = "\n".join(out)
         except Exception as exc:
-            out = "Can't create html table %s" % str(exc)
+            out = "Can't create html table %s" % unicodify(exc)
         return out
 
     def display_peek(self, dataset):
diff --git a/lib/galaxy/datatypes/gis.py b/lib/galaxy/datatypes/gis.py
new file mode 100644
index 00000000000..276de5cb97c
--- /dev/null
+++ b/lib/galaxy/datatypes/gis.py
@@ -0,0 +1,64 @@
+"""
+GIS classes
+"""
+
+from galaxy.datatypes.binary import Binary
+
+
+class Shapefile(Binary):
+    """ The Shapefile data format:
+            For more information please see http://en.wikipedia.org/wiki/Shapefile
+    """
+
+    composite_type = 'auto_primary_file'
+    file_ext = "shp"
+    allow_datatype_change = False
+
+    def __init__(self, **kwd):
+        Binary.__init__(self, **kwd)
+        self.add_composite_file('shapefile.shp', description='Geometry File (shp)', is_binary=True, optional=False)
+        self.add_composite_file('shapefile.shx', description='Geometry index File (shx)', is_binary=True, optional=False)
+        self.add_composite_file('shapefile.dbf', description='Columnar attributes for each shape (dbf)', is_binary=True, optional=False)
+        # optional
+        self.add_composite_file('shapefile.prj', description='Projection description (prj)', is_binary=False, optional=True)
+        self.add_composite_file('shapefile.sbn', description='Spatial index of the features (sbn)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.sbx', description='Spatial index of the features (sbx)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.fbn', description='Read only spatial index of the features (fbn)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.fbx', description='Read only spatial index of the features (fbx)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.ain', description='Attribute index of the active fields in a table (ain)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.aih', description='Attribute index of the active fields in a table (aih)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.atx', description='Attribute index for the dbf file (atx)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.ixs', description='Geocoding index (ixs)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.mxs', description='Geocoding index in ODB format (mxs)', is_binary=True, optional=True)
+        self.add_composite_file('shapefile.shp.xml', description='Geospatial metadata in XML format (xml)', is_binary=False, optional=True)
+
+    def generate_primary_file(self, dataset=None):
+        rval = ['<html><head><title>Shapefile Galaxy Composite Dataset</title></head><p/>']
+        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
+            fn = composite_name
+            opt_text = ''
+            if composite_file.optional:
+                opt_text = ' (optional)'
+            if composite_file.get('description'):
+                rval.append('<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text))
+            else:
+                rval.append('<li><a href="%s" type="application/binary">%s</a>%s</li>' % (fn, fn, opt_text))
+        rval.append('</ul></div></html>\n')
+        return "\n".join(rval)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text."""
+        if not dataset.dataset.purged:
+            dataset.peek = "Shapefile data"
+            dataset.blurb = "Shapefile data"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def display_peek(self, dataset):
+        """Create HTML content, used for displaying peek."""
+        try:
+            return dataset.peek
+        except Exception:
+            return "Shapefile data"
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index ee747aa91b0..2bf578bf038 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -772,9 +772,8 @@ class Gff(Tabular, _RemoteCallMixin):
                         break
                 if seqid is not None:
                     return (seqid, str(start), str(stop))  # Necessary to return strings?
-            except Exception as e:
-                # unexpected error
-                log.exception(str(e))
+            except Exception:
+                log.exception('Unexpected error')
         return (None, None, None)  # could not determine viewport
 
     def ucsc_links(self, dataset, type, app, base_url):
@@ -1141,9 +1140,8 @@ class Wiggle(Tabular, _RemoteCallMixin):
                         break
                 if chrom is not None:
                     return (chrom, str(start), str(end))  # Necessary to return strings?
-            except Exception as e:
-                # unexpected error
-                log.exception(str(e))
+            except Exception:
+                log.exception('Unexpected error')
         return (None, None, None)  # could not determine viewport
 
     def gbrowse_links(self, dataset, type, app, base_url):
@@ -1323,9 +1321,8 @@ class CustomTrack(Tabular):
                     if not max_line_count:
                         # exceeded viewport or total line count to check
                         break
-            except Exception as e:
-                # unexpected error
-                log.exception(str(e))
+            except Exception:
+                log.exception('Unexpected error')
         return (None, None, None)  # could not determine viewport
 
     def ucsc_links(self, dataset, type, app, base_url):
diff --git a/lib/galaxy/datatypes/isa.py b/lib/galaxy/datatypes/isa.py
index d11f6454612..793265a471e 100644
--- a/lib/galaxy/datatypes/isa.py
+++ b/lib/galaxy/datatypes/isa.py
@@ -14,7 +14,6 @@ import re
 import shutil
 import sys
 import tempfile
-from cgi import escape
 
 # Imports isatab after turning off warnings inside logger settings to avoid pandas warning making uploads fail.
 logging.getLogger("isatools.isatab").setLevel(logging.ERROR)
@@ -22,6 +21,7 @@ from isatools import (
     isajson,
     isatab_meta
 )
+from markupsafe import escape
 
 from galaxy import util
 from galaxy.datatypes import data
@@ -195,7 +195,7 @@ class _Isa(data.Data):
             out.append('</table>')
             out = "".join(out)
         except Exception as exc:
-            out = "Can't create peek %s" % str(exc)
+            out = "Can't create peek: %s" % util.unicodify(exc)
         return out
 
     # Generate primary file {{{2
diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index b4556e5d366..3fbdbed5d1c 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -19,6 +19,7 @@ from galaxy.datatypes.sniff import (
 from galaxy.datatypes.tabular import Tabular
 from galaxy.datatypes.util.generic_util import count_special_lines
 from galaxy.datatypes.xml import GenericXml
+from galaxy.util import unicodify
 
 log = logging.getLogger(__name__)
 
@@ -167,7 +168,7 @@ class SDF(GenericMolFile):
             if sdf_lines_accumulated:
                 _write_part_sdf_file(sdf_lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s' % str(e))
+            log.error('Unable to split files: %s', unicodify(e))
             raise
     split = classmethod(split)
 
@@ -254,7 +255,7 @@ class MOL2(GenericMolFile):
             if mol2_lines_accumulated:
                 _write_part_mol2_file(mol2_lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s' % str(e))
+            log.error('Unable to split files: %s', unicodify(e))
             raise
     split = classmethod(split)
 
@@ -333,7 +334,7 @@ class FPS(GenericMolFile):
             if lines_accumulated:
                 _write_part_fingerprint_file(header_lines + lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s' % str(e))
+            log.error('Unable to split files: %s', unicodify(e))
             raise
     split = classmethod(split)
 
@@ -503,7 +504,7 @@ class PDB(GenericMolFile):
                             chain_ids.add(line[21])
             dataset.metadata.chain_ids = list(chain_ids)
         except Exception as e:
-            log.error('Error finding chain_ids: %s' % str(e))
+            log.error('Error finding chain_ids: %s', unicodify(e))
             raise
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -656,7 +657,7 @@ class PQR(GenericMolFile):
                         chain_ids.add(match.groups()[5])
             dataset.metadata.chain_ids = list(chain_ids)
         except Exception as e:
-            log.error('Error finding chain_ids: %s' % str(e))
+            log.error('Error finding chain_ids: %s', unicodify(e))
             raise
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -898,7 +899,7 @@ class CML(GenericXml):
             if cml_lines_accumulated:
                 _write_part_cml_file(cml_lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s' % str(e))
+            log.error('Unable to split files: %s', unicodify(e))
             raise
     split = classmethod(split)
 
diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py
index 689ff667c9e..14df3e8f183 100644
--- a/lib/galaxy/datatypes/mothur.py
+++ b/lib/galaxy/datatypes/mothur.py
@@ -13,6 +13,7 @@ from galaxy.datatypes.sniff import (
     iter_headers
 )
 from galaxy.datatypes.tabular import Tabular
+from galaxy.util import unicodify
 
 log = logging.getLogger(__name__)
 
@@ -981,7 +982,7 @@ class SffFlow(Tabular):
             out += self.make_html_peek_rows(dataset, skipchars=skipchars)
             out += '</table>'
         except Exception as exc:
-            out = "Can't create peek %s" % str(exc)
+            out = "Can't create peek: %s" % unicodify(exc)
         return out
 
 
diff --git a/lib/galaxy/datatypes/msa.py b/lib/galaxy/datatypes/msa.py
index 770f797e444..c0673166721 100644
--- a/lib/galaxy/datatypes/msa.py
+++ b/lib/galaxy/datatypes/msa.py
@@ -8,7 +8,10 @@ from galaxy.datatypes.data import get_file_peek, Text
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import build_sniff_from_prefix
 from galaxy.datatypes.util import generic_util
-from galaxy.util import nice_size
+from galaxy.util import (
+    nice_size,
+    unicodify,
+)
 
 log = logging.getLogger(__name__)
 
@@ -214,7 +217,7 @@ class Stockholm_1_0(Text):
             if stockholm_lines_accumulated:
                 _write_part_stockholm_file(stockholm_lines_accumulated)
         except Exception as e:
-            log.error('Unable to split files: %s' % str(e))
+            log.error('Unable to split files: %s', unicodify(e))
             raise
     split = classmethod(split)
 
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index b1897586918..7a4261f5378 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -82,7 +82,7 @@ class Registry(object):
         self.display_sites = {}
         self.legacy_build_sites = {}
 
-    def load_datatypes(self, root_dir=None, config=None, deactivate=False, override=True):
+    def load_datatypes(self, root_dir=None, config=None, deactivate=False, override=True, use_converters=True, use_display_applications=True, use_build_sites=True):
         """
         Parse a datatypes XML file located at root_dir/config (if processing the Galaxy distributed config) or contained within
         an installed Tool Shed repository.  If deactivate is True, an installed Tool Shed repository that includes custom datatypes
@@ -119,14 +119,16 @@ class Registry(object):
                 root = config
             registration = root.find('registration')
             # Set default paths defined in local datatypes_conf.xml.
-            if not self.converters_path:
-                self.converters_path_attr = registration.get('converters_path', 'lib/galaxy/datatypes/converters')
-                self.converters_path = os.path.join(root_dir, self.converters_path_attr)
-                if not os.path.isdir(self.converters_path):
-                    raise ConfigurationError("Directory does not exist: %s" % self.converters_path)
-            if not self.display_applications_path:
-                self.display_path_attr = registration.get('display_path', 'display_applications')
-                self.display_applications_path = os.path.join(root_dir, self.display_path_attr)
+            if use_converters:
+                if not self.converters_path:
+                    self.converters_path_attr = registration.get('converters_path', 'lib/galaxy/datatypes/converters')
+                    self.converters_path = os.path.join(root_dir, self.converters_path_attr)
+                    if not os.path.isdir(self.converters_path):
+                        raise ConfigurationError("Directory does not exist: %s" % self.converters_path)
+            if use_display_applications:
+                if not self.display_applications_path:
+                    self.display_path_attr = registration.get('display_path', 'display_applications')
+                    self.display_applications_path = os.path.join(root_dir, self.display_path_attr)
             # Proprietary datatype's <registration> tag may have special attributes, proprietary_converter_path and proprietary_display_path.
             proprietary_converter_path = registration.get('proprietary_converter_path', None)
             proprietary_display_path = registration.get('proprietary_display_path', None)
@@ -222,7 +224,7 @@ class Registry(object):
                                             datatype_class = getattr(imported_module, datatype_class_name)
                                     except Exception as e:
                                         full_path = os.path.join(proprietary_path, proprietary_datatype_module)
-                                        self.log.debug("Exception importing proprietary code file %s: %s" % (str(full_path), str(e)))
+                                        self.log.debug("Exception importing proprietary code file %s: %s", full_path, galaxy.util.unicodify(e))
                                 # Either the above exception was thrown because the proprietary_datatype_module is not derived from a class
                                 # in the repository, or we are loading Galaxy's datatypes. In either case we'll look in the registry.
                                 if datatype_class is None:
@@ -367,7 +369,8 @@ class Registry(object):
                                         compressed_sniffers=compressed_sniffers)
             self.upload_file_formats.sort()
             # Load build sites
-            self._load_build_sites(root)
+            if use_build_sites:
+                self._load_build_sites(root)
         self.set_default_values()
 
         def append_to_sniff_order():
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index ee03f53e21d..ffa11e25a2f 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -9,10 +9,10 @@ import re
 import string
 import subprocess
 import sys
-from cgi import escape
 from itertools import islice
 
 import bx.align.maf
+from markupsafe import escape
 
 from galaxy import util
 from galaxy.datatypes import metadata
@@ -451,7 +451,7 @@ class Fasta(Sequence):
                     start_offset = f.tell()
                 part_file.write(line)
         except Exception as e:
-            log.error('Unable to size split FASTA file: %s' % str(e))
+            log.error('Unable to size split FASTA file: %s', util.unicodify(e))
             raise
         finally:
             f.close()
@@ -488,7 +488,7 @@ class Fasta(Sequence):
                         rec_count = 1
                 part_file.write(line)
         except Exception as e:
-            log.error('Unable to count split FASTA file: %s' % str(e))
+            log.error('Unable to count split FASTA file: %s', util.unicodify(e))
             raise
         finally:
             f.close()
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 404f9c53a11..e057cfb03c6 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -14,15 +14,16 @@ import sys
 import tempfile
 import zipfile
 
-from six import StringIO, text_type
+from six import (
+    PY3,
+    StringIO,
+    text_type,
+)
 from six.moves import filter
 from six.moves.urllib.request import urlopen
 
 from galaxy import util
-from galaxy.util import (
-    compression_utils,
-    smart_str
-)
+from galaxy.util import compression_utils
 from galaxy.util.checkers import (
     check_binary,
     check_bz2,
@@ -59,39 +60,24 @@ def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source
     """Writes a stream to the provided file descriptor, returns the file name. Closes file descriptor"""
     # signature and behavor is somewhat odd, due to backwards compatibility, but this can/should be done better
     CHUNK_SIZE = 1048576
-    data_checked = False
-    is_compressed = False
-    is_binary = False
     try:
         codecs.lookup(target_encoding)
     except Exception:
         target_encoding = util.DEFAULT_ENCODING  # utf-8
-    if not source_encoding:
-        source_encoding = util.DEFAULT_ENCODING  # sys.getdefaultencoding() would mimic old behavior (defaults to ascii)
     while True:
         chunk = stream.read(CHUNK_SIZE)
         if not chunk:
             break
-        if not data_checked:
-            # See if we're uploading a compressed file
-            try:
-                # Convert chunk to a bytestring if it is not already.
-                # Check if the first 2 bytes of the chunk are equal to the
-                # gzip magic number.
-                if smart_str(chunk)[:2] == util.gzip_magic:
-                    is_compressed = True
-            except Exception:
-                pass
-            if not is_compressed:
-                is_binary = util.is_binary(chunk)
-            data_checked = True
-        if not is_compressed and not is_binary:
+        if source_encoding is not None:
+            # If a source encoding is given we use it to convert to the target encoding
             if not isinstance(chunk, text_type):
                 chunk = chunk.decode(source_encoding, source_error)
             os.write(fd, chunk.encode(target_encoding, target_error))
         else:
             # Compressed files must be encoded after they are uncompressed in the upload utility,
             # while binary files should not be encoded at all.
+            if isinstance(chunk, text_type):
+                chunk = chunk.encode(target_encoding, target_error)
             os.write(fd, chunk)
     os.close(fd)
     return filename
@@ -103,28 +89,40 @@ def stream_to_file(stream, suffix='', prefix='', dir=None, text=False, **kwd):
     return stream_to_open_named_file(stream, fd, temp_name, **kwd)
 
 
-def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload"):
+def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload", block_size=128 * 1024, regexp=None):
     """
     Converts in place a file from universal line endings
     to Posix line endings.
-
-    >>> fname = get_test_fname('temp.txt')
-    >>> with open(fname, 'wt') as fh:
-    ...     _ = fh.write("1 2\\r3 4")
-    >>> convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
-    (2, None)
-    >>> open(fname).read()
-    '1 2\\n3 4\\n'
     """
     fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
-    with io.open(fd, mode="wt", encoding='utf-8') as fp:
-        i = None
-        for i, line in enumerate(io.open(fname, encoding='utf-8')):
-            fp.write("%s\n" % line.rstrip("\r\n"))
-    if i is None:
-        i = 0
+    i = 0
+    if PY3:
+        NEWLINE_BYTE = 10
+        CR_BYTE = 13
     else:
-        i += 1
+        NEWLINE_BYTE = "\n"
+        CR_BYTE = "\r"
+    with io.open(fd, mode="wb") as fp, io.open(fname, mode="rb") as fi:
+        last_char = None
+        block = fi.read(block_size)
+        last_block = b""
+        while block:
+            if last_char == CR_BYTE and block.startswith(b"\n"):
+                # Last block ended with CR, new block startswith newline.
+                # Since we replace CR with newline in the previous iteration we skip the first byte
+                block = block[1:]
+            if block:
+                last_char = block[-1]
+                block = block.replace(b"\r\n", b"\n").replace(b"\r", b"\n")
+                if regexp:
+                    block = b"\t".join(regexp.split(block))
+                fp.write(block)
+                i += block.count(b"\n")
+                last_block = block
+                block = fi.read(block_size)
+        if last_block and last_block[-1] != NEWLINE_BYTE:
+            i += 1
+            fp.write(b"\n")
     if in_place:
         shutil.move(temp_name, fname)
         # Return number of lines in file.
@@ -133,47 +131,9 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload"):
         return (i, temp_name)
 
 
-def sep2tabs(fname, in_place=True, patt=r"\s+", tmp_dir=None, tmp_prefix="gxupload"):
+def convert_newlines_sep2tabs(fname, in_place=True, patt=br"[^\S\n]+", tmp_dir=None, tmp_prefix="gxupload"):
     """
-    Transforms in place a 'sep' separated file to a tab separated one
-
-    >>> fname = get_test_fname('temp.txt')
-    >>> with open(fname, 'wt') as fh:
-    ...     _ = fh.write(u"1 2\\n3 4\\n")
-    >>> sep2tabs(fname)
-    (2, None)
-    >>> open(fname).read()
-    '1\\t2\\n3\\t4\\n'
-    """
-    regexp = re.compile(patt)
-    fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
-    with io.open(fd, mode="wt", encoding='utf-8') as fp:
-        i = None
-        for i, line in enumerate(io.open(fname, encoding='utf-8')):
-            if line.endswith("\r"):
-                line = line.rstrip('\r')
-                elems = regexp.split(line)
-                fp.write(u"%s\r" % '\t'.join(elems))
-            else:
-                line = line.rstrip('\n')
-                elems = regexp.split(line)
-                fp.write(u"%s\n" % '\t'.join(elems))
-    if i is None:
-        i = 0
-    else:
-        i += 1
-    if in_place:
-        shutil.move(temp_name, fname)
-        # Return number of lines in file.
-        return (i, None)
-    else:
-        return (i, temp_name)
-
-
-def convert_newlines_sep2tabs(fname, in_place=True, patt=r"\s+", tmp_dir=None, tmp_prefix="gxupload"):
-    """
-    Combines above methods: convert_newlines() and sep2tabs()
-    so that files do not need to be read twice
+    Converts newlines in a file to posix newlines and replaces spaces with tabs.
 
     >>> fname = get_test_fname('temp.txt')
     >>> with open(fname, 'wt') as fh:
@@ -184,18 +144,7 @@ def convert_newlines_sep2tabs(fname, in_place=True, patt=r"\s+", tmp_dir=None, t
     '1\\t2\\n3\\t4\\n'
     """
     regexp = re.compile(patt)
-    fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
-    with io.open(fd, mode="wt", encoding='utf-8') as fp:
-        for i, line in enumerate(io.open(fname, encoding='utf-8')):
-            line = line.rstrip('\r\n')
-            elems = regexp.split(line)
-            fp.write(u"%s\n" % '\t'.join(elems))
-    if in_place:
-        shutil.move(temp_name, fname)
-        # Return number of lines in file.
-        return (i + 1, None)
-    else:
-        return (i + 1, temp_name)
+    return convert_newlines(fname, in_place, tmp_dir, tmp_prefix, regexp=regexp)
 
 
 def iter_headers(fname_or_file_prefix, sep, count=60, comment_designator=None):
@@ -474,6 +423,9 @@ def guess_ext(fname, sniff_order, is_binary=False):
     >>> fname = get_test_fname('1.mtx')
     >>> guess_ext(fname, sniff_order)
     'mtx'
+    >>> fname = get_test_fname('1imzml')
+    >>> guess_ext(fname, sniff_order)  # This test case is ensuring doesn't throw exception, actual value could change if non-utf encoding handling improves.
+    'data'
     """
     file_prefix = FilePrefix(fname)
     file_ext = run_sniffers_raw(file_prefix, sniff_order, is_binary)
@@ -555,8 +507,9 @@ def zip_single_fileobj(path):
 class FilePrefix(object):
 
     def __init__(self, filename):
-        binary = False
+        non_utf8_error = None
         compressed_format = None
+        contents_header_bytes = None
         contents_header = None  # First MAX_BYTES of the file.
         truncated = False
         # A future direction to optimize sniffing even more for sniffers at the top of the list
@@ -565,20 +518,23 @@ class FilePrefix(object):
         # populates contents_header while providing a StringIO-like interface until the file is read
         # but then would fallback to native string_io()
         try:
-            compressed_format, f = compression_utils.get_fileobj_raw(filename)
+            compressed_format, f = compression_utils.get_fileobj_raw(filename, "rb")
             try:
-                contents_header = f.read(SNIFF_PREFIX_BYTES)
-                truncated = len(contents_header) == SNIFF_PREFIX_BYTES
+                contents_header_bytes = f.read(SNIFF_PREFIX_BYTES)
+                truncated = len(contents_header_bytes) == SNIFF_PREFIX_BYTES
+                contents_header = contents_header_bytes.decode("utf-8")
             finally:
                 f.close()
-        except UnicodeDecodeError:
-            binary = True
+        except UnicodeDecodeError as e:
+            non_utf8_error = e
 
         self.truncated = truncated
         self.filename = filename
-        self.binary = binary
+        self.non_utf8_error = non_utf8_error
+        self.binary = non_utf8_error is not None  # obviously wrong
         self.compressed_format = compressed_format
         self.contents_header = contents_header
+        self.contents_header_bytes = contents_header_bytes
         self._file_size = None
 
     @property
@@ -588,8 +544,8 @@ class FilePrefix(object):
         return self._file_size
 
     def string_io(self):
-        if self.binary:
-            raise Exception("Attempting to create a StringIO object for binary data.")
+        if self.non_utf8_error is not None:
+            raise self.non_utf8_error
         rval = StringIO(self.contents_header)
         return rval
 
@@ -703,7 +659,7 @@ def handle_compressed_file(
                 os.close(fd)
                 os.remove(uncompressed)
                 compressed_file.close()
-                raise IOError('Problem uncompressing %s data, please try retrieving the data uncompressed: %s' % (compressed_type, e))
+                raise IOError('Problem uncompressing %s data, please try retrieving the data uncompressed: %s' % (compressed_type, util.unicodify(e)))
             if not chunk:
                 break
             os.write(fd, chunk)
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 1d04a03a4a6..57744ed41f2 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -4,6 +4,7 @@ Tabular datatype
 from __future__ import absolute_import
 
 import abc
+import binascii
 import csv
 import logging
 import os
@@ -12,10 +13,10 @@ import shutil
 import subprocess
 import sys
 import tempfile
-from cgi import escape
 from json import dumps
 
 import pysam
+from markupsafe import escape
 
 from galaxy import util
 from galaxy.datatypes import binary, data, metadata
@@ -128,7 +129,7 @@ class TabularData(data.Text):
             out.append('</table>')
             out = "".join(out)
         except Exception as exc:
-            out = "Can't create peek %s" % str(exc)
+            out = "Can't create peek: %s" % util.unicodify(exc)
         return out
 
     def make_html_peek_header(self, dataset, skipchars=None, column_names=None, column_number_format='%s', column_parameter_alias=None, **kwargs):
@@ -174,7 +175,7 @@ class TabularData(data.Text):
             out.append('</tr>')
         except Exception as exc:
             log.exception('make_html_peek_header failed on HDA %s', dataset.id)
-            raise Exception("Can't create peek header %s" % str(exc))
+            raise Exception("Can't create peek header: %s" % util.unicodify(exc))
         return "".join(out)
 
     def make_html_peek_rows(self, dataset, skipchars=None, **kwargs):
@@ -205,7 +206,7 @@ class TabularData(data.Text):
                         out.append('</tr>')
         except Exception as exc:
             log.exception('make_html_peek_rows failed on HDA %s', dataset.id)
-            raise Exception("Can't create peek rows %s" % str(exc))
+            raise Exception("Can't create peek rows: %s" % util.unicodify(exc))
         return "".join(out)
 
     def display_peek(self, dataset):
@@ -691,11 +692,11 @@ class BaseVcf(Tabular):
     MetadataElement(name="viz_filter_cols", desc="Score column for visualization", default=[5], param=metadata.ColumnParameter, optional=True, multiple=True, visible=False)
     MetadataElement(name="sample_names", default=[], desc="Sample names", readonly=True, visible=False, optional=True, no_value=[])
 
-    def sniff_prefix(self, file_prefix):
+    def _sniff(self, fname_or_file_prefix):
         # Because this sniffer is run on compressed files that might be BGZF (due to the VcfGz subclass), we should
         # handle unicode decode errors. This should ultimately be done in get_headers(), but guess_ext() currently
         # relies on get_headers() raising this exception.
-        headers = get_headers(file_prefix, '\n', count=1)
+        headers = get_headers(fname_or_file_prefix, '\n', count=1)
         return headers[0][0].startswith("##fileformat=VCF")
 
     def display_peek(self, dataset):
@@ -745,14 +746,29 @@ class BaseVcf(Tabular):
 class Vcf(BaseVcf):
     file_ext = 'vcf'
 
+    def sniff_prefix(self, file_prefix):
+        return self._sniff(file_prefix)
+
 
 class VcfGz(BaseVcf, binary.Binary):
+    # This class name is a misnomer, should be VcfBgzip
     file_ext = 'vcf_bgzip'
     compressed = True
     compressed_format = "gzip"
 
     MetadataElement(name="tabix_index", desc="Vcf Index File", param=metadata.FileParameter, file_ext="tbi", readonly=True, no_value=None, visible=False, optional=True)
 
+    def sniff(self, filename):
+        if not self._sniff(filename):
+            return False
+        # Check that the file is compressed with bgzip (not gzip), i.e. the
+        # compressed format is BGZF, as explained in
+        # http://samtools.github.io/hts-specs/SAMv1.pdf
+        with open(filename, 'rb') as fh:
+            fh.seek(-28, 2)
+            last28 = fh.read()
+            return binascii.hexlify(last28) == b'1f8b08040000000000ff0600424302001b0003000000000000000000'
+
     def set_meta(self, dataset, **kwd):
         super(BaseVcf, self).set_meta(dataset, **kwd)
         """ Creates the index for the VCF file. """
@@ -764,7 +780,7 @@ class VcfGz(BaseVcf, binary.Binary):
         try:
             pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf', force=True)
         except Exception as e:
-            raise Exception('Error setting VCF.gz metadata: %s' % (str(e)))
+            raise Exception('Error setting VCF.gz metadata: %s' % (util.unicodify(e)))
         dataset.metadata.tabix_index = index_file
 
 
diff --git a/lib/galaxy/datatypes/test/0_nonewline b/lib/galaxy/datatypes/test/0_nonewline
new file mode 100644
index 00000000000..c227083464f
--- /dev/null
+++ b/lib/galaxy/datatypes/test/0_nonewline
@@ -0,0 +1 @@
+0
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/test/1imzml b/lib/galaxy/datatypes/test/1imzml
new file mode 100644
index 00000000000..6b45d2a3667
--- /dev/null
+++ b/lib/galaxy/datatypes/test/1imzml
@@ -0,0 +1,380 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" xmlns="http://psi.hupo.org/ms/mzml" version="1.1">
+  <cvList count="4">
+    <cv URI="http://ontologies.berkeleybop.org/pato.obo" fullName="Phenotype And Trait Ontology" id="PATO" version="releases/2017-07-10"/>
+    <cv URI="http://ontologies.berkeleybop.org/uo.obo" fullName="Units of Measurement Ontology" id="UO" version="releases/2017-09-25"/>
+    <cv URI="https://raw.githubusercontent.com/hupo-psi/psi-ms-cv/master/psi-ms.obo" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" id="MS" version="4.1.0"/>
+    <cv URI="https://raw.githubusercontent.com/imzML/imzML/master/imagingMS.obo" fullName="Mass Spectrometry Imaging Ontology" id="IMS" version="1.1.0"/>
+  </cvList>
+  <fileDescription>
+    <fileContent>
+      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
+      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
+      <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9d501bdc53444916b7e97e795b02c856"/>
+      <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7e8fdb93053915d3edb51b70aa0619ac209964df"/>
+      <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
+    </fileContent>
+    <sourceFileList count="1">
+      <sourceFile id="sf1" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\" name="Example.raw">
+        <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format"/>
+        <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/>
+        <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
+      </sourceFile>
+    </sourceFileList>
+    <contact>
+      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
+      <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Institut für Anorganische und Analytische Chemie"/>
+      <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/>
+      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
+    </contact>
+  </fileDescription>
+  <referenceableParamGroupList count="4">
+    <referenceableParamGroup id="mzArray">
+      <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
+      <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
+      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="intensityArray">
+      <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
+      <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
+      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
+      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="scan1">
+      <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan"/>
+      <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="spectrum1">
+      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
+      <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
+      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
+      <cvParam cvRef="MS" accession="MS:1000129" name="negative scan"/>
+    </referenceableParamGroup>
+  </referenceableParamGroupList>
+  <sampleList count="1">
+    <sample id="sample1" name="Sample1">
+      <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
+    </sample>
+  </sampleList>
+  <softwareList count="2">
+    <software id="Xcalibur" version="2.2">
+      <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur"/>
+    </software>
+    <software id="TMC" version="1.1 beta">
+      <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
+    </software>
+  </softwareList>
+  <scanSettingsList count="1">
+    <scanSettings id="scansettings1">
+      <cvParam cvRef="IMS" accession="IMS:1000401" name="top down"/>
+      <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback"/>
+      <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan"/>
+      <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right"/>
+      <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixels x" value="3"/>
+      <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixels y" value="3"/>
+      <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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+      <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
+    </scanSettings>
+  </scanSettingsList>
+  <instrumentConfigurationList count="1">
+    <instrumentConfiguration id="LTQFTUltra0">
+      <cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra"/>
+      <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/>
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+        <source order="1">
+          <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization"/>
+          <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet"/>
+          <cvParam cvRef="MS" accession="MS:1000844" name="focus diameter x" value="10.0"/>
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+        </source>
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+        </analyzer>
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+          <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier"/>
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+        </detector>
+      </componentList>
+      <softwareRef ref="Xcalibur"/>
+    </instrumentConfiguration>
+  </instrumentConfigurationList>
+  <dataProcessingList count="2">
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+    </dataProcessing>
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+        <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML"/>
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+    </dataProcessing>
+  </dataProcessingList>
+  <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
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+        </scanList>
+        <binaryDataArrayList count="2">
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+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=2" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="1">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="182.31835420101888"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
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+            <referenceableParamGroupRef ref="mzArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=3" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="2">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="161.8091904482675"/>
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+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=4" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="3">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="200.9633277092539"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=5" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="4">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="135.30584173158496"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
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+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=6" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="5">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="108.39597418421639"/>
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+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
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+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
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+        </scanList>
+        <binaryDataArrayList count="2">
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+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=7" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="6">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="127.84664447846832"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
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+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
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+        <referenceableParamGroupRef ref="spectrum1"/>
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+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
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+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
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+          </binaryDataArray>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=9" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="8">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="243.5395066031077"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+    </spectrumList>
+  </run>
+</mzML>
diff --git a/lib/galaxy/datatypes/test/dosimzml b/lib/galaxy/datatypes/test/dosimzml
new file mode 100644
index 00000000000..6ff4f5c078d
--- /dev/null
+++ b/lib/galaxy/datatypes/test/dosimzml
@@ -0,0 +1,380 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" xmlns="http://psi.hupo.org/ms/mzml" version="1.1">
+  <cvList count="4">
+    <cv URI="http://ontologies.berkeleybop.org/pato.obo" fullName="Phenotype And Trait Ontology" id="PATO" version="releases/2017-07-10"/>
+    <cv URI="http://ontologies.berkeleybop.org/uo.obo" fullName="Units of Measurement Ontology" id="UO" version="releases/2017-09-25"/>
+    <cv URI="https://raw.githubusercontent.com/hupo-psi/psi-ms-cv/master/psi-ms.obo" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" id="MS" version="4.1.0"/>
+    <cv URI="https://raw.githubusercontent.com/imzML/imzML/master/imagingMS.obo" fullName="Mass Spectrometry Imaging Ontology" id="IMS" version="1.1.0"/>
+  </cvList>
+  <fileDescription>
+    <fileContent>
+      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
+      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
+      <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9d501bdc53444916b7e97e795b02c856"/>
+      <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7e8fdb93053915d3edb51b70aa0619ac209964df"/>
+      <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
+    </fileContent>
+    <sourceFileList count="1">
+      <sourceFile id="sf1" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\" name="Example.raw">
+        <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format"/>
+        <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/>
+        <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
+      </sourceFile>
+    </sourceFileList>
+    <contact>
+      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
+      <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Institut für Anorganische und Analytische Chemie"/>
+      <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/>
+      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
+    </contact>
+  </fileDescription>
+  <referenceableParamGroupList count="4">
+    <referenceableParamGroup id="mzArray">
+      <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
+      <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
+      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="intensityArray">
+      <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
+      <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
+      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
+      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="scan1">
+      <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan"/>
+      <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="spectrum1">
+      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
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+      <cvParam cvRef="MS" accession="MS:1000129" name="negative scan"/>
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+  <sampleList count="1">
+    <sample id="sample1" name="Sample1">
+      <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
+    </sample>
+  </sampleList>
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+      <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
+    </scanSettings>
+  </scanSettingsList>
+  <instrumentConfigurationList count="1">
+    <instrumentConfiguration id="LTQFTUltra0">
+      <cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra"/>
+      <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/>
+      <componentList count="3">
+        <source order="1">
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+        <analyzer order="2">
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+    </instrumentConfiguration>
+  </instrumentConfigurationList>
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+    <dataProcessing id="TMCConversion">
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+        <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML"/>
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+  </dataProcessingList>
+  <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
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+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=2" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="1">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="182.31835420101888"/>
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+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
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+        </scanList>
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+      </spectrum>
+      <spectrum id="Scan=3" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="2">
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+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=4" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="3">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="200.9633277092539"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=5" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="4">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="135.30584173158496"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=6" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="5">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="108.39597418421639"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=7" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="6">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="127.84664447846832"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
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+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=8" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="7">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="168.27018147522492"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="Scan=9" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="8">
+        <referenceableParamGroupRef ref="spectrum1"/>
+        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="243.5395066031077"/>
+        <scanList count="1">
+          <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
+          <scan instrumentConfigurationRef="LTQFTUltra0">
+            <referenceableParamGroupRef ref="scan1"/>
+            <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
+            <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="mzArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+          <binaryDataArray encodedLength="0">
+            <referenceableParamGroupRef ref="intensityArray"/>
+            <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
+            <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>
+            <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
+            <binary />
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+    </spectrumList>
+  </run>
+</mzML>
diff --git a/lib/galaxy/datatypes/test/gis.geojson b/lib/galaxy/datatypes/test/gis.geojson
new file mode 100644
index 00000000000..ebe0b5d4071
--- /dev/null
+++ b/lib/galaxy/datatypes/test/gis.geojson
@@ -0,0 +1,44 @@
+{
+  "type": "FeatureCollection",
+  "features": [
+    {
+      "type": "Feature",
+      "geometry": {
+        "type": "Point",
+        "coordinates": [102.0, 0.5]
+      },
+      "properties": {
+        "prop0": "value0"
+      }
+    },
+    {
+      "type": "Feature",
+      "geometry": {
+        "type": "LineString",
+        "coordinates": [
+          [102.0, 0.0], [103.0, 1.0], [104.0, 0.0], [105.0, 1.0]
+        ]
+      },
+      "properties": {
+        "prop0": "value0",
+        "prop1": 0.0
+      }
+    },
+    {
+      "type": "Feature",
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [100.0, 0.0], [101.0, 0.0], [101.0, 1.0],
+            [100.0, 1.0], [100.0, 0.0]
+          ]
+        ]
+      },
+      "properties": {
+        "prop0": "value0",
+        "prop1": { "this": "that" }
+      }
+    }
+  ]
+}
diff --git a/lib/galaxy/datatypes/test/matrix.mcool b/lib/galaxy/datatypes/test/matrix.mcool
new file mode 100644
index 00000000000..bf42ef345fe
Binary files /dev/null and b/lib/galaxy/datatypes/test/matrix.mcool differ
diff --git a/lib/galaxy/datatypes/test/vcf_gzipped.vcf.gz b/lib/galaxy/datatypes/test/vcf_gzipped.vcf.gz
new file mode 100644
index 00000000000..67e5ea92790
Binary files /dev/null and b/lib/galaxy/datatypes/test/vcf_gzipped.vcf.gz differ
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index fab7ef0469c..3964696ff4e 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -15,7 +15,11 @@ from six.moves import shlex_quote
 from galaxy.datatypes.data import get_file_peek, Text
 from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
 from galaxy.datatypes.sniff import build_sniff_from_prefix, iter_headers
-from galaxy.util import nice_size, string_as_bool
+from galaxy.util import (
+    nice_size,
+    string_as_bool,
+    unicodify,
+)
 
 log = logging.getLogger(__name__)
 
@@ -363,6 +367,53 @@ class ImgtJson(Json):
                     return
 
 
+@build_sniff_from_prefix
+class GeoJson(Json):
+    """
+        GeoJSON is a geospatial data interchange format based on JavaScript Object Notation (JSON).
+        https://tools.ietf.org/html/rfc7946
+    """
+    file_ext = "geojson"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        super(GeoJson, self).set_peek(dataset)
+        if not dataset.dataset.purged:
+            dataset.blurb = "GeoJSON"
+
+    def sniff_prefix(self, file_prefix):
+        """
+        Determines whether the file is in json format with imgt elements
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname( '1.json' )
+        >>> GeoJson().sniff( fname )
+        False
+        >>> fname = get_test_fname( 'gis.geojson' )
+        >>> GeoJson().sniff( fname )
+        True
+        """
+        is_geojson = False
+        if self._looks_like_json(file_prefix):
+            is_geojson = self._looks_like_geojson(file_prefix)
+        return is_geojson
+
+    def _looks_like_geojson(self, file_prefix, load_size=5000):
+        """
+        One of "Point", "MultiPoint", "LineString", "MultiLineString", "Polygon", "MultiPolygon", and "GeometryCollection" needs to be present.
+        All of "type", "geometry", and "coordinates" needs to be present.
+        """
+        is_geojson = False
+        try:
+            with open(file_prefix.filename, "r") as fh:
+                segment_str = fh.read(load_size)
+                if any(x in segment_str for x in ["Point", "MultiPoint", "LineString", "MultiLineString", "Polygon", "MultiPolygon", "GeometryCollection"]):
+                    if all(x in segment_str for x in ["type", "geometry", "coordinates"]):
+                        return True
+        except Exception:
+            pass
+        return is_geojson
+
+
 @build_sniff_from_prefix
 class Obo(Text):
     """
@@ -637,12 +688,12 @@ class SnpSiftDbNSFP(Text):
                                 headers = lines[0].split('\t')
                                 dataset.metadata.annotation = headers[4:]
                         except Exception as e:
-                            log.warning("set_meta fname: %s  %s" % (fname, str(e)))
+                            log.warning("set_meta fname: %s  %s", fname, unicodify(e))
                     if fname.endswith('.tbi'):
                         dataset.metadata.index = fname
             self.regenerate_primary_file(dataset)
         except Exception as e:
-            log.warning("set_meta fname: %s  %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
+            log.warning("set_meta fname: %s  %s", dataset.file_name if dataset and dataset.file_name else 'Unkwown', unicodify(e))
 
         def set_peek(self, dataset, is_multi_byte=False):
             if not dataset.dataset.purged:
diff --git a/lib/galaxy/datatypes/upload_util.py b/lib/galaxy/datatypes/upload_util.py
index 84d2c8c8560..7f8168a11e0 100644
--- a/lib/galaxy/datatypes/upload_util.py
+++ b/lib/galaxy/datatypes/upload_util.py
@@ -54,7 +54,7 @@ def handle_upload(
                 convert_spaces_to_tabs=convert_spaces_to_tabs,
             )
         except sniff.InappropriateDatasetContentError as exc:
-            raise UploadProblemException(str(exc))
+            raise UploadProblemException(exc)
     elif requested_ext == 'auto':
         ext = sniff.guess_ext(path, registry.sniff_order, is_binary=is_binary)
     else:
diff --git a/lib/galaxy/datatypes/util/gff_util.py b/lib/galaxy/datatypes/util/gff_util.py
index 1d17a0c2b32..1e64e9ef2f8 100644
--- a/lib/galaxy/datatypes/util/gff_util.py
+++ b/lib/galaxy/datatypes/util/gff_util.py
@@ -6,6 +6,7 @@ import copy
 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper, ParseError
 from bx.tabular.io import Comment, Header
 
+from galaxy.util import unicodify
 from galaxy.util.odict import odict
 
 FASTA_DIRECTIVE = '##FASTA'
@@ -171,7 +172,7 @@ class GFFReaderWrapper(NiceReaderWrapper):
             self.skipped += 1
             # no reason to stuff an entire bad file into memmory
             if self.skipped < 10:
-                self.skipped_lines.append((self.linenum, self.current_line, str(e)))
+                self.skipped_lines.append((self.linenum, self.current_line, unicodify(e)))
 
             # For debugging, uncomment this to propogate parsing exceptions up.
             # I.e. the underlying reason for an unexpected StopIteration exception
diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 06162cf7b96..e3c614ecdb0 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -34,20 +34,47 @@ class ConditionalDependencies(object):
 
     def parse_configs(self):
         self.config = load_app_properties(config_file=self.config_file)
-        job_conf_xml = self.config.get(
-            "job_config_file",
-            join(dirname(self.config_file), 'job_conf.xml'))
-        try:
-            for plugin in ElementTree.parse(job_conf_xml).find('plugins').findall('plugin'):
-                if 'load' in plugin.attrib:
-                    self.job_runners.append(plugin.attrib['load'])
-        except (OSError, IOError):
-            pass
-        try:
-            for plugin in ElementTree.parse(job_conf_xml).findall('.//destination/param[@id="rules_module"]'):
-                self.job_rule_modules.append(plugin.text)
-        except (OSError, IOError):
-            pass
+
+        def load_job_config_dict(job_conf_dict):
+            for runner in job_conf_dict.get("runners"):
+                if "load" in runner:
+                    self.job_runners.append(runner.get("load"))
+                if "rules_module" in runner:
+                    self.job_rule_modules.append(plugin.text)
+                if "params" in runner:
+                    runner_params = runner["params"]
+                    if "rules_module" in runner_params:
+                        self.job_rule_modules.append(plugin.text)
+
+        if "job_config" in self.config:
+            load_job_config_dict(self.config.get("job_config"))
+        else:
+            job_conf_path = self.config.get(
+                "job_config_file",
+                join(dirname(self.config_file), 'job_conf.xml'))
+            if '.xml' in job_conf_path:
+                try:
+                    try:
+                        for plugin in ElementTree.parse(job_conf_path).find('plugins').findall('plugin'):
+                            if 'load' in plugin.attrib:
+                                self.job_runners.append(plugin.attrib['load'])
+                    except (OSError, IOError):
+                        pass
+                    try:
+                        for plugin in ElementTree.parse(job_conf_path).findall('.//destination/param[@id="rules_module"]'):
+                            self.job_rule_modules.append(plugin.text)
+                    except (OSError, IOError):
+                        pass
+                except ElementTree.ParseError:
+                    pass
+            else:
+                try:
+                    with open("job_conf_path", "r") as f:
+                        job_conf_dict = yaml.safe_load(f)
+                    load_job_config_dict(job_conf_dict)
+                except (OSError, IOError):
+                    pass
+
         object_store_conf_xml = self.config.get(
             "object_store_config_file",
             join(dirname(self.config_file), 'object_store_conf.xml'))
diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index 6741c925615..8980b46000a 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -15,6 +15,7 @@ mock = "*"
 NoseHTML = "*"
 pygithub3 = {version = "*", markers = "python_version < '3'"}
 pytest = "*"
+pytest-cov = "*"
 pytest-html = "*"
 pytest-pythonpath = "*"
 pytest-postgresql = "*"
@@ -75,8 +76,8 @@ pyparsing = "*"
 "Fabric3" = "*"
 paramiko = "*"
 python-genomespaceclient = "<2.0"
-social_auth_core = {version = "==3.1.0", extras = ['openidconnect']}
-cloudauthz = "<=0.2.0"
+social_auth_core = {version = "==3.1.0+gx0", extras = ['openidconnect']}
+cloudauthz = "<=0.4.0"
 gxformat2 = "*"
 
 [requires]
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 64d6a17b4ad..bb14cf2fbde 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -4,45 +4,49 @@ alabaster==0.7.12
 argh==0.26.2
 atomicwrites==1.3.0
 attrs==19.1.0
-babel==2.6.0
-certifi==2019.3.9
+babel==2.7.0
+certifi==2019.6.16
 chardet==3.0.4
-commonmark==0.8.1
+commonmark==0.9.0
+configparser==3.7.4 ; python_version < '3.2'
+contextlib2==0.5.5 ; python_version < '3.5'
+coverage==4.5.3
 docutils==0.14
 funcsigs==1.0.2 ; python_version < '3.3'
 future==0.17.1
 gunicorn==19.9.0
 idna==2.8
 imagesize==1.1.0
+importlib-metadata==0.18
 jinja2==2.10.1
-lxml==4.3.3
+lxml==4.3.4
 markdown==2.6.11
 markupsafe==1.1.1
 mirakuru==1.1.0
-mock==2.0.0
+mock==3.0.5
 more-itertools==5.0.0
 nose==1.3.7
 nosehtml==0.4.5
 packaging==19.0
 pathlib2==2.3.2 ; python_version < '3'
 pathtools==0.1.2
-pbr==5.1.3
-pluggy==0.9.0
+pluggy==0.12.0
 port-for==0.4
-psutil==5.6.1
+psutil==5.6.3
 py==1.8.0
 pygithub3==0.5.1 ; python_version < '3'
-pygments==2.3.1
+pygments==2.4.2
 pyparsing==2.4.0
+pytest-cov==2.7.1
 pytest-html==1.20.0
 pytest-metadata==1.8.0
-pytest-postgresql==1.4.0
+pytest-postgresql==1.4.1
 pytest-pythonpath==0.7.3
-pytest==4.4.0
+pytest==4.6.3
 pytz==2019.1
-pyyaml==5.1
+pyyaml==5.1.1
 recommonmark==0.5.0
-requests==2.21.0
+requests==2.22.0
 scandir==1.10.0 ; python_version < '3.5'
 selenium==3.141.0
 six==1.11.0
@@ -50,9 +54,11 @@ snowballstemmer==1.2.1
 sphinx-markdown-tables==0.0.9
 sphinx-rtd-theme==0.4.3
 sphinx==1.8.5
-sphinxcontrib-websupport==1.1.0
-testfixtures==6.7.0
+sphinxcontrib-websupport==1.1.2
+testfixtures==6.9.0
 twill==0.9.1 ; python_version < '3'
 typing==3.6.6 ; python_version < '3.5'
-urllib3==1.24.1 ; python_version == '2.7'
+urllib3==1.25.3 ; python_version == '2.7'
 watchdog==0.9.0
+wcwidth==0.1.7 ; sys_platform != 'win32'
+zipp==0.5.1
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 0277247d436..8a4e6c136ad 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -1,9 +1,10 @@
 -i https://wheels.galaxyproject.org/simple
 --extra-index-url https://pypi.python.org/simple
 adal==1.2.1
-amqp==2.4.2
+amqp==2.5.0
 appdirs==1.4.3
 asn1crypto==0.24.0
+attrs==19.1.0
 avro==1.8.1 ; python_version < '3'
 azure-common==1.1.14
 azure-cosmosdb-nspkg==2.0.2
@@ -16,9 +17,9 @@ azure-mgmt-resource==2.0.0
 azure-mgmt-storage==2.0.0
 azure-nspkg==3.0.2
 azure-storage-blob==1.3.1
-azure-storage-common==1.4.0
+azure-storage-common==1.4.2
 azure-storage-nspkg==3.1.0
-babel==2.6.0
+babel==2.7.0
 bagit==1.6.4
 bcrypt==3.1.6
 bdbag==1.4.1
@@ -28,21 +29,21 @@ bleach==3.1.0
 boltons==19.1.0
 boto3==1.9.114
 boto==2.49.0
-botocore==1.12.130
+botocore==1.12.169
 bx-python==0.8.2
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
-cachetools==3.1.0
-certifi==2019.3.9
-cffi==1.12.2
+cachetools==3.1.1
+certifi==2019.6.16
+cffi==1.12.3
 chardet==3.0.4
-cheetah3==3.2.1
-cliff==2.14.1
-cloudauthz==0.2.0
+cheetah3==3.2.3
+cliff==2.15.0
+cloudauthz==0.4.0
 cloudbridge==2.0.0
 cmd2==0.8.9
 contextlib2==0.5.5 ; python_version < '3.5'
-cryptography==2.6.1
+cryptography==2.7
 cwltool==1.0.20180721142728
 debtcollector==1.21.0
 decorator==4.4.0
@@ -52,7 +53,7 @@ dictobj==0.4
 docopt==0.6.2
 docutils==0.14
 dogpile.cache==0.7.1
-ecdsa==0.13
+ecdsa==0.13.2
 enum34==1.1.6 ; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2 ; python_version < '3.3'
@@ -63,9 +64,9 @@ galaxy-sequence-utils==1.1.3
 google-api-python-client==1.7.8
 google-auth-httplib2==0.0.3
 google-auth==1.6.3
-gxformat2==0.8.2
+gxformat2==0.8.3
 h5py==2.9.0
-httplib2==0.12.1
+httplib2==0.13.0
 idna==2.8
 ipaddress==1.0.22 ; python_version < '3.3'
 isa-rwval==0.10.7
@@ -74,12 +75,12 @@ isodate==0.6.0
 jmespath==0.9.4
 jsonpatch==1.23
 jsonpointer==2.0
-jsonschema==2.6.0
-keystoneauth1==3.13.1
-kombu==4.5.0
+jsonschema==3.0.1
+keystoneauth1==3.14.0
+kombu==4.6.3
 lockfile==0.12.2
-lxml==4.3.3
-mako==1.0.9
+lxml==4.3.4
+mako==1.0.12
 markupsafe==1.1.1
 mercurial==3.7.3 ; python_version < '3'
 mistune==0.8.4
@@ -94,35 +95,35 @@ netifaces==0.10.9
 networkx==1.11
 nodeenv==1.3.3
 nose==1.3.7
-numpy==1.16.2
+numpy==1.16.4
 oauth2client==4.1.3
 oauthlib==3.0.1
 openstacksdk==0.17.0
 os-client-config==1.32.0
-os-service-types==1.6.0
+os-service-types==1.7.0
 osc-lib==1.12.1
-oslo.config==6.8.1
+oslo.config==6.10.0
 oslo.context==2.22.1
 oslo.i18n==3.23.1
-oslo.log==3.42.3
-oslo.serialization==2.28.2
-oslo.utils==3.40.3
+oslo.log==3.44.0
+oslo.serialization==2.29.1
+oslo.utils==3.41.0
 packaging==19.0
-paramiko==2.4.2
+paramiko==2.5.0
 parsley==1.3
 paste==3.0.8
 pastedeploy==2.0.1
 pastescript==3.1.0
 pathlib2==2.3.2 ; python_version < '3'
-pbr==5.1.3
+pbr==5.3.0
 prettytable==0.7.2
 prov==1.5.1
-psutil==5.6.1
-pulsar-galaxy-lib==0.9.0
-pyasn1-modules==0.2.4
+psutil==5.6.3
+pulsar-galaxy-lib==0.12.1
+pyasn1-modules==0.2.5
 pyasn1==0.4.5
 pycparser==2.19
-pycryptodome==3.8.1
+pycryptodome==3.8.2
 pyeventsystem==0.1.0
 pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
 pyjwt==1.7.1
@@ -131,6 +132,7 @@ pynacl==1.3.0
 pyopenssl==19.0.0
 pyparsing==2.4.0
 pyperclip==1.7.0
+pyrsistent==0.15.2
 pysam==0.15.2
 pysftp==0.2.9
 python-cinderclient==4.0.0
@@ -144,32 +146,32 @@ python-novaclient==11.0.0
 python-openid==2.2.5 ; python_version < '3.0'
 python-swiftclient==3.6.0
 pytz==2019.1
-pyyaml==5.1
+pyyaml==5.1.1
 rdflib-jsonld==0.4.0
 rdflib==4.2.2
 repoze.lru==0.7
 requests-oauthlib==1.2.0
 requests-toolbelt==0.9.1
-requests==2.21.0
+requests==2.22.0
 requestsexceptions==1.4.0
-rfc3986==1.2.0
+rfc3986==1.3.2
 routes==2.4.1
 rsa==4.0
 ruamel.ordereddict==0.4.13 ; platform_python_implementation == 'CPython' and python_version <= '2.7'
-ruamel.yaml==0.15.91
-s3transfer==0.2.0
+ruamel.yaml==0.15.97
+s3transfer==0.2.1
 scandir==1.10.0 ; python_version < '3.5'
 schema-salad==2.7.20181126142424
 shellescape==3.4.1
 simplejson==3.16.0
 six==1.11.0
-social-auth-core[openidconnect]==3.1.0
+social-auth-core[openidconnect]==3.1.0+gx0
 sqlalchemy-migrate==0.12.0
-sqlalchemy-utils==0.33.11
-sqlalchemy==1.2.18
+sqlalchemy-utils==0.34.0
+sqlalchemy==1.3.4
 sqlparse==0.3.0
 stevedore==1.30.1
-subprocess32==3.5.3 ; python_version < '3.0'
+subprocess32==3.5.4 ; python_version < '3.0'
 svgwrite==1.2.1
 tempita==0.5.2
 tenacity==4.12.0
@@ -178,10 +180,10 @@ typing==3.6.6 ; python_version < '3.5'
 tzlocal==1.5.1
 unicodecsv==0.14.1 ; python_version < '3.0'
 uritemplate==3.0.0
-urllib3==1.24.1 ; python_version == '2.7'
+urllib3==1.25.3 ; python_version == '2.7'
 uwsgi==2.0.18
 vine==1.3.0
-warlock==1.3.0
+warlock==1.3.3
 wcwidth==0.1.7 ; sys_platform != 'win32'
 webencodings==0.5.1
 webob==1.8.5
diff --git a/lib/galaxy/dependencies/pipfiles/update.sh b/lib/galaxy/dependencies/pipfiles/update.sh
index ff67d81805c..edafb36cb7e 100755
--- a/lib/galaxy/dependencies/pipfiles/update.sh
+++ b/lib/galaxy/dependencies/pipfiles/update.sh
@@ -65,6 +65,7 @@ for env in $ENVS; do
                 -e "s/^futures==\([^ ;]\{1,\}\).*$/futures==\1 ; python_version == '2.6' or python_version == '2.7'/" \
                 -e "s/^monotonic==\([^ ;]\{1,\}\).*$/monotonic==\1/" \
                 -e "s/^more-itertools==\([^ ;]\{1,\}\).*$/more-itertools==\1/" \
+                -e "s/^paste==\([^ ;]\{1,\}\).*$/paste==\1/" \
                 -e "s/^py2-ipaddress==\([^ ;]\{1,\}\).*$/py2-ipaddress==\1 ; python_version < '3'/" \
                 -e "s/^pyinotify==\([^ ;]\{1,\}\).*$/pyinotify==\1 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'/" \
                 -e "s/^python-dateutil==\([^ ;]\{1,\}\).*$/python-dateutil==\1/" \
diff --git a/lib/galaxy/tools/deps/mulled/__init__.py b/lib/galaxy/job_execution/__init__.py
similarity index 100%
rename from lib/galaxy/tools/deps/mulled/__init__.py
rename to lib/galaxy/job_execution/__init__.py
diff --git a/lib/galaxy/jobs/datasets.py b/lib/galaxy/job_execution/datasets.py
similarity index 100%
rename from lib/galaxy/jobs/datasets.py
rename to lib/galaxy/job_execution/datasets.py
diff --git a/lib/galaxy/tools/parameters/output_collect.py b/lib/galaxy/job_execution/output_collect.py
similarity index 88%
rename from lib/galaxy/tools/parameters/output_collect.py
rename to lib/galaxy/job_execution/output_collect.py
index caca15031cd..d670e3faada 100644
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/job_execution/output_collect.py
@@ -4,6 +4,7 @@ import logging
 import operator
 import os
 import re
+from tempfile import NamedTemporaryFile
 
 import galaxy.model
 from galaxy.model.dataset_collections import builder
@@ -20,13 +21,14 @@ from galaxy.model.store.discover import (
     RegexCollectedDatasetMatch,
     UNSET,
 )
-from galaxy.tools.parser.output_collection_def import (
+from galaxy.tool_util.parser.output_collection_def import (
     DEFAULT_DATASET_COLLECTOR_DESCRIPTION,
     INPUT_DBKEY_TOKEN,
     ToolProvidedMetadataDatasetCollection,
 )
 from galaxy.util import (
-    odict
+    odict,
+    unicodify
 )
 
 DATASET_ID_TOKEN = "DATASET_ID"
@@ -316,6 +318,7 @@ def collect_primary_datasets(job_context, output, input_ext):
                 extra_files_path = new_primary_datasets_attributes.get('extra_files', None)
                 if extra_files_path:
                     extra_files_path_joined = os.path.join(job_working_directory, extra_files_path)
+                    primary_data.dataset.create_extra_files_path()
                     for root, dirs, files in os.walk(extra_files_path_joined):
                         extra_dir = os.path.join(primary_data.extra_files_path, root.replace(extra_files_path_joined, '', 1).lstrip(os.path.sep))
                         extra_dir = os.path.normpath(extra_dir)
@@ -417,7 +420,7 @@ class DatasetCollector(object):
     def __init__(self, dataset_collection_description):
         self.discover_via = dataset_collection_description.discover_via
         # dataset_collection_description is an abstract description
-        # built from the tool parsing module - see galaxy.tools.parser.output_colleciton_def
+        # built from the tool parsing module - see galaxy.tool_util.parser.output_colleciton_def
         self.sort_key = dataset_collection_description.sort_key
         self.sort_reverse = dataset_collection_description.sort_reverse
         self.sort_comp = dataset_collection_description.sort_comp
@@ -462,3 +465,63 @@ def _compose(f, g):
 
 DEFAULT_DATASET_COLLECTOR = DatasetCollector(DEFAULT_DATASET_COLLECTOR_DESCRIPTION)
 DEFAULT_TOOL_PROVIDED_DATASET_COLLECTOR = ToolMetadataDatasetCollector(ToolProvidedMetadataDatasetCollection())
+
+
+def read_exit_code_from(exit_code_file, id_tag):
+    """Read exit code reported for a Galaxy job."""
+    try:
+        # This should be an 8-bit exit code, but read ahead anyway:
+        exit_code_str = open(exit_code_file, "r").read(32)
+    except Exception:
+        # By default, the exit code is 0, which typically indicates success.
+        exit_code_str = "0"
+
+    try:
+        # Decode the exit code. If it's bogus, then just use 0.
+        exit_code = int(exit_code_str)
+    except ValueError:
+        galaxy_id_tag = id_tag
+        log.warning("(%s) Exit code '%s' invalid. Using 0." % (galaxy_id_tag, exit_code_str))
+        exit_code = 0
+
+    return exit_code
+
+
+def default_exit_code_file(files_dir, id_tag):
+    return os.path.join(files_dir, 'galaxy_%s.ec' % id_tag)
+
+
+def collect_extra_files(object_store, dataset, job_working_directory):
+    store_by = getattr(object_store, "store_by", "id")
+    file_name = "dataset_%s_files" % getattr(dataset.dataset, store_by)
+    temp_file_path = os.path.join(job_working_directory, file_name)
+    extra_dir = None
+    try:
+        # This skips creation of directories - object store
+        # automatically creates them.  However, empty directories will
+        # not be created in the object store at all, which might be a
+        # problem.
+        for root, dirs, files in os.walk(temp_file_path):
+            extra_dir = root.replace(job_working_directory, '', 1).lstrip(os.path.sep)
+            for f in files:
+                object_store.update_from_file(
+                    dataset.dataset,
+                    extra_dir=extra_dir,
+                    alt_name=f,
+                    file_name=os.path.join(root, f),
+                    create=True,
+                    preserve_symlinks=True
+                )
+    except Exception as e:
+        log.debug("Error in collect_associated_files: %s", unicodify(e))
+
+    # Handle composite datatypes of auto_primary_file type
+    if dataset.datatype.composite_type == 'auto_primary_file' and not dataset.has_data():
+        try:
+            with NamedTemporaryFile(mode='w') as temp_fh:
+                temp_fh.write(dataset.datatype.generate_primary_file(dataset))
+                temp_fh.flush()
+                object_store.update_from_file(dataset.dataset, file_name=temp_fh.name, create=True)
+                dataset.set_size()
+        except Exception as e:
+            log.warning('Unable to generate primary composite file automatically for %s: %s', dataset.dataset.id, unicodify(e))
diff --git a/lib/galaxy/jobs/metrics/__init__.py b/lib/galaxy/job_metrics/__init__.py
similarity index 93%
rename from lib/galaxy/jobs/metrics/__init__.py
rename to lib/galaxy/job_metrics/__init__.py
index 14413a8ab1d..83f3c026ca6 100644
--- a/lib/galaxy/jobs/metrics/__init__.py
+++ b/lib/galaxy/job_metrics/__init__.py
@@ -16,7 +16,7 @@ import os
 
 from galaxy import util
 from galaxy.util import plugin_config
-from ..metrics import formatting
+from ..job_metrics import formatting
 
 log = logging.getLogger(__name__)
 
@@ -59,8 +59,8 @@ class JobMetrics(object):
         return self.job_instrumenters[destination_id].collect_properties(job_id, job_directory)
 
     def __plugins_dict(self):
-        import galaxy.jobs.metrics.instrumenters
-        return plugin_config.plugins_dict(galaxy.jobs.metrics.instrumenters, 'plugin_type')
+        import galaxy.job_metrics.instrumenters
+        return plugin_config.plugins_dict(galaxy.job_metrics.instrumenters, 'plugin_type')
 
 
 class NullJobInstrumenter(object):
@@ -108,15 +108,15 @@ class JobInstrumenter(object):
         return "\n".join([c for c in commands if c])
 
     def collect_properties(self, job_id, job_directory):
-        per_plugin_properites = {}
+        per_plugin_properties = {}
         for plugin in self.plugins:
             try:
                 properties = plugin.job_properties(job_id, job_directory)
                 if properties:
-                    per_plugin_properites[plugin.plugin_type] = properties
+                    per_plugin_properties[plugin.plugin_type] = properties
             except Exception:
                 log.exception("Failed to collect job properties for plugin %s", plugin)
-        return per_plugin_properites
+        return per_plugin_properties
 
     def __plugins_from_source(self, plugins_source):
         return plugin_config.load_plugins(self.plugin_classes, plugins_source, self.extra_kwargs)
diff --git a/lib/galaxy/jobs/metrics/collectl/__init__.py b/lib/galaxy/job_metrics/collectl/__init__.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/collectl/__init__.py
rename to lib/galaxy/job_metrics/collectl/__init__.py
diff --git a/lib/galaxy/jobs/metrics/collectl/cli.py b/lib/galaxy/job_metrics/collectl/cli.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/collectl/cli.py
rename to lib/galaxy/job_metrics/collectl/cli.py
diff --git a/lib/galaxy/jobs/metrics/collectl/processes.py b/lib/galaxy/job_metrics/collectl/processes.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/collectl/processes.py
rename to lib/galaxy/job_metrics/collectl/processes.py
diff --git a/lib/galaxy/jobs/metrics/collectl/stats.py b/lib/galaxy/job_metrics/collectl/stats.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/collectl/stats.py
rename to lib/galaxy/job_metrics/collectl/stats.py
diff --git a/lib/galaxy/jobs/metrics/collectl/subsystems.py b/lib/galaxy/job_metrics/collectl/subsystems.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/collectl/subsystems.py
rename to lib/galaxy/job_metrics/collectl/subsystems.py
diff --git a/lib/galaxy/jobs/metrics/formatting.py b/lib/galaxy/job_metrics/formatting.py
similarity index 68%
rename from lib/galaxy/jobs/metrics/formatting.py
rename to lib/galaxy/job_metrics/formatting.py
index 6bda18418c2..0e0ce11fbc3 100644
--- a/lib/galaxy/jobs/metrics/formatting.py
+++ b/lib/galaxy/job_metrics/formatting.py
@@ -11,8 +11,8 @@ class JobMetricFormatter(object):
 def seconds_to_str(value):
     """Convert seconds to a simple simple string describing the amount of time."""
     if value < 60:
-        return "%s seconds" % value
+        return "%s seconds" % round(value, 2)
     elif value < 3600:
-        return "%s minutes" % (value / 60)
+        return "%s minutes" % round(value / 60, 2)
     else:
-        return "%s hours and %s minutes" % (value / 3600, (value % 3600) / 60)
+        return "%s hours and %s minutes" % (round(value / 3600, 2), round((value % 3600) / 60, 2))
diff --git a/lib/galaxy/jobs/metrics/instrumenters/__init__.py b/lib/galaxy/job_metrics/instrumenters/__init__.py
similarity index 98%
rename from lib/galaxy/jobs/metrics/instrumenters/__init__.py
rename to lib/galaxy/job_metrics/instrumenters/__init__.py
index 952ec6f4b55..9137ffc9020 100644
--- a/lib/galaxy/jobs/metrics/instrumenters/__init__.py
+++ b/lib/galaxy/job_metrics/instrumenters/__init__.py
@@ -10,7 +10,7 @@ from abc import (
 
 import six
 
-from ...metrics import formatting
+from .. import formatting
 
 INSTRUMENT_FILE_PREFIX = "__instrument"
 
diff --git a/lib/galaxy/jobs/metrics/instrumenters/cgroup.py b/lib/galaxy/job_metrics/instrumenters/cgroup.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/instrumenters/cgroup.py
rename to lib/galaxy/job_metrics/instrumenters/cgroup.py
diff --git a/lib/galaxy/jobs/metrics/instrumenters/collectl.py b/lib/galaxy/job_metrics/instrumenters/collectl.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/instrumenters/collectl.py
rename to lib/galaxy/job_metrics/instrumenters/collectl.py
diff --git a/lib/galaxy/jobs/metrics/instrumenters/core.py b/lib/galaxy/job_metrics/instrumenters/core.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/instrumenters/core.py
rename to lib/galaxy/job_metrics/instrumenters/core.py
diff --git a/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py b/lib/galaxy/job_metrics/instrumenters/cpuinfo.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
rename to lib/galaxy/job_metrics/instrumenters/cpuinfo.py
diff --git a/lib/galaxy/jobs/metrics/instrumenters/env.py b/lib/galaxy/job_metrics/instrumenters/env.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/instrumenters/env.py
rename to lib/galaxy/job_metrics/instrumenters/env.py
diff --git a/lib/galaxy/jobs/metrics/instrumenters/hostname.py b/lib/galaxy/job_metrics/instrumenters/hostname.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/instrumenters/hostname.py
rename to lib/galaxy/job_metrics/instrumenters/hostname.py
diff --git a/lib/galaxy/jobs/metrics/instrumenters/meminfo.py b/lib/galaxy/job_metrics/instrumenters/meminfo.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/instrumenters/meminfo.py
rename to lib/galaxy/job_metrics/instrumenters/meminfo.py
diff --git a/lib/galaxy/jobs/metrics/instrumenters/uname.py b/lib/galaxy/job_metrics/instrumenters/uname.py
similarity index 100%
rename from lib/galaxy/jobs/metrics/instrumenters/uname.py
rename to lib/galaxy/job_metrics/instrumenters/uname.py
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index e3460c38fc8..7ec38255bb9 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -16,29 +16,35 @@ import time
 import traceback
 from abc import ABCMeta, abstractmethod
 from json import loads
-from tempfile import NamedTemporaryFile
 from xml.etree import ElementTree
 
 import six
+import yaml
 from pulsar.client.staging import COMMAND_VERSION_FILENAME
 
 import galaxy
 from galaxy import model, util
 from galaxy.datatypes import sniff
 from galaxy.exceptions import ObjectInvalid, ObjectNotFound
+from galaxy.job_execution.datasets import (
+    DatasetPath,
+    NullDatasetPathRewriter,
+    OutputsToWorkingDirectoryPathRewriter,
+    TaskPathRewriter
+)
+from galaxy.job_execution.output_collect import collect_extra_files
 from galaxy.jobs.actions.post import ActionBox
-from galaxy.jobs.mapper import JobRunnerMapper
+from galaxy.jobs.mapper import JobMappingException, JobRunnerMapper
 from galaxy.jobs.runners import BaseJobRunner, JobState
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.objectstore import ObjectStorePopulator
+from galaxy.tool_util.deps import requirements
+from galaxy.tool_util.output_checker import check_output, DETECTED_JOB_STATE
 from galaxy.util import safe_makedirs, unicodify
 from galaxy.util.bunch import Bunch
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.xml_macros import load
-from galaxy.web.stack.handlers import ConfiguresHandlers
-from .datasets import (DatasetPath, NullDatasetPathRewriter,
-    OutputsToWorkingDirectoryPathRewriter, TaskPathRewriter)
-from .output_checker import check_output, DETECTED_JOB_STATE
+from galaxy.web_stack.handlers import ConfiguresHandlers
 
 log = logging.getLogger(__name__)
 
@@ -46,7 +52,7 @@ log = logging.getLogger(__name__)
 # that import Galaxy internals - but it shouldn't be used in Galaxy's code
 # itself.
 TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json'
-TOOL_PROVIDED_JOB_METADATA_KEYS = ['name', 'info', 'dbkey']
+TOOL_PROVIDED_JOB_METADATA_KEYS = ['name', 'info', 'dbkey', 'created_from_basename']
 
 # Override with config.default_job_shell.
 DEFAULT_JOB_SHELL = '/bin/bash'
@@ -80,10 +86,6 @@ class JobDestination(Bunch):
 
         super(JobDestination, self).__init__(**kwds)
 
-        # Store tags as a list
-        if self.tags is not None:
-            self['tags'] = [x.strip() for x in self.tags.split(',')]
-
 
 class JobToolConfiguration(Bunch):
     """
@@ -112,6 +114,139 @@ def config_exception(e, file):
     return Exception(message)
 
 
+def job_config_xml_to_dict(config, root):
+    config_dict = {}
+
+    runners = {}
+    config_dict["runners"] = runners
+
+    # Parser plugins section populate 'runners' and 'dynamic' in config_dict.
+    plugins = root.find('plugins')
+    if plugins is not None:
+        for plugin in ConfiguresHandlers._findall_with_required(plugins, 'plugin', ('id', 'type', 'load')):
+            if plugin.get('type') == 'runner':
+                workers = plugin.get('workers', plugins.get('workers', JobConfiguration.DEFAULT_NWORKERS))
+                runner_kwds = JobConfiguration.get_params(config, plugin)
+                plugin_id = plugin.get('id')
+                runner_info = dict(id=plugin_id,
+                                   load=plugin.get('load'),
+                                   workers=int(workers),
+                                   kwds=runner_kwds)
+                runners[plugin_id] = runner_info
+            else:
+                log.error('Unknown plugin type: %s' % plugin.get('type'))
+
+        for plugin in ConfiguresHandlers._findall_with_required(plugins, 'plugin', ('id', 'type')):
+            if plugin.get('id') == 'dynamic' and plugin.get('type') == 'runner':
+                config_dict["dynamic"] = JobConfiguration.get_params(config, plugin)
+
+    handling_config_dict = ConfiguresHandlers.xml_to_dict(config, root.find("handlers"))
+    config_dict["handling"] = handling_config_dict
+
+    # Parse destinations
+    environments = []
+
+    destinations = root.find('destinations')
+    for destination in ConfiguresHandlers._findall_with_required(destinations, 'destination', ('id', 'runner')):
+        destination_id = destination.get('id')
+        destination_metrics = destination.get("metrics", None)
+
+        environment = {"id": destination_id}
+
+        metrics_to_dict = {"src": "default"}
+        if destination_metrics:
+            if not util.asbool(destination_metrics):
+                metrics_to_dict = {"src": "disabled"}
+            else:
+                metrics_to_dict = {"src": "path", "path": destination_metrics}
+        else:
+            metrics_elements = ConfiguresHandlers._findall_with_required(destination, 'job_metrics', ())
+            if metrics_elements:
+                metrics_to_dict = {"src": "xml_element", 'xml_element': metrics_elements[0]}
+
+        environment["metrics"] = metrics_to_dict
+
+        params = JobConfiguration.get_params(config, destination)
+        # TODO: handle enabled/disabled in configure_from
+        environment['params'] = params
+        environment['env'] = JobConfiguration.get_envs(destination)
+        destination_resubmits = JobConfiguration.get_resubmits(destination)
+        if destination_resubmits:
+            environment['resubmit'] = destination_resubmits
+        # TODO: handle empty resubmits defaults in configure_from
+
+        runner = destination.get('runner')
+        if runner:
+            environment['runner'] = runner
+
+        tags = destination.get('tags')
+        # Store tags as a list
+        if tags is not None:
+            tags = [x.strip() for x in tags.split(',')]
+            environment['tags'] = tags
+
+        environments.append(environment)
+
+    config_dict['execution'] = {
+        'environments': environments,
+    }
+    default_destination = ConfiguresHandlers.get_xml_default(config, destinations)
+    if default_destination:
+        config_dict['execution']['default'] = default_destination
+
+    resources_config_dict = {}
+    resource_groups = {}
+
+    # Parse resources...
+    resources = root.find('resources')
+    if resources is not None:
+        default_resource_group = resources.get("default", None)
+        if default_resource_group:
+            resources_config_dict["default"] = default_resource_group
+
+        for group in ConfiguresHandlers._findall_with_required(resources, 'group'):
+            group_id = group.get('id')
+            fields_str = group.get('fields', None) or group.text or ''
+            fields = [f for f in fields_str.split(",") if f]
+            resource_groups[group_id] = fields
+
+    resources_config_dict["groups"] = resource_groups
+    config_dict["resources"] = resources_config_dict
+
+    # Parse tool mappings
+    tools = root.find('tools')
+    config_dict['tools'] = []
+    if tools is not None:
+        for tool in ConfiguresHandlers._findall_with_required(tools, 'tool'):
+            # There can be multiple definitions with identical ids, but different params
+            tool_mapping_conf = {}
+            for key in ['handler', 'destination', 'id', 'resources']:
+                value = tool.get(key)
+                if value:
+                    if key == "destination":
+                        key = "environment"
+                    tool_mapping_conf[key] = value
+            tool_mapping_conf["params"] = JobConfiguration.get_params(config, tool)
+            config_dict['tools'].append(tool_mapping_conf)
+
+    limits_config = []
+    limits = root.find('limits')
+    if limits is not None:
+        for limit in JobConfiguration._findall_with_required(limits, 'limit', ('type',)):
+            limit_dict = {}
+            for key in ['type', 'tag', 'id', 'window']:
+                if key == 'type' and key.startswith('destination_'):
+                    key = 'environment_%s' % key[len("destination_"):]
+                value = limit.get(key)
+                if value:
+                    limit_dict[key] = value
+                limit_dict['value'] = limit.text
+            limits_config.append(limit_dict)
+
+    config_dict['limits'] = limits_config
+    return config_dict
+
+
 class JobConfiguration(ConfiguresHandlers):
     """A parser and interface to advanced job management features.
 
@@ -141,7 +276,7 @@ class JobConfiguration(ConfiguresHandlers):
         self.default_handler_id = None
         self.handler_assignment_methods = None
         self.handler_assignment_methods_configured = False
-        self.handler_max_grab = 1
+        self.handler_max_grab = None
         self.destinations = {}
         self.destination_tags = {}
         self.default_destination_id = None
@@ -162,7 +297,7 @@ class JobConfiguration(ConfiguresHandlers):
         default_resubmit_condition = self.app.config.default_job_resubmission_condition
         if default_resubmit_condition:
             default_resubmits.append(dict(
-                destination=None,
+                environment=None,
                 condition=default_resubmit_condition,
                 handler=None,
                 delay=None,
@@ -171,10 +306,26 @@ class JobConfiguration(ConfiguresHandlers):
 
         self.__parse_resource_parameters()
         # Initialize the config
-        job_config_file = self.app.config.job_config_file
         try:
-            tree = load(job_config_file)
-            self.__parse_job_conf_xml(tree)
+            if 'job_config' in self.app.config.config_dict:
+                job_config_dict = self.app.config.config_dict["job_config"]
+            else:
+                job_config_file = self.app.config.job_config_file
+                if '.xml' in job_config_file:
+                    tree = load(job_config_file)
+                    job_config_dict = self.__parse_job_conf_xml(tree)
+                else:
+                    with open(job_config_file, "r") as f:
+                        job_config_dict = yaml.safe_load(f)
+
+            # Load tasks if configured
+            if self.app.config.use_tasked_jobs:
+                job_config_dict["runners"]["tasks"] = dict(id='tasks', load='tasks', workers=self.app.config.local_task_queue_workers, kwds={})
+
+            self._configure_from_dict(job_config_dict)
+
+            log.debug('Done loading job configuration')
+
         except IOError:
             log.warning('Job configuration "%s" does not exist, using default job configuration',
                         self.app.config.job_config_file)
@@ -182,43 +333,33 @@ class JobConfiguration(ConfiguresHandlers):
         except Exception as e:
             raise config_exception(e, job_config_file)
 
-    def __parse_job_conf_xml(self, tree):
-        """Loads the new-style job configuration from options in the job config file (by default, job_conf.xml).
-
-        :param tree: Object representing the root ``<job_conf>`` object in the job config file.
-        :type tree: ``xml.etree.ElementTree.Element``
-        """
-        root = tree.getroot()
-        log.debug('Loading job configuration from %s' % self.app.config.job_config_file)
-
-        # Parse job plugins
-        plugins = root.find('plugins')
-        if plugins is not None:
-            for plugin in self._findall_with_required(plugins, 'plugin', ('id', 'type', 'load')):
-                if plugin.get('type') == 'runner':
-                    workers = plugin.get('workers', plugins.get('workers', JobConfiguration.DEFAULT_NWORKERS))
-                    runner_kwds = self.__get_params(plugin)
-                    if not self.__is_enabled(runner_kwds):
+    def _configure_from_dict(self, job_config_dict):
+        for runner_id, runner_info in job_config_dict["runners"].items():
+            if "kwds" not in runner_info:
+                # convert all 'extra' parameters into kwds, allows defining a runner
+                # with a flat dictionary.
+                kwds = {}
+                for key, value in runner_info.items():
+                    if key in ['id', 'load', 'workers']:
                         continue
-                    runner_info = dict(id=plugin.get('id'),
-                                       load=plugin.get('load'),
-                                       workers=int(workers),
-                                       kwds=runner_kwds)
-                    self.runner_plugins.append(runner_info)
-                else:
-                    log.error('Unknown plugin type: %s' % plugin.get('type'))
-            for plugin in self._findall_with_required(plugins, 'plugin', ('id', 'type')):
-                if plugin.get('id') == 'dynamic' and plugin.get('type') == 'runner':
-                    self.dynamic_params = self.__get_params(plugin)
+                    kwds[key] = value
+                runner_info["kwds"] = kwds
 
-        # Load tasks if configured
-        if self.app.config.use_tasked_jobs:
-            self.runner_plugins.append(dict(id='tasks', load='tasks', workers=self.app.config.local_task_queue_workers))
+            if not self.__is_enabled(runner_info.get("kwds")):
+                continue
+            runner_info["id"] = runner_id
+            if runner_id == "dynamic":
+                log.warning('Deprecated treatment of dynamic running configuration as an actual job runner.')
+                self.dynamic_params = runner_info["kwds"]
+                continue
+            self.runner_plugins.append(runner_info)
+        if "dynamic" in job_config_dict:
+            self.dynamic_params = job_config_dict.get("dynamic", None)
 
         # Parse handlers
-        handlers_conf = root.find('handlers')
-        self._init_handler_assignment_methods(handlers_conf)
-        self._init_handlers(handlers_conf)
+        handling_config_dict = job_config_dict.get("handling", {})
+        self._init_handler_assignment_methods(handling_config_dict)
+        self._init_handlers(handling_config_dict)
         if not self.handler_assignment_methods_configured:
             self._set_default_handler_assignment_methods()
         else:
@@ -227,38 +368,51 @@ class JobConfiguration(ConfiguresHandlers):
         for tag, handlers in [(t, h) for t, h in self.handlers.items() if isinstance(h, list)]:
             log.info("Tag [%s] handlers: %s", tag, ', '.join(handlers))
 
-        # Parse destinations
-        destinations = root.find('destinations')
+        # Parse environments
         job_metrics = self.app.job_metrics
-        for destination in self._findall_with_required(destinations, 'destination', ('id', 'runner')):
-            id = destination.get('id')
-            destination_metrics = destination.get("metrics", None)
-            if destination_metrics:
-                if not util.asbool(destination_metrics):
-                    # disable
-                    job_metrics.set_destination_instrumenter(id, None)
-                else:
-                    metrics_conf_path = self.app.config.resolve_path(destination_metrics)
-                    job_metrics.set_destination_conf_file(id, metrics_conf_path)
-            else:
-                metrics_elements = self._findall_with_required(destination, 'job_metrics', ())
-                if metrics_elements:
-                    job_metrics.set_destination_conf_element(id, metrics_elements[0])
-            job_destination = JobDestination(**dict(destination.items()))
-            params = self.__get_params(destination)
-            if not self.__is_enabled(params):
+        execution_dict = job_config_dict.get('execution', {})
+        environments = execution_dict.get("environments", [])
+        enviroment_iter = map(lambda e: (e["id"], e), environments) if isinstance(environments, list) else environments.items()
+        for environment_id, environment_dict in enviroment_iter:
+            metrics = environment_dict.get("metrics") or {"src": "default"}
+            metrics_src = metrics.get("src") or "default"
+            if metrics_src != "default":
+                # customized metrics for this environment.
+                if metrics_src == "disabled":
+                    job_metrics.set_destination_instrumenter(environment_id, None)
+                elif metrics_src == "xml_element":
+                    metrics_element = metrics.get("xml_element")
+                    job_metrics.set_destination_conf_element(environment_id, metrics_element)
+                elif metrics_src == "path":
+                    metrics_conf_path = self.app.config.resolve_path(metrics.get("path"))
+                    job_metrics.set_destination_conf_file(environment_id, metrics_conf_path)
+
+            destination_kwds = {}
+
+            params = environment_dict.get("params")
+            if params is None:
+                # Treat the excess keys in the environment as the destination parameters
+                # allowing a flat configuration of these things.
+                params = {}
+                for key, value in environment_dict.items():
+                    if key in ['id', 'tags', 'runner', 'shell', 'env', 'resubmit']:
+                        continue
+                    params[key] = value
+                environment_dict["params"] = params
+
+            for key in ['tags', 'runner', 'shell', 'env', 'resubmit', 'params']:
+                if key in environment_dict:
+                    destination_kwds[key] = environment_dict[key]
+            destination_kwds["id"] = environment_id
+            job_destination = JobDestination(**destination_kwds)
+            if not self.__is_enabled(job_destination.params):
                 continue
 
-            job_destination['params'] = params
-            job_destination['env'] = self.__get_envs(destination)
-            destination_resubmits = self.__get_resubmits(destination)
-            if destination_resubmits:
-                resubmits = destination_resubmits
-            else:
+            if not job_destination.resubmit:
                 resubmits = self.default_resubmits
-            job_destination["resubmit"] = resubmits
+                job_destination.resubmit = resubmits
 
-            self.destinations[id] = (job_destination,)
+            self.destinations[environment_id] = (job_destination,)
             if job_destination.tags is not None:
                 for tag in job_destination.tags:
                     if tag not in self.destinations:
@@ -266,29 +420,30 @@ class JobConfiguration(ConfiguresHandlers):
                     self.destinations[tag].append(job_destination)
 
         # Determine the default destination
-        self.default_destination_id = self._get_default(
-            self.app.config, destinations, list(self.destinations.keys()), auto=True)
+        self.default_destination_id = self._ensure_default_set(execution_dict.get("default"), list(self.destinations.keys()), auto=True)
 
-        # Parse resources...
-        resources = root.find('resources')
-        if resources is not None:
-            self.default_resource_group = resources.get("default", None)
-            for group in self._findall_with_required(resources, 'group'):
-                id = group.get('id')
-                fields_str = group.get('fields', None) or group.text or ''
-                fields = [f for f in fields_str.split(",") if f]
-                self.resource_groups[id] = fields
+        # Read in resources
+        resources = job_config_dict.get("resources", {})
+        self.default_resource_group = resources.get("default", None)
+        for group_id, fields in resources.get("groups", {}).items():
+            self.resource_groups[group_id] = fields
 
-        # Parse tool mappings
-        tools = root.find('tools')
-        if tools is not None:
-            for tool in self._findall_with_required(tools, 'tool'):
-                # There can be multiple definitions with identical ids, but different params
-                id = tool.get('id').lower().rstrip('/')
-                if id not in self.tools:
-                    self.tools[id] = list()
-                self.tools[id].append(JobToolConfiguration(**dict(tool.items())))
-                self.tools[id][-1]['params'] = self.__get_params(tool)
+        tools = job_config_dict.get('tools', [])
+        for tool in tools:
+            tool_id = tool.get('id').lower().rstrip('/')
+            if tool_id not in self.tools:
+                self.tools[tool_id] = list()
+            params = tool.get("params")
+            if params is None:
+                params = {}
+                for key, value in tool.items():
+                    if key in ["environment", "handler", "id"]:
+                        continue
+                    params[key] = value
+                tool["params"] = params
+            if "environment" in tool:
+                tool["destination"] = tool.pop("environment")
+            self.tools[tool_id].append(JobToolConfiguration(**dict(tool.items())))
 
         types = dict(registered_user_concurrent_jobs=int,
                      anonymous_user_concurrent_jobs=int,
@@ -297,26 +452,28 @@ class JobConfiguration(ConfiguresHandlers):
                      output_size=util.size_to_bytes)
 
         # Parse job limits
-        limits = root.find('limits')
-        if limits is not None:
-            for limit in self._findall_with_required(limits, 'limit', ('type',)):
-                type = limit.get('type')
-                # concurrent_jobs renamed to destination_user_concurrent_jobs in job_conf.xml
-                if type in ('destination_user_concurrent_jobs', 'concurrent_jobs', 'destination_total_concurrent_jobs'):
-                    id = limit.get('tag', None) or limit.get('id')
-                    if type == 'destination_total_concurrent_jobs':
-                        self.limits.destination_total_concurrent_jobs[id] = int(limit.text)
-                    else:
-                        self.limits.destination_user_concurrent_jobs[id] = int(limit.text)
-                elif type == 'total_walltime':
-                    self.limits.total_walltime["window"] = (
-                        int(limit.get('window')) or 30
-                    )
-                    self.limits.total_walltime["raw"] = (
-                        types.get(type, str)(limit.text)
-                    )
-                elif limit.text:
-                    self.limits.__dict__[type] = types.get(type, str)(limit.text)
+        for limit_dict in job_config_dict.get("limits", []):
+            limit_type = limit_dict.get('type')
+            if limit_type.startswith("environment_"):
+                limit_type = 'destination_%s' % limit_type[len("environment_"):]
+
+            limit_value = limit_dict.get("value")
+            # concurrent_jobs renamed to destination_user_concurrent_jobs in job_conf.xml
+            if limit_type in ('destination_user_concurrent_jobs', 'concurrent_jobs', 'destination_total_concurrent_jobs'):
+                id = limit_dict.get('tag', None) or limit_dict.get('id')
+                if limit_type == 'destination_total_concurrent_jobs':
+                    self.limits.destination_total_concurrent_jobs[id] = int(limit_value)
+                else:
+                    self.limits.destination_user_concurrent_jobs[id] = int(limit_value)
+            elif limit_type == 'total_walltime':
+                self.limits.total_walltime["window"] = (
+                    int(limit_dict.get('window')) or 30
+                )
+                self.limits.total_walltime["raw"] = (
+                    types.get(limit_type, str)(limit_value)
+                )
+            elif limit_value:
+                self.limits.__dict__[limit_type] = types.get(limit_type, str)(limit_value)
 
         if self.limits.walltime is not None:
             h, m, s = [int(v) for v in self.limits.walltime.split(':')]
@@ -329,13 +486,23 @@ class JobConfiguration(ConfiguresHandlers):
                 0, s, 0, 0, m, h
             )
 
-        log.debug('Done loading job configuration')
+    def __parse_job_conf_xml(self, tree):
+        """Loads the new-style job configuration from options in the job config file (by default, job_conf.xml).
 
-    def _parse_handler(self, handler_id, handler_element):
-        for plugin in handler_element.findall('plugin'):
+        :param tree: Object representing the root ``<job_conf>`` object in the job config file.
+        :type tree: ``xml.etree.ElementTree.Element``
+        """
+        root = tree.getroot()
+        log.debug('Loading job configuration from %s' % self.app.config.job_config_file)
+
+        job_config_dict = job_config_xml_to_dict(self.app.config, root)
+        return job_config_dict
+
+    def _parse_handler(self, handler_id, process_dict):
+        for plugin_id in process_dict.get("plugins") or []:
             if handler_id not in self.handler_runner_plugins:
                 self.handler_runner_plugins[handler_id] = []
-            self.handler_runner_plugins[handler_id].append(plugin.get('id'))
+            self.handler_runner_plugins[handler_id].append(plugin_id)
 
     def __set_default_job_conf(self):
         # Run jobs locally
@@ -383,19 +550,12 @@ class JobConfiguration(ConfiguresHandlers):
     def __parse_resource_parameters(self):
         self.resource_parameters = util.parse_resource_parameters(self.app.config.job_resource_params_file)
 
-    def __get_params(self, parent):
-        """Parses any child <param> tags in to a dictionary suitable for persistence.
-
-        :param parent: Parent element in which to find child <param> tags.
-        :type parent: ``xml.etree.ElementTree.Element``
-
-        :returns: dict
-        """
+    @staticmethod
+    def get_params(config, parent):
         rval = {}
         for param in parent.findall('param'):
             key = param.get('id')
             if key in ["container", "container_override"]:
-                from galaxy.tools.deps import requirements
                 containers = map(requirements.container_from_element, param.findall('container'))
                 param_value = list(map(lambda c: c.to_dict(), containers))
             else:
@@ -406,12 +566,23 @@ class JobConfiguration(ConfiguresHandlers):
                 param_value = os.environ.get(environ_var, param_value)
             elif 'from_config' in param.attrib:
                 config_val = param.attrib['from_config']
-                param_value = self.app.config.config_dict.get(config_val, param_value)
+                param_value = config.config_dict.get(config_val, param_value)
 
             rval[key] = param_value
         return rval
 
-    def __get_envs(self, parent):
+    def __get_params(self, parent):
+        """Parses any child <param> tags in to a dictionary suitable for persistence.
+
+        :param parent: Parent element in which to find child <param> tags.
+        :type parent: ``xml.etree.ElementTree.Element``
+
+        :returns: dict
+        """
+        return JobConfiguration.get_params(self.app.config, parent)
+
+    @staticmethod
+    def get_envs(parent):
         """Parses any child <env> tags in to a dictionary suitable for persistence.
 
         :param parent: Parent element in which to find child <env> tags.
@@ -430,7 +601,8 @@ class JobConfiguration(ConfiguresHandlers):
             ))
         return rval
 
-    def __get_resubmits(self, parent):
+    @staticmethod
+    def get_resubmits(parent):
         """Parses any child <resubmit> tags in to a dictionary suitable for persistence.
 
         :param parent: Parent element in which to find child <resubmit> tags.
@@ -442,7 +614,7 @@ class JobConfiguration(ConfiguresHandlers):
         for resubmit in parent.findall('resubmit'):
             rval.append(dict(
                 condition=resubmit.get('condition'),
-                destination=resubmit.get('destination'),
+                environment=resubmit.get('destination'),
                 handler=resubmit.get('handler'),
                 delay=resubmit.get('delay'),
             ))
@@ -451,7 +623,7 @@ class JobConfiguration(ConfiguresHandlers):
     def __is_enabled(self, params):
         """Check for an enabled parameter - pop it out - and return as boolean."""
         enabled = True
-        if "enabled" in params:
+        if "enabled" in (params or {}):
             raw_enabled = params.pop("enabled")
             enabled = util.asbool(raw_enabled)
 
@@ -596,7 +768,7 @@ class JobConfiguration(ConfiguresHandlers):
                     log.warning("Job runner classes must be subclassed from BaseJobRunner, %s has bases: %s" % (id, runner_class.__bases__))
                     continue
                 try:
-                    rval[id] = runner_class(self.app, runner['workers'], **runner.get('kwds', {}))
+                    rval[id] = runner_class(self.app, runner.get('workers', JobConfiguration.DEFAULT_NWORKERS), **runner.get('kwds', {}))
                 except TypeError:
                     log.exception("Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load",
                                   module_name, class_name)
@@ -703,7 +875,7 @@ class JobWrapper(HasResourceParameters):
         self.output_hdas_and_paths = None
         self.tool_provided_job_metadata = None
         # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
-        self.external_output_metadata = get_metadata_compute_strategy(self.app, job.id)
+        self.external_output_metadata = get_metadata_compute_strategy(self.app.config, job.id)
         self.job_runner_mapper = JobRunnerMapper(self, queue.dispatcher.url_to_destination, self.app.job_config)
         self.params = None
         if job.params:
@@ -749,6 +921,10 @@ class JobWrapper(HasResourceParameters):
     def requires_containerization(self):
         return util.asbool(self.get_destination_configuration("require_container", "False"))
 
+    @property
+    def use_metadata_binary(self):
+        return util.asbool(self.get_destination_configuration('use_metadata_binary', "False"))
+
     def can_split(self):
         # Should the job handler split this job up?
         return self.app.config.use_tasked_jobs and self.tool.parallelism
@@ -922,6 +1098,10 @@ class JobWrapper(HasResourceParameters):
                 job, base_dir='job_work', dir_only=True, obj_dir=True)
         return self.__working_directory
 
+    def working_directory_exists(self):
+        job = self.get_job()
+        return self.app.object_store.exists(job, base_dir='job_work', dir_only=True, obj_dir=True)
+
     @property
     def tool_working_directory(self):
         return os.path.join(self.working_directory, "working")
@@ -994,6 +1174,21 @@ class JobWrapper(HasResourceParameters):
         """
         job = self.get_job()
         self.sa_session.refresh(job)
+
+        # If this fail method is being called because a dynamic rule raised JobMappingException, the call to
+        # self.get_destination_configuration() below accesses self.job_destination and will just cause
+        # JobMappingException to be raised again.
+        try:
+            self.job_destination
+        except JobMappingException as exc:
+            log.debug("(%s) fail(): Job destination raised JobMappingException('%s'), caching fake '__fail__' "
+                      "destination for completion of fail method", self.get_id_tag(), unicodify(exc.failure_message))
+            self.job_runner_mapper.cached_job_destination = JobDestination(id='__fail__')
+
+        # Might be AssertionError or other exception
+        message = str(message)
+        working_directory_exists = self.working_directory_exists()
+
         # if the job was deleted, don't fail it
         if not job.state == job.states.DELETED:
             # Check if the failure is due to an exception
@@ -1006,13 +1201,13 @@ class JobWrapper(HasResourceParameters):
                 etype, evalue, tb = sys.exc_info()
 
             outputs_to_working_directory = util.asbool(self.get_destination_configuration("outputs_to_working_directory", False))
-            if outputs_to_working_directory and not self.__link_file_check():
+            if outputs_to_working_directory and not self.__link_file_check() and working_directory_exists:
                 for dataset_path in self.get_output_fnames():
                     try:
                         shutil.move(dataset_path.false_path, dataset_path.real_path)
-                        log.debug("fail(): Moved %s to %s" % (dataset_path.false_path, dataset_path.real_path))
+                        log.debug("fail(): Moved %s to %s", dataset_path.false_path, dataset_path.real_path)
                     except (IOError, OSError) as e:
-                        log.error("fail(): Missing output file in working directory: %s" % e)
+                        log.error("fail(): Missing output file in working directory: %s", unicodify(e))
             for dataset_assoc in job.output_datasets + job.output_library_datasets:
                 dataset = dataset_assoc.dataset
                 self.sa_session.refresh(dataset)
@@ -1049,7 +1244,8 @@ class JobWrapper(HasResourceParameters):
                 # the partial files to the object store regardless of whether job.state == DELETED
                 self.__update_output(job, dataset, clean_only=True)
 
-        self._fix_output_permissions()
+        if working_directory_exists:
+            self._fix_output_permissions()
         self._report_error()
         # Perform email action even on failure.
         for pja in [pjaa.post_job_action for pjaa in job.post_job_actions if pjaa.post_job_action.action_type == "EmailAction"]:
@@ -1211,6 +1407,87 @@ class JobWrapper(HasResourceParameters):
         job.object_store_id = object_store_populator.object_store_id
         self._setup_working_directory(job=job)
 
+    def _finish_dataset(self, output_name, dataset, job, context, final_job_state, remote_metadata_directory):
+        implicit_collection_jobs = job.implicit_collection_jobs_association
+        purged = dataset.dataset.purged
+        if not purged and dataset.dataset.external_filename is None:
+            trynum = 0
+            while trynum < self.app.config.retry_job_output_collection:
+                try:
+                    # Attempt to short circuit NFS attribute caching
+                    os.stat(dataset.dataset.file_name)
+                    os.chown(dataset.dataset.file_name, os.getuid(), -1)
+                    trynum = self.app.config.retry_job_output_collection
+                except (OSError, ObjectNotFound) as e:
+                    trynum += 1
+                    log.warning('Error accessing dataset with ID %i, will retry: %s', dataset.dataset.id, unicodify(e))
+                    time.sleep(2)
+        if getattr(dataset, "hidden_beneath_collection_instance", None):
+            dataset.visible = False
+        dataset.blurb = 'done'
+        dataset.peek = 'no peek'
+        dataset.info = (dataset.info or '')
+        if context['stdout'].strip():
+            # Ensure white space between entries
+            dataset.info = dataset.info.rstrip() + "\n" + context['stdout'].strip()
+        if context['stderr'].strip():
+            # Ensure white space between entries
+            dataset.info = dataset.info.rstrip() + "\n" + context['stderr'].strip()
+        dataset.tool_version = self.version_string
+        dataset.set_size()
+        if 'uuid' in context:
+            dataset.dataset.uuid = context['uuid']
+        self.__update_output(job, dataset)
+        if not purged:
+            collect_extra_files(self.object_store, dataset, self.working_directory)
+        if job.states.ERROR == final_job_state:
+            dataset.blurb = "error"
+            if not implicit_collection_jobs:
+                # Only unhide dataset outputs that are not part of a implicit collection
+                dataset.mark_unhidden()
+        elif not purged:
+            # If the tool was expected to set the extension, attempt to retrieve it
+            if dataset.ext == 'auto':
+                dataset.extension = context.get('ext', 'data')
+                dataset.init_meta(copy_from=dataset)
+            # if a dataset was copied, it won't appear in our dictionary:
+            # either use the metadata from originating output dataset, or call set_meta on the copies
+            # it would be quicker to just copy the metadata from the originating output dataset,
+            # but somewhat trickier (need to recurse up the copied_from tree), for now we'll call set_meta()
+            retry_internally = util.asbool(self.get_destination_configuration("retry_metadata_internally", True))
+            metadata_set_successfully = self.external_output_metadata.external_metadata_set_successfully(dataset, output_name, self.sa_session, working_directory=self.working_directory)
+            if retry_internally and not metadata_set_successfully:
+                # If Galaxy was expected to sniff type and didn't - do so.
+                if dataset.ext == "_sniff_":
+                    extension = sniff.handle_uploaded_dataset_file(dataset.dataset.file_name, self.app.datatypes_registry)
+                    dataset.extension = extension
+
+                # call datatype.set_meta directly for the initial set_meta call during dataset creation
+                dataset.datatype.set_meta(dataset, overwrite=False)
+            elif (job.states.ERROR != final_job_state and not metadata_set_successfully):
+                dataset._state = model.Dataset.states.FAILED_METADATA
+            else:
+                self.external_output_metadata.load_metadata(dataset, output_name, self.sa_session, working_directory=self.working_directory, remote_metadata_directory=remote_metadata_directory)
+            line_count = context.get('line_count', None)
+            try:
+                # Certain datatype's set_peek methods contain a line_count argument
+                dataset.set_peek(line_count=line_count)
+            except TypeError:
+                # ... and others don't
+                dataset.set_peek()
+        else:
+            # Handle purged datasets.
+            dataset.blurb = "empty"
+            if dataset.ext == 'auto':
+                dataset.extension = context.get('ext', 'txt')
+
+        for context_key in TOOL_PROVIDED_JOB_METADATA_KEYS:
+            if context_key in context:
+                context_value = context[context_key]
+                setattr(dataset, context_key, context_value)
+
+        self.sa_session.add(dataset)
+
     def finish(
         self,
         tool_stdout,
@@ -1220,6 +1497,7 @@ class JobWrapper(HasResourceParameters):
         job_stderr=None,
         check_output_detected_state=None,
         remote_metadata_directory=None,
+        job_metrics_directory=None,
     ):
         """
         Called to indicate that the associated command has been run. Updates
@@ -1274,7 +1552,8 @@ class JobWrapper(HasResourceParameters):
             if not os.path.exists(version_filename):
                 version_filename = self.get_version_string_path_legacy()
             if os.path.exists(version_filename):
-                self.version_string = open(version_filename).read()
+                with open(version_filename, 'rb') as fh:
+                    self.version_string = galaxy.util.shrink_and_unicodify(fh.read())
                 os.unlink(version_filename)
 
         outputs_to_working_directory = util.asbool(self.get_destination_configuration("outputs_to_working_directory", False))
@@ -1296,101 +1575,15 @@ class JobWrapper(HasResourceParameters):
                         return self.fail("Job %s's output dataset(s) could not be read" % job.id)
 
         job_context = ExpressionContext(dict(stdout=job.stdout, stderr=job.stderr))
-        implicit_collection_jobs = job.implicit_collection_jobs_association
         for dataset_assoc in job.output_datasets + job.output_library_datasets:
             context = self.get_dataset_finish_context(job_context, dataset_assoc)
             # should this also be checking library associations? - can a library item be added from a history before the job has ended? -
             # lets not allow this to occur
             # need to update all associated output hdas, i.e. history was shared with job running
             for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations:
-                purged = dataset.dataset.purged
-                if not purged and dataset.dataset.external_filename is None:
-                    trynum = 0
-                    while trynum < self.app.config.retry_job_output_collection:
-                        try:
-                            # Attempt to short circuit NFS attribute caching
-                            os.stat(dataset.dataset.file_name)
-                            os.chown(dataset.dataset.file_name, os.getuid(), -1)
-                            trynum = self.app.config.retry_job_output_collection
-                        except (OSError, ObjectNotFound) as e:
-                            trynum += 1
-                            log.warning('Error accessing dataset with ID %i, will retry: %s', dataset.dataset.id, e)
-                            time.sleep(2)
-                if getattr(dataset, "hidden_beneath_collection_instance", None):
-                    dataset.visible = False
-                dataset.blurb = 'done'
-                dataset.peek = 'no peek'
-                dataset.info = (dataset.info or '')
-                if context['stdout'].strip():
-                    # Ensure white space between entries
-                    dataset.info = dataset.info.rstrip() + "\n" + context['stdout'].strip()
-                if context['stderr'].strip():
-                    # Ensure white space between entries
-                    dataset.info = dataset.info.rstrip() + "\n" + context['stderr'].strip()
-                dataset.tool_version = self.version_string
-                dataset.set_size()
-                if 'uuid' in context:
-                    dataset.dataset.uuid = context['uuid']
-                self.__update_output(job, dataset)
-                if not purged:
-                    self._collect_extra_files(dataset.dataset, self.working_directory)
-                # Handle composite datatypes of auto_primary_file type
-                if dataset.datatype.composite_type == 'auto_primary_file' and not dataset.has_data():
-                    try:
-                        with NamedTemporaryFile() as temp_fh:
-                            temp_fh.write(dataset.datatype.generate_primary_file(dataset))
-                            temp_fh.flush()
-                            self.object_store.update_from_file(dataset.dataset, file_name=temp_fh.name, create=True)
-                            dataset.set_size()
-                    except Exception as e:
-                        log.warning('Unable to generate primary composite file automatically for %s: %s', dataset.dataset.id, e)
-                if job.states.ERROR == final_job_state:
-                    dataset.blurb = "error"
-                    if not implicit_collection_jobs:
-                        # Only unhide dataset outputs that are not part of a implicit collection
-                        dataset.mark_unhidden()
-                elif not purged:
-                    # If the tool was expected to set the extension, attempt to retrieve it
-                    if dataset.ext == 'auto':
-                        dataset.extension = context.get('ext', 'data')
-                        dataset.init_meta(copy_from=dataset)
-                    # if a dataset was copied, it won't appear in our dictionary:
-                    # either use the metadata from originating output dataset, or call set_meta on the copies
-                    # it would be quicker to just copy the metadata from the originating output dataset,
-                    # but somewhat trickier (need to recurse up the copied_from tree), for now we'll call set_meta()
-                    retry_internally = util.asbool(self.get_destination_configuration("retry_metadata_internally", True))
-                    metadata_set_successfully = self.external_output_metadata.external_metadata_set_successfully(dataset, dataset_assoc.name, self.sa_session, working_directory=self.working_directory)
-                    if retry_internally and not metadata_set_successfully:
-                        # If Galaxy was expected to sniff type and didn't - do so.
-                        if dataset.ext == "_sniff_":
-                            extension = sniff.handle_uploaded_dataset_file(dataset.dataset.file_name, self.app.datatypes_registry)
-                            dataset.extension = extension
-
-                        # call datatype.set_meta directly for the initial set_meta call during dataset creation
-                        dataset.datatype.set_meta(dataset, overwrite=False)
-                    elif (job.states.ERROR != final_job_state and not metadata_set_successfully):
-                        dataset._state = model.Dataset.states.FAILED_METADATA
-                    else:
-                        self.external_output_metadata.load_metadata(dataset, dataset_assoc.name, self.sa_session, working_directory=self.working_directory, remote_metadata_directory=remote_metadata_directory)
-                    line_count = context.get('line_count', None)
-                    try:
-                        # Certain datatype's set_peek methods contain a line_count argument
-                        dataset.set_peek(line_count=line_count)
-                    except TypeError:
-                        # ... and others don't
-                        dataset.set_peek()
-                else:
-                    # Handle purged datasets.
-                    dataset.blurb = "empty"
-                    if dataset.ext == 'auto':
-                        dataset.extension = context.get('ext', 'txt')
-
-                for context_key in TOOL_PROVIDED_JOB_METADATA_KEYS:
-                    if context_key in context:
-                        context_value = context[context_key]
-                        setattr(dataset, context_key, context_value)
-
-                self.sa_session.add(dataset)
+                self._finish_dataset(
+                    dataset_assoc.name, dataset, job, context, final_job_state, remote_metadata_directory
+                )
             if job.states.ERROR == final_job_state:
                 log.debug("(%s) setting dataset %s state to ERROR", job.id, dataset_assoc.dataset.dataset.id)
                 # TODO: This is where the state is being set to error. Change it!
@@ -1459,7 +1652,7 @@ class JobWrapper(HasResourceParameters):
         job.set_final_state(final_job_state)
         if not job.tasks:
             # If job was composed of tasks, don't attempt to recollect statisitcs
-            self._collect_metrics(job)
+            self._collect_metrics(job, job_metrics_directory)
         self.sa_session.flush()
         log.debug('job %d ended (finish() executed in %s)' % (self.job_id, finish_timer))
         if job.state == job.states.ERROR:
@@ -1521,36 +1714,12 @@ class JobWrapper(HasResourceParameters):
         except Exception:
             log.exception("Unable to cleanup job %d", self.job_id)
 
-    def _collect_extra_files(self, dataset, job_working_directory):
-        object_store = self.app.object_store
-        store_by = getattr(object_store, "store_by", "id")
-        file_name = "dataset_%s_files" % getattr(dataset, store_by)
-        temp_file_path = os.path.join(job_working_directory, file_name)
-        extra_dir = None
-        try:
-            # This skips creation of directories - object store
-            # automatically creates them.  However, empty directories will
-            # not be created in the object store at all, which might be a
-            # problem.
-            for root, dirs, files in os.walk(temp_file_path):
-                extra_dir = root.replace(job_working_directory, '', 1).lstrip(os.path.sep)
-                for f in files:
-                    self.object_store.update_from_file(
-                        dataset,
-                        extra_dir=extra_dir,
-                        alt_name=f,
-                        file_name=os.path.join(root, f),
-                        create=True,
-                        preserve_symlinks=True
-                    )
-        except Exception as e:
-            log.debug("Error in collect_associated_files: %s" % (e))
-
-    def _collect_metrics(self, has_metrics):
+    def _collect_metrics(self, has_metrics, job_metrics_directory=None):
         job = has_metrics.get_job()
-        per_plugin_properties = self.app.job_metrics.collect_properties(job.destination_id, self.job_id, self.working_directory)
+        job_metrics_directory = job_metrics_directory or self.working_directory
+        per_plugin_properties = self.app.job_metrics.collect_properties(job.destination_id, self.job_id, job_metrics_directory)
         if per_plugin_properties:
-            log.info("Collecting metrics for %s %s" % (type(has_metrics).__name__, getattr(has_metrics, 'id', None)))
+            log.info("Collecting metrics for %s %s in %s" % (type(has_metrics).__name__, getattr(has_metrics, 'id', None), job_metrics_directory))
         for plugin, properties in per_plugin_properties.items():
             for metric_name, metric_value in properties.items():
                 if metric_value is not None:
@@ -1629,7 +1798,7 @@ class JobWrapper(HasResourceParameters):
         return paths
 
     def get_output_basenames(self):
-        return list(map(os.path.basename, map(str, self.get_output_fnames())))
+        return [os.path.basename(str(fname)) for fname in self.get_output_fnames()]
 
     def get_output_fnames(self):
         if self.output_paths is None:
@@ -1762,7 +1931,8 @@ class JobWrapper(HasResourceParameters):
         if config_file is None:
             config_file = self.app.config.config_file
         if datatypes_config is None:
-            datatypes_config = os.path.join(self.working_directory, 'registry.xml')
+            datatypes_config = os.path.join(self.working_directory, 'metadata', 'registry.xml')
+            safe_makedirs(os.path.join(self.working_directory, 'metadata'))
             self.app.datatypes_registry.to_xml_file(path=datatypes_config)
 
         output_datasets = {}
diff --git a/lib/galaxy/jobs/actions/post.py b/lib/galaxy/jobs/actions/post.py
index d33aba36280..9a43a5eedc1 100644
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -7,7 +7,10 @@ import socket
 
 from markupsafe import escape
 
-from galaxy.util import send_mail
+from galaxy.util import (
+    send_mail,
+    unicodify,
+)
 from galaxy.util.logging import get_logger
 
 log = get_logger(__name__)
@@ -55,7 +58,7 @@ class EmailAction(DefaultJobAction):
         try:
             send_mail(frm, to, subject, body, app.config)
         except Exception as e:
-            log.error("EmailAction PJA Failed, exception: %s" % e)
+            log.error("EmailAction PJA Failed, exception: %s", unicodify(e))
 
     @classmethod
     def get_short_str(cls, pja):
@@ -282,9 +285,10 @@ class ColumnSetAction(DefaultJobAction):
                 for k, v in action.action_arguments.items():
                     if v:
                         # Try to use both pure integer and 'cX' format.
-                        if v[0] == 'c':
-                            v = v[1:]
-                        v = int(v)
+                        if not isinstance(v, int):
+                            if v[0] == 'c':
+                                v = v[1:]
+                            v = int(v)
                         if v != 0:
                             setattr(dataset_assoc.dataset.metadata, k, v)
 
diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index ad99b0e1e56..adccf42b427 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -140,7 +140,7 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
         tool_commands
     )
     write_script(local_container_script, script_contents, config)
-    commands = local_container_script
+    commands = "%s %s" % (shell, local_container_script)
     if 'working_directory' in remote_command_params:
         commands = "%s %s" % (shell, join(remote_command_params['working_directory'], script_name))
     commands += " > ../tool_stdout 2> ../tool_stderr"
@@ -204,6 +204,7 @@ def __handle_metadata(commands_builder, job_wrapper, runner, remote_command_para
         datatypes_config=datatypes_config,
         compute_tmp_dir=compute_tmp_dir,
         resolve_metadata_dependencies=resolve_metadata_dependencies,
+        use_bin=job_wrapper.use_metadata_binary,
         kwds={'overwrite': False}
     ) or ''
     metadata_command = metadata_command.strip()
diff --git a/lib/galaxy/jobs/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py
index 709ec15c3c4..e2bebc4e3bc 100755
--- a/lib/galaxy/jobs/dynamic_tool_destination.py
+++ b/lib/galaxy/jobs/dynamic_tool_destination.py
@@ -12,7 +12,7 @@ from functools import reduce
 from xml.etree import ElementTree as ET
 
 import numpy as np
-from yaml import load
+import yaml
 
 __version__ = '1.1.0'
 
@@ -727,7 +727,7 @@ def parse_yaml(path="/config/tool_destinations.yml",
     # Import file from path
     try:
         if test:
-            config = load(path)
+            config = yaml.safe_load(path)
         else:
             if path == "/config/tool_destinations.yml":
                 # os.path.realpath gets the path of DynamicToolDestination.py
@@ -741,7 +741,7 @@ def parse_yaml(path="/config/tool_destinations.yml",
                 opt_file = path
 
             with open(opt_file, 'r') as stream:
-                config = load(stream)
+                config = yaml.safe_load(stream)
 
         # Test imported file
         try:
diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index 046163fb59b..942eac7d16c 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -28,9 +28,10 @@ from galaxy.jobs import (
     TaskWrapper
 )
 from galaxy.jobs.mapper import JobNotReadyException
+from galaxy.util import unicodify
 from galaxy.util.monitors import Monitors
-from galaxy.web.stack.handlers import HANDLER_ASSIGNMENT_METHODS
-from galaxy.web.stack.message import JobHandlerMessage
+from galaxy.web_stack.handlers import HANDLER_ASSIGNMENT_METHODS
+from galaxy.web_stack.message import JobHandlerMessage
 
 log = logging.getLogger(__name__)
 
@@ -107,8 +108,9 @@ class JobHandlerQueue(Monitors):
             .where(and_(
                 model.Job.table.c.handler.in_(self.app.job_config.self_handler_tags),
                 model.Job.table.c.state == model.Job.states.NEW)) \
-            .order_by(model.Job.table.c.id) \
-            .limit(self.app.job_config.handler_max_grab)
+            .order_by(model.Job.table.c.id)
+        if self.app.job_config.handler_max_grab:
+            subq = subq.limit(self.app.job_config.handler_max_grab)
         if method == HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED:
             subq = subq.with_for_update(skip_locked=True)
         self.__grab_query = model.Job.table.update() \
@@ -268,7 +270,7 @@ class JobHandlerQueue(Monitors):
                 # If this is a serialization failure on PostgreSQL, then e.orig is a psycopg2 TransactionRollbackError
                 # and should have attribute `code`. Other engines should just report the message and move on.
                 if int(getattr(e.orig, 'pgcode', -1)) != 40001:
-                    log.debug('Grabbing job failed (serialization failures are ok): %s', str(e))
+                    log.debug('Grabbing job failed (serialization failures are ok): %s', unicodify(e))
                 trans.rollback()
 
     def __handle_waiting_jobs(self):
@@ -433,7 +435,7 @@ class JobHandlerQueue(Monitors):
                 model.Dataset.deleted,
                 model.Dataset.purged,
                 model.Dataset.state,
-            ).join(job_to_input) \
+            ).join(job_to_input.job) \
                 .join(input_association) \
                 .join(model.Dataset) \
                 .filter(model.Job.id.in_(job_ids_to_check)) \
@@ -450,13 +452,15 @@ class JobHandlerQueue(Monitors):
             if hda_deleted or dataset_deleted:
                 if dataset_purged:
                     # If the dataset has been purged we can't resume the job by undeleting the input
-                    jobs_to_fail[job_id].append("Input dataset '%s' was deleted before the job started" % (hda_name))
+                    jobs_to_fail[job_id].append("Input dataset '%s' was deleted before the job started" % hda_name)
                 else:
-                    jobs_to_pause[job_id].append("Input dataset '%s' was deleted before the job started" % (hda_name))
+                    jobs_to_pause[job_id].append("Input dataset '%s' was deleted before the job started" % hda_name)
             elif hda_state == model.HistoryDatasetAssociation.states.FAILED_METADATA:
-                jobs_to_pause[job_id].append("Input dataset '%s' failed to properly set metadata" % (hda_name))
+                jobs_to_pause[job_id].append("Input dataset '%s' failed to properly set metadata" % hda_name)
             elif dataset_state == model.Dataset.states.PAUSED:
-                jobs_to_pause[job_id].append("Input dataset '%s' was paused before the job started" % (hda_name))
+                jobs_to_pause[job_id].append("Input dataset '%s' was paused before the job started" % hda_name)
+            elif dataset_state == model.Dataset.states.ERROR:
+                jobs_to_pause[job_id].append("Input dataset '%s' is in error state" % hda_name)
             elif dataset_state != model.Dataset.states.OK:
                 jobs_to_ignore[job_id].append("Input dataset '%s' is in %s state" % (hda_name, dataset_state))
         for job_id in sorted(jobs_to_pause):
diff --git a/lib/galaxy/jobs/manager.py b/lib/galaxy/jobs/manager.py
index 931278ce786..d44707a8720 100644
--- a/lib/galaxy/jobs/manager.py
+++ b/lib/galaxy/jobs/manager.py
@@ -9,7 +9,7 @@ from sqlalchemy.sql.expression import null
 from galaxy.exceptions import HandlerAssignmentError, ToolExecutionError
 from galaxy.jobs import handler, NoopQueue
 from galaxy.model import Job
-from galaxy.web.stack.message import JobHandlerMessage
+from galaxy.web_stack.message import JobHandlerMessage
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py
index d97bba62df6..8d50ad0a9b8 100644
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -1,10 +1,10 @@
 import importlib
-import inspect
 import logging
 
 import galaxy.jobs.rules
 from galaxy.jobs import stock_rules
 from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination
+from galaxy.util.getargspec import getfullargspec
 from galaxy.util.submodules import import_submodules
 from .rule_helper import RuleHelper
 
@@ -56,7 +56,7 @@ class JobRunnerMapper(object):
             self.rules_module = importlib.import_module(module_name)
 
     def __invoke_expand_function(self, expand_function, destination):
-        function_arg_names = inspect.getargspec(expand_function).args
+        function_arg_names = getfullargspec(expand_function).args
         app = self.job_wrapper.app
         possible_args = {
             "job_id": self.job_wrapper.job_id,
@@ -207,6 +207,10 @@ class JobRunnerMapper(object):
         return job_destination
 
     def __determine_job_destination(self, params, raw_job_destination=None):
+        if self.job_wrapper.tool is None:
+            raise JobMappingException(
+                "Can't map job to destination, tool '%s' is unavailable" % self.job_wrapper.get_job().tool_id
+            )
         if raw_job_destination is None:
             raw_job_destination = self.job_wrapper.tool.get_job_destination(params)
         if raw_job_destination.runner == DYNAMIC_RUNNER_NAME:
diff --git a/lib/galaxy/jobs/rule_helper.py b/lib/galaxy/jobs/rule_helper.py
index 2dd339d6ae4..cca29fa7477 100644
--- a/lib/galaxy/jobs/rule_helper.py
+++ b/lib/galaxy/jobs/rule_helper.py
@@ -9,7 +9,7 @@ from galaxy import (
     model,
     util
 )
-from galaxy.tools.deps.dependencies import ToolInfo
+from galaxy.tool_util.deps.dependencies import ToolInfo
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index 88867243703..89e2d4e836b 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -18,23 +18,25 @@ from six.moves.queue import (
 
 import galaxy.jobs
 from galaxy import model
+from galaxy.job_execution.output_collect import default_exit_code_file, read_exit_code_from
 from galaxy.jobs.command_factory import build_command
-from galaxy.jobs.output_checker import DETECTED_JOB_STATE
 from galaxy.jobs.runners.util.env import env_to_statement
 from galaxy.jobs.runners.util.job_script import (
     job_script,
     write_script
 )
-from galaxy.tools.deps.dependencies import (
+from galaxy.tool_util.deps.dependencies import (
     JobInfo,
     ToolInfo
 )
+from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
 from galaxy.util import (
     DATABASE_MAX_STRING_SIZE,
     ExecutionTimer,
     in_directory,
     ParamsWithSpecs,
-    shrink_stream_by_size
+    shrink_stream_by_size,
+    unicodify,
 )
 from galaxy.util.bunch import Bunch
 from galaxy.util.monitors import Monitors
@@ -130,6 +132,11 @@ class BaseJobRunner(object):
                 method(arg)
             except Exception:
                 log.exception("(%s) Unhandled exception calling %s" % (job_id, name))
+                if not isinstance(arg, JobState):
+                    job_state = JobState(job_wrapper=arg, job_destination={})
+                else:
+                    job_state = arg
+                self.work_queue.put((self.fail_job, job_state))
 
     # Causes a runner's `queue_job` method to be called from a worker thread
     def put(self, job_wrapper):
@@ -230,8 +237,8 @@ class BaseJobRunner(object):
                 stderr_file=stderr_file,
             )
         except Exception as e:
-            log.exception("(%s) Failure preparing job" % job_id)
-            job_wrapper.fail(str(e), exception=True)
+            log.exception("(%s) Failure preparing job", job_id)
+            job_wrapper.fail(unicodify(e), exception=True)
             return False
 
         if not job_wrapper.runner_command_line:
@@ -544,7 +551,7 @@ class JobState(object):
                 self.job_file = JobState.default_job_file(files_dir, id_tag)
                 self.output_file = os.path.join(files_dir, 'galaxy_%s.o' % id_tag)
                 self.error_file = os.path.join(files_dir, 'galaxy_%s.e' % id_tag)
-                self.exit_code_file = os.path.join(files_dir, 'galaxy_%s.ec' % id_tag)
+                self.exit_code_file = default_exit_code_file(files_dir, id_tag)
             job_name = 'g%s' % id_tag
             if self.job_wrapper.tool.old_id:
                 job_name += '_%s' % self.job_wrapper.tool.old_id
@@ -556,27 +563,8 @@ class JobState(object):
     def default_job_file(files_dir, id_tag):
         return os.path.join(files_dir, 'galaxy_%s.sh' % id_tag)
 
-    @staticmethod
-    def default_exit_code_file(files_dir, id_tag):
-        return os.path.join(files_dir, 'galaxy_%s.ec' % id_tag)
-
     def read_exit_code(self):
-        try:
-            # This should be an 8-bit exit code, but read ahead anyway:
-            exit_code_str = open(self.exit_code_file, "r").read(32)
-        except Exception:
-            # By default, the exit code is 0, which typically indicates success.
-            exit_code_str = "0"
-
-        try:
-            # Decode the exit code. If it's bogus, then just use 0.
-            exit_code = int(exit_code_str)
-        except ValueError:
-            galaxy_id_tag = self.job_wrapper.get_id_tag()
-            log.warning("(%s) Exit code '%s' invalid. Using 0." % (galaxy_id_tag, exit_code_str))
-            exit_code = 0
-
-        return exit_code
+        return read_exit_code_from(self.exit_code_file, self.job_wrapper.get_id_tag())
 
     def cleanup(self):
         for file in [getattr(self, a) for a in self.cleanup_file_attributes if hasattr(self, a)]:
@@ -589,7 +577,7 @@ class JobState(object):
                     prefix = "(%s)" % self.job_wrapper.get_id_tag()
                 else:
                     prefix = "(%s/%s)" % (self.job_wrapper.get_id_tag(), self.job_id)
-                log.debug("%s Unable to cleanup %s: %s" % (prefix, file, str(e)))
+                log.debug("%s Unable to cleanup %s: %s" % (prefix, file, unicodify(e)))
 
 
 class AsynchronousJobState(JobState):
@@ -753,7 +741,7 @@ class AsynchronousJobRunner(BaseJobRunner, Monitors):
                 if which_try == self.app.config.retry_job_output_collection:
                     stdout = ''
                     stderr = job_state.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER
-                    log.error('(%s/%s) %s: %s' % (galaxy_id_tag, external_job_id, stderr, str(e)))
+                    log.error('(%s/%s) %s: %s', galaxy_id_tag, external_job_id, stderr, unicodify(e))
                     collect_output_success = False
                 else:
                     time.sleep(1)
diff --git a/lib/galaxy/jobs/runners/chronos.py b/lib/galaxy/jobs/runners/chronos.py
index 8d88a4482ff..98f6fbf8241 100644
--- a/lib/galaxy/jobs/runners/chronos.py
+++ b/lib/galaxy/jobs/runners/chronos.py
@@ -5,6 +5,7 @@ import logging
 
 from galaxy import model
 from galaxy.jobs.runners import AsynchronousJobRunner, AsynchronousJobState
+from galaxy.util import unicodify
 
 CHRONOS_IMPORT_MSG = ('The Python \'chronos\' package is required to use '
                       'this feature, please install it or correct the '
@@ -20,7 +21,7 @@ try:
     )
 except ImportError as e:
     chronos = None
-    CHRONOS_IMPORT_MSG.format(msg=str(e))
+    CHRONOS_IMPORT_MSG.format(msg=unicodify(e))
 
 
 __all__ = ('ChronosJobRunner',)
@@ -40,7 +41,7 @@ def handle_exception_call(func):
         try:
             return func(*args, **kwargs)
         except chronos_exceptions as e:
-            LOGGER.error(str(e))
+            LOGGER.error(unicodify(e))
 
     return wrapper
 
diff --git a/lib/galaxy/jobs/runners/cli.py b/lib/galaxy/jobs/runners/cli.py
index a0c4fd1abe5..2da5643a6ce 100644
--- a/lib/galaxy/jobs/runners/cli.py
+++ b/lib/galaxy/jobs/runners/cli.py
@@ -181,6 +181,8 @@ class ShellJobRunner(AsynchronousJobRunner):
                     # Try to find out the reason for exiting
                     self.__handle_out_of_memory(ajs, external_job_id)
                     self.work_queue.put((self.mark_as_failed, ajs))
+                    # Don't add the job to the watched items once it fails, deals with https://github.com/galaxyproject/galaxy/issues/7820
+                    continue
             if state == model.Job.states.RUNNING and not ajs.running:
                 ajs.running = True
             ajs.old_state = state
diff --git a/lib/galaxy/jobs/runners/godocker.py b/lib/galaxy/jobs/runners/godocker.py
index fd00c446585..4cb0cf7eace 100644
--- a/lib/galaxy/jobs/runners/godocker.py
+++ b/lib/galaxy/jobs/runners/godocker.py
@@ -10,6 +10,7 @@ from galaxy.jobs.runners import (
     AsynchronousJobRunner,
     AsynchronousJobState
 )
+from galaxy.util import unicodify
 
 
 log = logging.getLogger(__name__)
@@ -297,11 +298,11 @@ class GodockerJobRunner(AsynchronousJobRunner):
                 log_file.write(out_log)
                 log_file.close()
                 f.close()
-                log.debug("CREATE OUTPUT FILE: " + str(job_state.output_file))
-                log.debug("CREATE ERROR FILE: " + str(job_state.error_file))
-                log.debug("CREATE EXIT CODE FILE: " + str(job_state.exit_code_file))
+                log.debug("CREATE OUTPUT FILE: " + job_state.output_file)
+                log.debug("CREATE ERROR FILE: " + job_state.error_file)
+                log.debug("CREATE EXIT CODE FILE: " + job_state.exit_code_file)
             except IOError as e:
-                log.error('Could not access task log file %s' % str(e))
+                log.error('Could not access task log file: %s', unicodify(e))
                 log.debug("IO Error occurred when accessing the files.")
                 return False
         return True
diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index 3594e044cb7..1dba8c47281 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -14,22 +14,18 @@ from galaxy.jobs.runners import (
     AsynchronousJobState,
     JobState
 )
+from galaxy.jobs.runners.util.pykube_util import (
+    DEFAULT_JOB_API_VERSION,
+    ensure_pykube,
+    Job,
+    job_object_dict,
+    Pod,
+    produce_unique_k8s_job_name,
+    pull_policy,
+    pykube_client_from_dict,
+)
 from galaxy.util.bytesize import ByteSize
 
-# pykube imports:
-try:
-    from pykube.config import KubeConfig
-    from pykube.http import HTTPClient
-    from pykube.objects import (
-        Job,
-        Pod
-    )
-except ImportError as exc:
-    KubeConfig = None
-    K8S_IMPORT_MESSAGE = ('The Python pykube package is required to use '
-                          'this feature, please install it or correct the '
-                          'following error:\nImportError %s' % str(exc))
-
 log = logging.getLogger(__name__)
 
 __all__ = ('KubernetesJobRunner', )
@@ -43,22 +39,25 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
     def __init__(self, app, nworkers, **kwargs):
         # Check if pykube was importable, fail if not
-        assert KubeConfig is not None, K8S_IMPORT_MESSAGE
+        ensure_pykube()
         runner_param_specs = dict(
-            k8s_config_path=dict(map=str, default=os.environ.get('KUBECONFIG', None)),
+            k8s_config_path=dict(map=str, default=None),
             k8s_use_service_account=dict(map=bool, default=False),
             k8s_persistent_volume_claims=dict(map=str),
             k8s_namespace=dict(map=str, default="default"),
             k8s_galaxy_instance_id=dict(map=str),
             k8s_timeout_seconds_job_deletion=dict(map=int, valid=lambda x: int > 0, default=30),
-            k8s_job_api_version=dict(map=str, default="batch/v1"),
+            k8s_job_api_version=dict(map=str, default=DEFAULT_JOB_API_VERSION),
             k8s_supplemental_group_id=dict(map=str),
             k8s_pull_policy=dict(map=str, default="Default"),
+            k8s_run_as_user_id=dict(map=str, valid=lambda s: s == "$uid" or s.isdigit()),
+            k8s_run_as_group_id=dict(map=str, valid=lambda s: s == "$gid" or s.isdigit()),
             k8s_fs_group_id=dict(map=int),
             k8s_default_requests_cpu=dict(map=str, default=None),
             k8s_default_requests_memory=dict(map=str, default=None),
             k8s_default_limits_cpu=dict(map=str, default=None),
             k8s_default_limits_memory=dict(map=str, default=None),
+            k8s_pod_retries=dict(map=int, valid=lambda x: int >= 0, default=3),
             k8s_pod_retrials=dict(map=int, valid=lambda x: int >= 0, default=3))
 
         if 'runner_param_specs' not in kwargs:
@@ -68,13 +67,11 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         """Start the job runner parent object """
         super(KubernetesJobRunner, self).__init__(app, nworkers, **kwargs)
 
-        if "k8s_use_service_account" in self.runner_params and self.runner_params["k8s_use_service_account"]:
-            self._pykube_api = HTTPClient(KubeConfig.from_service_account())
-        else:
-            self._pykube_api = HTTPClient(KubeConfig.from_file(self.runner_params["k8s_config_path"]))
-
+        self._pykube_api = pykube_client_from_dict(self.runner_params)
         self._galaxy_instance_id = self.__get_galaxy_instance_id()
 
+        self._run_as_user_id = self.__get_run_as_user_id()
+        self._run_as_group_id = self.__get_run_as_group_id()
         self._supplemental_group = self.__get_supplemental_group()
         self._fs_group = self.__get_fs_group()
         self._default_pull_policy = self.__get_pull_policy()
@@ -117,18 +114,11 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
         # Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/
         k8s_job_name = self.__produce_unique_k8s_job_name(job_wrapper.get_id_tag())
-        k8s_job_obj = {
-            "apiVersion": self.runner_params['k8s_job_api_version'],
-            "kind": "Job",
-            "metadata": {
-                    # metadata.name is the name of the pod resource created, and must be unique
-                    # http://kubernetes.io/docs/user-guide/configuring-containers/
-                    "name": k8s_job_name,
-                    "namespace": self.runner_params['k8s_namespace'],
-                    "labels": {"app": k8s_job_name}
-            },
-            "spec": self.__get_k8s_job_spec(ajs)
-        }
+        k8s_job_obj = job_object_dict(
+            self.runner_params,
+            k8s_job_name,
+            self.__get_k8s_job_spec(ajs)
+        )
 
         # Checks if job exists and is trusted, or if it needs re-creation.
         job = Job(self._pykube_api, k8s_job_obj)
@@ -163,9 +153,24 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         self.monitor_queue.put(ajs)
 
     def __get_pull_policy(self):
-        if "k8s_pull_policy" in self.runner_params:
-            if self.runner_params['k8s_pull_policy'] in ["Always", "IfNotPresent", "Never"]:
-                return self.runner_params['k8s_pull_policy']
+        return pull_policy(self.runner_params)
+
+    def __get_run_as_user_id(self):
+        if "k8s_run_as_user_id" in self.runner_params:
+            run_as_user = self.runner_params["k8s_run_as_user_id"]
+            if run_as_user == "$uid":
+                return os.getuid()
+            else:
+                return int(self.runner_params["k8s_run_as_user_id"])
+        return None
+
+    def __get_run_as_group_id(self):
+        if "k8s_run_as_group_id" in self.runner_params:
+            run_as_group = self.runner_params["k8s_run_as_group_id"]
+            if run_as_group == "$gid":
+                return self.app.config.gid
+            else:
+                return int(self.runner_params["k8s_run_as_group_id"])
         return None
 
     def __get_supplemental_group(self):
@@ -211,10 +216,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
     def __produce_unique_k8s_job_name(self, galaxy_internal_job_id):
         # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers.
-        instance_id = ""
-        if self._galaxy_instance_id and len(self._galaxy_instance_id) > 0:
-            instance_id = self._galaxy_instance_id + "-"
-        return "galaxy-" + instance_id + galaxy_internal_job_id
+        instance_id = self._galaxy_instance_id or ''
+        return produce_unique_k8s_job_name(app_prefix='galaxy', instance_id=instance_id, job_id=galaxy_internal_job_id)
 
     def __get_k8s_job_spec(self, ajs):
         """Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template."""
@@ -237,17 +240,21 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         }
         # TODO include other relevant elements that people might want to use from
         # TODO http://kubernetes.io/docs/api-reference/v1/definitions/#_v1_podspec
-
-        if self._supplemental_group and self._supplemental_group > 0:
-            k8s_spec_template["spec"]["securityContext"] = dict(supplementalGroups=[self._supplemental_group])
-        if self._fs_group and self._fs_group > 0:
-            if "securityContext" in k8s_spec_template["spec"]:
-                k8s_spec_template["spec"]["securityContext"]["fsGroup"] = self._fs_group
-            else:
-                k8s_spec_template["spec"]["securityContext"] = dict(fsGroup=self._fs_group)
-
+        k8s_spec_template["spec"]["securityContext"] = self.__get_k8s_security_context()
         return k8s_spec_template
 
+    def __get_k8s_security_context(self):
+        security_context = {}
+        if self._run_as_user_id:
+            security_context["runAsUser"] = self._run_as_user_id
+        if self._run_as_group_id:
+            security_context["runAsGroup"] = self._run_as_group_id
+        if self._supplemental_group and self._supplemental_group > 0:
+            security_context["supplementalGroups"] = [self._supplemental_group]
+        if self._fs_group and self._fs_group > 0:
+            security_context["fsGroup"] = self._fs_group
+        return security_context
+
     def __get_k8s_restart_policy(self, job_wrapper):
         """The default Kubernetes restart policy for Jobs"""
         return "Never"
@@ -396,11 +403,17 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             active = 0
             failed = 0
 
-            max_pod_retrials = 1
-            if 'k8s_pod_retrials' in self.runner_params:
-                max_pod_retrials = int(self.runner_params['k8s_pod_retrials'])
-            if 'max_pod_retrials' in job_destination.params:
-                max_pod_retrials = int(job_destination.params['max_pod_retrials'])
+            max_pod_retries = 1
+            if 'max_pod_retries' in job_destination.params:
+                max_pod_retries = int(job_destination.params['max_pod_retries'])
+            elif 'k8s_pod_retries' in self.runner_params:
+                max_pod_retries = int(self.runner_params['k8s_pod_retries'])
+            elif 'max_pod_retrials' in job_destination.params:
+                # For backward compatibility
+                max_pod_retries = int(job_destination.params['max_pod_retrials'])
+            elif 'k8s_pod_retrials' in self.runner_params:
+                # For backward compatibility
+                max_pod_retries = int(self.runner_params['max_pod_retrials'])
 
             if 'succeeded' in job.obj['status']:
                 succeeded = job.obj['status']['succeeded']
@@ -416,12 +429,12 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 return None
             elif failed > 0 and self.__job_failed_due_to_low_memory(job_state):
                 return self._handle_job_failure(job, job_state, reason="OOM")
-            elif active > 0 and failed <= max_pod_retrials:
+            elif active > 0 and failed <= max_pod_retries:
                 if not job_state.running:
                     job_state.running = True
                     job_state.job_wrapper.change_state(model.Job.states.RUNNING)
                 return job_state
-            elif failed > max_pod_retrials:
+            elif failed > max_pod_retries:
                 return self._handle_job_failure(job, job_state)
             elif job_state.job_wrapper.get_job().state == model.Job.states.DELETED:
                 # Job has been deleted via stop_job, cleanup and remove from watched_jobs by returning `None`
@@ -443,7 +456,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             # there is more than one job associated to the expected unique job id used as selector.
             log.error("More than one Kubernetes Job associated to job id '%s'", job_state.job_id)
             with open(job_state.error_file, 'w') as error_file:
-                error_file.write("More than one Kubernetes Job associated to job id '%s'\n" % job_state.job_id)
+                error_file.write("More than one Kubernetes Job associated with job id '%s'\n" % job_state.job_id)
             self.mark_as_failed(job_state)
             return job_state
 
@@ -468,7 +481,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         marks the job for resubmission (resubmit logic is part of destinations).
         """
 
-        pods = Pod.objects(self._pykube_api).filter(selector="app=%s" % job_state.job_id)
+        pods = Pod.objects(self._pykube_api).filter(selector="app=%s" % job_state.job_id,
+                                                    namespace=self.runner_params['k8s_namespace'])
         pod = Pod(self._pykube_api, pods.response['items'][0])
 
         if pod.obj['status']['phase'] == "Failed" and \
@@ -481,8 +495,9 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         """Attempts to delete a dispatched job to the k8s cluster"""
         job = job_wrapper.get_job()
         try:
-            jobs = Job.objects(self._pykube_api).filter(selector="app=" +
-                                                                 self.__produce_unique_k8s_job_name(job.get_id_tag()))
+            jobs = Job.objects(self._pykube_api).filter(
+                selector="app=" + self.__produce_unique_k8s_job_name(job.get_id_tag()),
+                namespace=self.runner_params['k8s_namespace'])
             if len(jobs.response['items']) >= 0:
                 job_to_delete = Job(self._pykube_api, jobs.response['items'][0])
                 job_to_delete.scale(replicas=0)
diff --git a/lib/galaxy/jobs/runners/local.py b/lib/galaxy/jobs/runners/local.py
index 799187b127e..0f64d64129e 100644
--- a/lib/galaxy/jobs/runners/local.py
+++ b/lib/galaxy/jobs/runners/local.py
@@ -11,6 +11,7 @@ import threading
 from time import sleep
 
 from galaxy import model
+from galaxy.job_execution.output_collect import default_exit_code_file
 from galaxy.util import (
     asbool,
 )
@@ -65,7 +66,7 @@ class LocalJobRunner(BaseJobRunner):
 
         job_id = job_wrapper.get_id_tag()
         job_file = JobState.default_job_file(job_wrapper.working_directory, job_id)
-        exit_code_path = JobState.default_exit_code_file(job_wrapper.working_directory, job_id)
+        exit_code_path = default_exit_code_file(job_wrapper.working_directory, job_id)
         job_script_props = {
             'slots_statement': slots_statement,
             'command': command_line,
@@ -137,7 +138,7 @@ class LocalJobRunner(BaseJobRunner):
 
         job_destination = job_wrapper.job_destination
         job_state = JobState(job_wrapper, job_destination)
-        job_state.exit_code_file = JobState.default_exit_code_file(job_wrapper.working_directory, job_id)
+        job_state.exit_code_file = default_exit_code_file(job_wrapper.working_directory, job_id)
         job_state.stop_job = False
         self._finish_or_resubmit_job(job_state, stdout, stderr, job_id=job_id)
 
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 0e0f5c89b80..6ea38d13cd2 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -12,6 +12,7 @@ from time import sleep
 
 import packaging.version
 import pulsar.core
+import six
 import yaml
 from pulsar.client import (
     build_client_manager,
@@ -35,7 +36,7 @@ from galaxy.jobs.runners import (
     AsynchronousJobRunner,
     AsynchronousJobState
 )
-from galaxy.tools.deps import dependencies
+from galaxy.tool_util.deps import dependencies
 from galaxy.util import (
     galaxy_directory,
     specs,
@@ -55,6 +56,7 @@ __all__ = (
 MINIMUM_PULSAR_VERSIONS = {
     '_default_': packaging.version.parse("0.7.0.dev3"),
     'remote_metadata': packaging.version.parse("0.8.0"),
+    'remote_container_handling': packaging.version.parse("0.9.1.dev0")  # probably 0.10 ultimately?
 }
 
 NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory."
@@ -83,6 +85,10 @@ PULSAR_PARAM_SPECS = dict(
         map=specs.to_bool_or_none,
         default=None,
     ),
+    remote_container_handling=dict(
+        map=specs.to_bool,
+        default=False,
+    ),
     amqp_url=dict(
         map=specs.to_str_or_none,
         default=None,
@@ -272,7 +278,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
         job_destination = job_wrapper.job_destination
         self._populate_parameter_defaults(job_destination)
 
-        command_line, client, remote_job_config, compute_environment = self.__prepare_job(job_wrapper, job_destination)
+        command_line, client, remote_job_config, compute_environment, remote_container = self.__prepare_job(job_wrapper, job_destination)
 
         if not command_line:
             return
@@ -292,6 +298,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
             else:
                 metadata_directory = os.path.join(job_wrapper.working_directory, "metadata")
 
+            remote_pulsar_app_config = job_destination.params.get("pulsar_app_config", {})
             client_job_description = ClientJobDescription(
                 command_line=command_line,
                 input_files=self.get_input_files(job_wrapper),
@@ -305,6 +312,8 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 rewrite_paths=rewrite_paths,
                 arbitrary_files=unstructured_path_rewrites,
                 touch_outputs=output_names,
+                remote_pulsar_app_config=remote_pulsar_app_config,
+                container=None if not remote_container else remote_container.container_id,
             )
             job_id = pulsar_submit_job(client, client_job_description, remote_job_config)
             log.info("Pulsar job submitted with job_id %s" % job_id)
@@ -326,6 +335,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
     def __needed_features(self, client):
         return {
             'remote_metadata': PulsarJobRunner.__remote_metadata(client),
+            'remote_container_handling': PulsarJobRunner.__remote_container_handling(client),
         }
 
     def __prepare_job(self, job_wrapper, job_destination):
@@ -334,12 +344,20 @@ class PulsarJobRunner(AsynchronousJobRunner):
         client = None
         remote_job_config = None
         compute_environment = None
+        remote_container = None
 
         fail_or_resubmit = False
         try:
             client = self.get_client_from_wrapper(job_wrapper)
             tool = job_wrapper.tool
             remote_job_config = client.setup(tool.id, tool.version, tool.requires_galaxy_python_environment)
+            remote_container_handling = PulsarJobRunner.__remote_container_handling(client)
+            if remote_container_handling:
+                # Handle this remotely and don't pass it to build_command
+                remote_container = self._find_container(
+                    job_wrapper,
+                )
+
             needed_features = self.__needed_features(client)
             PulsarJobRunner.check_job_config(remote_job_config, check_features=needed_features)
             rewrite_parameters = PulsarJobRunner.__rewrite_parameters(client)
@@ -362,13 +380,15 @@ class PulsarJobRunner(AsynchronousJobRunner):
             # calculated at some other level.
             remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir))
             remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files"))
-            container = self._find_container(
-                job_wrapper,
-                compute_working_directory=remote_working_directory,
-                compute_tool_directory=remote_tool_directory,
-                compute_job_directory=remote_job_directory,
-            )
             job_wrapper.disable_commands_in_new_shell()
+            container = None
+            if remote_container is None:
+                container = self._find_container(
+                    job_wrapper,
+                    compute_working_directory=remote_working_directory,
+                    compute_tool_directory=remote_tool_directory,
+                    compute_job_directory=remote_job_directory,
+                )
 
             # Pulsar handles ``create_tool_working_directory`` and
             # ``include_work_dir_outputs`` details.
@@ -398,7 +418,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
             job_state = self._job_state(job_wrapper.get_job(), job_wrapper)
             self.work_queue.put((self.fail_job, job_state))
 
-        return command_line, client, remote_job_config, compute_environment
+        return command_line, client, remote_job_config, compute_environment, remote_container
 
     def __prepare_input_files_locally(self, job_wrapper):
         """Run task splitting commands locally."""
@@ -449,7 +469,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
         user = job_wrapper.get_job().user
         if user:
             for key, value in params.items():
-                if value:
+                if value and isinstance(value, six.string_types):
                     params[key] = model.User.expand_user_properties(user, value)
 
         env = getattr(job_wrapper.job_destination, "env", [])
@@ -516,11 +536,18 @@ class PulsarJobRunner(AsynchronousJobRunner):
             self._handle_metadata_externally(job_wrapper, resolve_requirements=True)
         # Finish the job
         try:
+            job_metrics_directory = os.path.join(job_wrapper.working_directory, "metadata")
+            # Following check is a hack for jobs started during 19.01 or earlier release
+            # and finishing with a 19.05 code base. Eliminate the hack in 19.09 or later
+            # along with hacks for legacy metadata compute strategy.
+            if not os.path.exists(job_metrics_directory) or not any(["__instrument" in f for f in os.listdir(job_metrics_directory)]):
+                job_metrics_directory = job_wrapper.working_directory
             job_wrapper.finish(
                 stdout,
                 stderr,
                 exit_code,
                 remote_metadata_directory=remote_metadata_directory,
+                job_metrics_directory=job_metrics_directory,
             )
         except Exception:
             log.exception("Job wrapper finish method failed")
@@ -615,9 +642,14 @@ class PulsarJobRunner(AsynchronousJobRunner):
     def __client_outputs(self, client, job_wrapper):
         work_dir_outputs = self.get_work_dir_outputs(job_wrapper)
         output_files = self.get_output_files(job_wrapper)
+        if self.app.config.metadata_strategy == "legacy":
+            # Drop this branch in 19.09.
+            metadata_directory = job_wrapper.working_directory
+        else:
+            metadata_directory = os.path.join(job_wrapper.working_directory, "metadata")
         client_outputs = ClientOutputs(
             working_directory=job_wrapper.tool_working_directory,
-            metadata_directory=job_wrapper.working_directory,
+            metadata_directory=metadata_directory,
             work_dir_outputs=work_dir_outputs,
             output_files=output_files,
             version_file=job_wrapper.get_version_string_path(),
@@ -662,6 +694,11 @@ class PulsarJobRunner(AsynchronousJobRunner):
         remote_metadata = string_as_bool_or_none(pulsar_client.destination_params.get("remote_metadata", False))
         return remote_metadata
 
+    @staticmethod
+    def __remote_container_handling(pulsar_client):
+        remote_container_handling = string_as_bool_or_none(pulsar_client.destination_params.get("remote_container_handling", False))
+        return remote_container_handling
+
     @staticmethod
     def __use_remote_datatypes_conf(pulsar_client):
         """Use remote metadata datatypes instead of Galaxy's.
@@ -686,7 +723,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
 
     def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, remote_job_config):
         metadata_kwds = {}
-        if remote_metadata:
+        if remote_metadata and not job_wrapper.use_metadata_binary:
             remote_system_properties = remote_job_config.get("system_properties", {})
             remote_galaxy_home = remote_system_properties.get("galaxy_home", None)
             if not remote_galaxy_home:
@@ -773,6 +810,36 @@ class PulsarMQJobRunner(PulsarJobRunner):
             # Nothing else to do? - Attempt to fail the job?
 
 
+class PulsarKubernetesCoexecutionJobRunner(PulsarMQJobRunner):
+    """Flavor of Pulsar job runner with sensible defaults for Kubernetes Pod co-execution."""
+
+    destination_defaults = dict(
+        default_file_action="remote_transfer",
+        rewrite_parameters="true",
+        dependency_resolution="none",
+        jobs_directory="/pulsar_staging",
+        pulsar_container_image="galaxy/pulsar-pod-staging:0.12.0",
+        remote_container_handling=True,
+        k8s_enabled=True,
+        url=PARAMETER_SPECIFICATION_IGNORED,
+        private_token=PARAMETER_SPECIFICATION_IGNORED,
+    )
+
+    def _populate_parameter_defaults(self, job_destination):
+        super(PulsarKubernetesCoexecutionJobRunner, self)._populate_parameter_defaults(job_destination)
+        params = job_destination.params
+        # Set some sensible defaults for Pulsar application that runs in staging container.
+        if "pulsar_app_config" not in params:
+            params["pulsar_app_config"] = {}
+        pulsar_app_config = params["pulsar_app_config"]
+        if "staging_directory" not in pulsar_app_config:
+            # coexecution always uses a fixed path for staging directory
+            pulsar_app_config["staging_directory"] = params.get("jobs_directory")
+        if "manager" not in pulsar_app_config and "managers" not in pulsar_app_config:
+            # coexecution always uses coexecution manager
+            pulsar_app_config["manager"] = {"type": "coexecution"}
+
+
 class PulsarRESTJobRunner(PulsarJobRunner):
     """Flavor of Pulsar job runner with sensible defaults for RESTful usage."""
 
diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py
index 333fd55d563..9b5b3b7600b 100644
--- a/lib/galaxy/jobs/runners/slurm.py
+++ b/lib/galaxy/jobs/runners/slurm.py
@@ -10,6 +10,7 @@ import time
 
 from galaxy import model
 from galaxy.jobs.runners.drmaa import DRMAAJobRunner
+from galaxy.util import unicodify
 from galaxy.util.logging import get_logger
 
 log = get_logger(__name__)
@@ -28,13 +29,9 @@ SLURM_MEMORY_LIMIT_EXCEEDED_MSG = 'slurmstepd: error: Exceeded job memory limit'
 SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS = [': Exceeded job memory limit at some point.',
                                                 ': Exceeded step memory limit at some point.']
 SLURM_MEMORY_LIMIT_SCAN_SIZE = 16 * 1024 * 1024  # 16MB
-SLURM_UNABLE_TO_ADD_TASK_TO_MEMORY_CG_MSG_RE = re.compile(r"""slurmstepd: error: task/cgroup: unable to add task\[pid=\d+\] to memory cg '\(null\)'$""")
-SLURM_UNABLE_TO_CREATE_CGROUP_MSG_RE = re.compile(r"""slurmstepd: error: xcgroup_instantiate: unable to create cgroup '[^']+' : No space left on device$""")
-SLURM_UNABLE_TO_INSTANCIATE_CGROUP_MSG_RE = re.compile(r"""slurmstepd: error: jobacct_gather/cgroup: unable to instanciate (job|user) \d+ memory cgroup$""")
+SLURM_CGROUP_RE = re.compile(r"""slurmstepd: .*cgroup.*$""")
 SLURM_TOP_WARNING_RES = (
-    SLURM_UNABLE_TO_ADD_TASK_TO_MEMORY_CG_MSG_RE,
-    SLURM_UNABLE_TO_CREATE_CGROUP_MSG_RE,
-    SLURM_UNABLE_TO_INSTANCIATE_CGROUP_MSG_RE
+    SLURM_CGROUP_RE,
 )
 
 # These messages are returned to the user
@@ -55,7 +52,7 @@ class SlurmJobRunner(DRMAAJobRunner):
             p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
             stdout, stderr = p.communicate()
             if p.returncode != 0:
-                stderr = stderr.strip()
+                stderr = unicodify(stderr).strip()
                 if stderr == 'SLURM accounting storage is disabled':
                     log.warning('SLURM accounting storage is not properly configured, unable to run sacct')
                     return
@@ -63,7 +60,7 @@ class SlurmJobRunner(DRMAAJobRunner):
             # First line is for 'job_id'
             # Second line is for 'job_id.batch' (only available after the batch job is complete)
             # Following lines are for the steps 'job_id.0', 'job_id.1', ... (but Galaxy does not use steps)
-            first_line = stdout.splitlines()[0]
+            first_line = unicodify(stdout).splitlines()[0]
             # Strip whitespaces and the final '+' (if present), only return the first word
             return first_line.strip().rstrip('+').split()[0]
 
@@ -81,6 +78,7 @@ class SlurmJobRunner(DRMAAJobRunner):
             stdout, stderr = p.communicate()
             if p.returncode != 0:
                 # Will need to be more clever here if this message is not consistent
+                stderr = unicodify(stderr)
                 if stderr == 'slurm_load_jobs error: Invalid job id specified\n':
                     # The job may be old, try to get its state with sacct
                     job_state = _get_slurm_state_with_sacct(job_id, cluster)
@@ -88,7 +86,7 @@ class SlurmJobRunner(DRMAAJobRunner):
                         return job_state
                     return 'NOT_FOUND'
                 raise Exception('`%s` returned %s, stderr: %s' % (' '.join(cmd), p.returncode, stderr))
-            stdout = stdout.strip()
+            stdout = unicodify(stdout).strip()
             # stdout is a single line in format "key1=value1 key2=value2 ..."
             job_info_keys = []
             job_info_values = []
diff --git a/lib/galaxy/jobs/runners/state_handlers/resubmit.py b/lib/galaxy/jobs/runners/state_handlers/resubmit.py
index f9cbd744f7c..69f9761e4d6 100644
--- a/lib/galaxy/jobs/runners/state_handlers/resubmit.py
+++ b/lib/galaxy/jobs/runners/state_handlers/resubmit.py
@@ -97,7 +97,8 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
         else:
             job_log_prefix = "(%s)" % (job_state.job_wrapper.job_id)
 
-        destination = resubmit['destination']
+        # Is destination needed here, might these be serialized to the database?
+        destination = resubmit.get('environment') or resubmit.get('destination')
         log.info("%s Job will be resubmitted to '%s' because %s at "
                  "the '%s' destination",
                  job_log_prefix,
diff --git a/lib/galaxy/jobs/runners/util/condor/__init__.py b/lib/galaxy/jobs/runners/util/condor/__init__.py
index a8a9003f01e..c71f79bb5bb 100644
--- a/lib/galaxy/jobs/runners/util/condor/__init__.py
+++ b/lib/galaxy/jobs/runners/util/condor/__init__.py
@@ -9,6 +9,7 @@ from subprocess import (
     STDOUT
 )
 
+from galaxy.util import unicodify
 from ..external import parse_external_id
 
 DEFAULT_QUERY_CLASSAD = dict(
@@ -82,7 +83,7 @@ def condor_submit(submit_file):
         else:
             message = PROBLEM_PARSING_EXTERNAL_ID
     except Exception as e:
-        message = str(e)
+        message = unicodify(e)
     return external_id, message
 
 
@@ -97,7 +98,7 @@ def condor_stop(external_id):
     except CalledProcessError:
         failure_message = "condor_rm failed"
     except Exception as e:
-        "error encountered calling condor_rm: %s" % e
+        failure_message = "error encountered calling condor_rm: %s" % unicodify(e)
     return failure_message
 
 
diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py
new file mode 100644
index 00000000000..a86601c324f
--- /dev/null
+++ b/lib/galaxy/jobs/runners/util/pykube_util.py
@@ -0,0 +1,89 @@
+"""Interface layer for pykube library shared between Galaxy and Pulsar."""
+import os
+import uuid
+
+try:
+    from pykube.config import KubeConfig
+    from pykube.http import HTTPClient
+    from pykube.objects import (
+        Job,
+        Pod
+    )
+except ImportError as exc:
+    KubeConfig = None
+    Job = None
+    Pod = None
+    K8S_IMPORT_MESSAGE = ('The Python pykube package is required to use '
+                          'this feature, please install it or correct the '
+                          'following error:\nImportError %s' % str(exc))
+
+DEFAULT_JOB_API_VERSION = "batch/v1"
+DEFAULT_NAMESPACE = "default"
+
+
+def ensure_pykube():
+    if KubeConfig is None:
+        raise Exception(K8S_IMPORT_MESSAGE)
+
+
+def pykube_client_from_dict(params):
+    if "k8s_use_service_account" in params and params["k8s_use_service_account"]:
+        pykube_client = HTTPClient(KubeConfig.from_service_account())
+    else:
+        config_path = params.get("k8s_config_path")
+        if config_path is None:
+            config_path = os.environ.get('KUBECONFIG', None)
+        if config_path is None:
+            config_path = '~/.kube/config'
+        pykube_client = HTTPClient(KubeConfig.from_file(config_path))
+    return pykube_client
+
+
+def produce_unique_k8s_job_name(app_prefix=None, instance_id=None, job_id=None):
+    if job_id is None:
+        job_id = str(uuid.uuid4())
+
+    job_name = ""
+    if app_prefix:
+        job_name += "%s-" % app_prefix
+
+    if instance_id and instance_id > 0:
+        job_name += "%s-" % instance_id
+
+    return job_name + job_id
+
+
+def pull_policy(params):
+    # If this doesn't validate it returns None, that seems odd?
+    if "k8s_pull_policy" in params:
+        if params['k8s_pull_policy'] in ["Always", "IfNotPresent", "Never"]:
+            return params['k8s_pull_policy']
+    return None
+
+
+def job_object_dict(params, job_name, spec):
+    k8s_job_obj = {
+        "apiVersion": params.get('k8s_job_api_version', DEFAULT_JOB_API_VERSION),
+        "kind": "Job",
+        "metadata": {
+                # metadata.name is the name of the pod resource created, and must be unique
+                # http://kubernetes.io/docs/user-guide/configuring-containers/
+                "name": job_name,
+                "namespace": params.get('k8s_namespace', DEFAULT_NAMESPACE),
+                "labels": {"app": job_name}
+        },
+        "spec": spec,
+    }
+    return k8s_job_obj
+
+
+__all__ = (
+    "DEFAULT_JOB_API_VERSION",
+    "ensure_pykube",
+    "Job",
+    "job_object_dict",
+    "Pod",
+    "produce_unique_k8s_job_name",
+    "pull_policy",
+    "pykube_client_from_dict",
+)
diff --git a/lib/galaxy/jobs/splitters/multi.py b/lib/galaxy/jobs/splitters/multi.py
index 4396c98d905..241f7f58cc7 100644
--- a/lib/galaxy/jobs/splitters/multi.py
+++ b/lib/galaxy/jobs/splitters/multi.py
@@ -1,9 +1,9 @@
-import inspect
 import logging
 import os
 import shutil
 
 from galaxy import model, util
+from galaxy.util.getargspec import getfullargspec
 
 
 log = logging.getLogger(__name__)
@@ -157,7 +157,7 @@ def do_merge(job_wrapper, task_wrappers):
                                   % (len(output_files), len(task_dirs), output_file_name))
                     # First two args to merge always output_files and path of dataset. More
                     # complicated merge methods may require more parameters. Set those up here.
-                    extra_merge_arg_names = inspect.getargspec(output_type.merge).args[2:]
+                    extra_merge_arg_names = getfullargspec(output_type.merge).args[2:]
                     extra_merge_args = {}
                     if "output_dataset" in extra_merge_arg_names:
                         extra_merge_args["output_dataset"] = output_dataset
@@ -181,7 +181,7 @@ def do_merge(job_wrapper, task_wrappers):
     except Exception as e:
         stdout = 'Error merging files'
         log.exception(stdout)
-        stderr = str(e)
+        stderr = util.unicodify(e)
 
     for tw in task_wrappers:
         # Prevent repetitive output, e.g. "Sequence File Aligned"x20
diff --git a/lib/galaxy/jobs/transfer_manager.py b/lib/galaxy/jobs/transfer_manager.py
index 3b85d7d5784..fedcacf302b 100644
--- a/lib/galaxy/jobs/transfer_manager.py
+++ b/lib/galaxy/jobs/transfer_manager.py
@@ -11,7 +11,11 @@ import threading
 
 from six.moves import shlex_quote
 
-from galaxy.util import listify, sleeper
+from galaxy.util import (
+    listify,
+    sleeper,
+    unicodify,
+)
 from galaxy.util.json import jsonrpc_request, validate_jsonrpc_response
 
 log = logging.getLogger(__name__)
@@ -113,7 +117,7 @@ class TransferManager(object):
                     self.sa_session.refresh(tj)
                     error = e.args
                     if type(error) != dict:
-                        error = dict(code=256, message='Error connecting to transfer daemon', data=str(e))
+                        error = dict(code=256, message='Error connecting to transfer daemon', data=unicodify(e))
                     rval.append(dict(transfer_job_id=tj.id, state=tj.state, error=error))
             else:
                 self.sa_session.refresh(tj)
diff --git a/lib/galaxy/managers/annotatable.py b/lib/galaxy/managers/annotatable.py
index 6195438e1e7..13cd9aed949 100644
--- a/lib/galaxy/managers/annotatable.py
+++ b/lib/galaxy/managers/annotatable.py
@@ -104,5 +104,6 @@ class AnnotatableFilterMixin(object):
 
     def _add_parsers(self):
         self.fn_filter_parsers.update({
-            'annotation'    : {'op': {'has': self.filter_annotation_contains, }},
+            'annotation'    : {'op': {'has': self.filter_annotation_contains,
+                                      'contains': self.filter_annotation_contains}},
         })
diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index ba16ea12562..26b0fe2e01b 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -36,9 +36,12 @@ from six import string_types
 from galaxy import exceptions
 from galaxy import model
 from galaxy.model import tool_shed_install
+from galaxy.util import namedtuple
 
 log = logging.getLogger(__name__)
 
+parsed_filter = namedtuple("ParsedFilter", "filter_type filter")
+
 
 # ==== accessors from base/controller.py
 def security_check(trans, item, check_ownership=False, check_accessible=False):
@@ -323,18 +326,16 @@ class ModelManager(object):
         if not isinstance(filters, list):
             filters = [filters]
         for filter_ in filters:
-            if self._is_fn_filter(filter_):
-                fn_filters.append(filter_)
-            else:
+            if not hasattr(filter_, 'filter_type'):
                 orm_filters.append(filter_)
+            elif filter_.filter_type == 'function':
+                fn_filters.append(filter_.filter)
+            elif filter_.filter_type == 'orm_function':
+                orm_filters.append(filter_.filter(self.model_class))
+            else:
+                orm_filters.append(filter_.filter)
         return (orm_filters, fn_filters)
 
-    def _is_fn_filter(self, filter_):
-        """
-        Returns True if `filter_` is a functional filter to be applied after the SQL query.
-        """
-        return callable(filter_)
-
     def _orm_list(self, query=None, **kwargs):
         """
         Sends kwargs to build the query return all models found.
@@ -380,7 +381,7 @@ class ModelManager(object):
         """
         if not ids:
             return []
-        ids_filter = self.model_class.id.in_(ids)
+        ids_filter = parsed_filter("orm", self.model_class.id.in_(ids))
         found = self.list(filters=self._munge_filters(ids_filter, filters), **kwargs)
         # TODO: this does not order by the original 'ids' array
 
@@ -899,6 +900,8 @@ class ModelFilterParser(HasAModelManager):
 
     #: model class
     model_class = None
+    subcontainer_model_class = None
+    parsed_filter = parsed_filter
 
     def __init__(self, app, **kwargs):
         """
@@ -931,6 +934,7 @@ class ModelFilterParser(HasAModelManager):
             'id'            : {'op': ('in')},
             'encoded_id'    : {'column' : 'id', 'op': ('in'), 'val': self.parse_id_list},
             # dates can be directly passed through the orm into a filter (no need to parse into datetime object)
+            'extension'     : {'op': ('eq', 'like', 'in')},
             'create_time'   : {'op': ('le', 'ge'), 'val': self.parse_date},
             'update_time'   : {'op': ('le', 'ge'), 'val': self.parse_date},
         })
@@ -997,7 +1001,7 @@ class ModelFilterParser(HasAModelManager):
             val = val_parser(val)
 
         # curry/partial and fold the val in there now
-        return lambda i: filter_fn(i, val)
+        return self.parsed_filter(filter_type="function", filter=lambda i: filter_fn(i, val))
 
     # ---- ORM filters
     def _parse_orm_filter(self, attr, op, val):
@@ -1011,6 +1015,8 @@ class ModelFilterParser(HasAModelManager):
         if not column_map:
             # no column mapping (not whitelisted)
             return None
+        if callable(column_map):
+            return self.parsed_filter(filter_type="orm_function", filter=column_map(attr, op, val))
         # attr must be a whitelisted column by attr name or by key passed in column_map
         # note: column_map[ 'column' ] takes precedence
         if 'column' in column_map:
@@ -1037,7 +1043,7 @@ class ModelFilterParser(HasAModelManager):
             val = val_parser(val)
 
         orm_filter = op(val)
-        return orm_filter
+        return self.parsed_filter(filter_type="orm", filter=orm_filter)
 
     #: these are the easier/shorter string equivalents to the python operator fn names that need '__' around them
     UNDERSCORED_OPS = ('lt', 'le', 'eq', 'ne', 'ge', 'gt')
@@ -1119,3 +1125,13 @@ class ModelFilterParser(HasAModelManager):
             date_string = ' '.join([group for group in match.groups() if group])
             return date_string
         raise ValueError('datetime strings must be in the ISO 8601 format and in the UTC')
+
+    def raise_filter_err(self, attr, op, val, msg):
+        raise exceptions.RequestParameterInvalidException(msg, column=attr, operation=op, val=val)
+
+
+def is_valid_slug(slug):
+    """Returns true iff slug is valid."""
+
+    VALID_SLUG_RE = re.compile(r"^[a-z0-9\-]+$")
+    return VALID_SLUG_RE.match(slug)
diff --git a/lib/galaxy/managers/citations.py b/lib/galaxy/managers/citations.py
index c4baac44001..bdae2df866e 100644
--- a/lib/galaxy/managers/citations.py
+++ b/lib/galaxy/managers/citations.py
@@ -1,6 +1,5 @@
 import functools
 import logging
-import os
 
 import requests
 from beaker.cache import CacheManager
@@ -26,8 +25,8 @@ class CitationsManager(object):
                 citation_collection.add(citation)
         return citation_collection.citations
 
-    def parse_citation(self, citation_elem, tool_directory):
-        return parse_citation(citation_elem, tool_directory, self)
+    def parse_citation(self, citation_elem):
+        return parse_citation(citation_elem, self)
 
     def _get_tool(self, tool_id):
         tool = self.app.toolbox.get_tool(tool_id)
@@ -55,17 +54,20 @@ class DoiCache(object):
         return self._cache.get(key=doi, createfunc=createfunc)
 
 
-def parse_citation(elem, directory, citation_manager):
-    """ Parse an abstract citation entry from the specified XML element.
-    The directory parameter should be used to find external files for this
-    citation.
+def parse_citation(elem, citation_manager):
+    """
+    Parse an abstract citation entry from the specified XML element.
     """
     citation_type = elem.attrib.get('type', None)
     citation_class = CITATION_CLASSES.get(citation_type, None)
     if not citation_class:
         log.warning("Unknown or unspecified citation type: %s" % citation_type)
         return None
-    return citation_class(elem, directory, citation_manager)
+    try:
+        citation = citation_class(elem, citation_manager)
+    except Exception as e:
+        raise Exception("Invalid citation of type '%s' with content '%s': %s" % (citation_type, elem.text, e))
+    return citation
 
 
 class CitationCollection(object):
@@ -114,16 +116,8 @@ class BaseCitation(object):
 
 class BibtexCitation(BaseCitation):
 
-    def __init__(self, elem, directory, citation_manager):
-        bibtex_file = elem.attrib.get("file", None)
-        if bibtex_file:
-            raw_bibtex = open(os.path.join(directory, bibtex_file), "r").read()
-        else:
-            raw_bibtex = elem.text.strip()
-        self._set_raw_bibtex(raw_bibtex)
-
-    def _set_raw_bibtex(self, raw_bibtex):
-        self.raw_bibtex = raw_bibtex
+    def __init__(self, elem, citation_manager):
+        self.raw_bibtex = elem.text.strip()
 
     def to_bibtex(self):
         return self.raw_bibtex
@@ -132,7 +126,7 @@ class BibtexCitation(BaseCitation):
 class DoiCitation(BaseCitation):
     BIBTEX_UNSET = object()
 
-    def __init__(self, elem, directory, citation_manager):
+    def __init__(self, elem, citation_manager):
         self.__doi = elem.text.strip()
         self.doi_cache = citation_manager.doi_cache
         self.raw_bibtex = DoiCitation.BIBTEX_UNSET
diff --git a/lib/galaxy/managers/cloud.py b/lib/galaxy/managers/cloud.py
index b43798c219e..f88eef13827 100644
--- a/lib/galaxy/managers/cloud.py
+++ b/lib/galaxy/managers/cloud.py
@@ -247,14 +247,14 @@ class CloudManager(sharable.SharableModelManager):
             if bucket is None:
                 raise RequestParameterInvalidException("The bucket `{}` not found.".format(bucket_name))
         except Exception as e:
-            raise ItemAccessibilityException("Could not get the bucket `{}`: {}".format(bucket_name, str(e)))
+            raise ItemAccessibilityException("Could not get the bucket `{}`: {}".format(bucket_name, util.unicodify(e)))
 
         datasets = []
         for obj in objects:
             try:
                 key = bucket.objects.get(obj)
             except Exception as e:
-                raise MessageException("The following error occurred while getting the object {}: {}".format(obj, str(e)))
+                raise MessageException("The following error occurred while getting the object {}: {}".format(obj, util.unicodify(e)))
             if key is None:
                 log.exception(
                     "Could not get object `{}` for user `{}`. Object may not exist, or the provided credentials are "
@@ -366,7 +366,7 @@ class CloudManager(sharable.SharableModelManager):
                             "job_id": trans.app.security.encode_id(job.id)
                         }))
                 except Exception as e:
-                    err_msg = "maybe invalid or unauthorized credentials. {}".format(e.message)
+                    err_msg = "maybe invalid or unauthorized credentials. {}".format(util.unicodify(e))
                     log.debug("Failed to send the dataset `{}` per user `{}` request to cloud, {}".format(
                         object_label, trans.user.id, err_msg))
                     failed.append(json.dumps(
diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py
index 3d879c3498d..1e5173f7b79 100644
--- a/lib/galaxy/managers/cloudauthzs.py
+++ b/lib/galaxy/managers/cloudauthzs.py
@@ -44,7 +44,8 @@ class CloudAuthzsSerializer(base.ModelSerializer):
             'authn_id',
             'last_update',
             'last_activity',
-            'create_time'
+            'create_time',
+            'description'
         ])
 
     def add_serializers(self):
@@ -63,7 +64,8 @@ class CloudAuthzsSerializer(base.ModelSerializer):
             'authn_id'     : lambda i, k, **c: self.app.security.encode_id(i.authn_id),
             'last_update'  : lambda i, k, **c: str(i.last_update),
             'last_activity': lambda i, k, **c: str(i.last_activity),
-            'create_time'  : lambda i, k, **c: str(i.create_time)
+            'create_time'  : lambda i, k, **c: str(i.create_time),
+            'description'  : lambda i, k, **c: str(i.description)
         })
 
 
@@ -80,7 +82,7 @@ class CloudAuthzsDeserializer(base.ModelDeserializer):
             'authn_id': self.deserialize_and_validate_authn_id,
             'provider': self.default_deserializer,
             'config': self.default_deserializer,
-            'deleted': self.default_deserializer
+            'description': self.default_deserializer
         })
 
     def deserialize_and_validate_authn_id(self, item, key, val, **context):
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index bee1eaae84a..26d5a0c9a04 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -74,7 +74,6 @@ class ConfigSerializer(base.ModelSerializer):
             # TODO: change this to (more generic) upload_path and incorporate config.nginx_upload_path into building it
             'nginx_upload_path'                 : lambda i, k, **c: getattr(i, k, False),
             'chunk_upload_size'                 : _defaults_to(104857600),
-            'ftp_upload_dir'                    : _defaults_to(None),
             'ftp_upload_site'                   : _defaults_to(None),
             'version_major'                     : _defaults_to(None),
             'require_login'                     : _defaults_to(None),
@@ -84,7 +83,7 @@ class ConfigSerializer(base.ModelSerializer):
             'message_box_class'                 : _defaults_to('info'),
             'server_startttime'                 : lambda i, k, **c: server_starttime,
             'mailing_join_addr'                 : _defaults_to('galaxy-announce-join@bx.psu.edu'),
-            'smtp_server'                       : _defaults_to(None),
+            'server_mail_configured'            : lambda i, k, **c: True if getattr(i, 'smtp_server', False) else False,
             'registration_warning_message'      : _defaults_to(None),
             'welcome_url'                       : _defaults_to(None),
             'show_welcome_with_login'           : _defaults_to(True),
diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py
index a7f47949457..af697af7d2a 100644
--- a/lib/galaxy/managers/folders.py
+++ b/lib/galaxy/managers/folders.py
@@ -17,6 +17,7 @@ from galaxy.exceptions import (
     MalformedId,
     RequestParameterInvalidException
 )
+from galaxy.util import unicodify
 
 log = logging.getLogger(__name__)
 
@@ -50,7 +51,7 @@ class FolderManager(object):
         except NoResultFound:
             raise RequestParameterInvalidException('No folder found with the id provided.')
         except Exception as e:
-            raise InternalServerError('Error loading from the database.' + str(e))
+            raise InternalServerError('Error loading from the database.' + unicodify(e))
         folder = self.secure(trans, folder, check_manageable, check_accessible)
         return folder
 
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 1842665ea78..08bd08e505f 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -300,7 +300,8 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
 
             'annotation',
 
-            'api_type'
+            'api_type',
+            'created_from_basename',
         ], include_keys_from='summary')
 
         self.add_view('extended', [
@@ -354,7 +355,8 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
             # TODO: to DatasetAssociationSerializer
             'accessible'    : lambda i, k, user=None, **c: self.manager.is_accessible(i, user, **c),
             'api_type'      : lambda *a, **c: 'file',
-            'type'          : lambda *a, **c: 'file'
+            'type'          : lambda *a, **c: 'file',
+            'created_from_basename' : lambda i, k, **c: i.created_from_basename,
         })
 
     def serialize(self, hda, keys, user=None, **context):
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index c495de58fa8..2b51ea99647 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -23,11 +23,14 @@ from galaxy import (
     model
 )
 from galaxy.managers import (
+    annotatable,
     base,
     containers,
     deletable,
     hdas,
-    hdcas
+    hdcas,
+    taggable,
+    tools
 )
 
 log = logging.getLogger(__name__)
@@ -56,6 +59,7 @@ class HistoryContentsManager(containers.ContainerManagerMixin):
         "type_id",
         "hid",
         # joining columns
+        "extension",
         "dataset_id",
         "collection_id",
         "name",
@@ -149,8 +153,8 @@ class HistoryContentsManager(containers.ContainerManagerMixin):
         Note: does not include deleted/hidden contents.
         """
         filters = [
-            sql.column('deleted') == false(),
-            sql.column('visible') == true()
+            base.ModelFilterParser.parsed_filter("orm", sql.column('deleted') == false()),
+            base.ModelFilterParser.parsed_filter("orm", sql.column('visible') == true())
         ]
         contents_subquery = self._union_of_contents_query(history, filters=filters).subquery()
         statement = (sql.select([sql.column('state'), func.count('*')])
@@ -245,15 +249,32 @@ class HistoryContentsManager(containers.ContainerManagerMixin):
 
         # cycle back over the union query to create an ordered list of the objects returned in queries 2 & 3 above
         contents = []
+        filters = kwargs.get('filters') or []
         # TODO: or as generator?
         for result in contents_results:
             result_type = self._get_union_type(result)
             contents_id = self._get_union_id(result)
             content = id_map[result_type][contents_id]
-            contents.append(content)
+            if self.passes_filters(content, filters):
+                contents.append(content)
         return contents
 
-    def _union_of_contents_query(self, container, filters=None, limit=None, offset=None, order_by=None, **kwargs):
+    @staticmethod
+    def passes_filters(content, filters):
+        for filter_fn in filters:
+            if filter_fn.filter_type == 'function':
+                if not filter_fn.filter(content):
+                    return False
+        return True
+
+    def _union_of_contents_query(self,
+                                 container,
+                                 filters=None,
+                                 limit=None,
+                                 offset=None,
+                                 order_by=None,
+                                 user_id=None,
+                                 **kwargs):
         """
         Returns a query for a limited and offset list of both types of contents,
         filtered and in some order.
@@ -271,13 +292,23 @@ class HistoryContentsManager(containers.ContainerManagerMixin):
         # note: I'm trying to keep these private functions as generic as possible in order to move them toward base later
 
         # query 1: create a union of common columns for which the component_classes can be filtered/limited
-        contained_query = self._contents_common_query_for_contained(container.id)
-        subcontainer_query = self._contents_common_query_for_subcontainer(container.id)
+        contained_query = self._contents_common_query_for_contained(history_id=container.id if container else None,
+                                                                    user_id=user_id)
+        subcontainer_query = self._contents_common_query_for_subcontainer(history_id=container.id if container else None,
+                                                                          user_id=user_id)
+
+        filters = filters or []
+        # Apply filters that are specific to a model
+        for orm_filter in filters:
+            if orm_filter.filter_type == "orm_function":
+                contained_query = contained_query.filter(orm_filter.filter(self.contained_class))
+                subcontainer_query = subcontainer_query.filter(orm_filter.filter(self.subcontainer_class))
         contents_query = contained_query.union(subcontainer_query)
 
-        # TODO: this needs the same fn/orm split that happens in the main query
-        for orm_filter in (filters or []):
-            contents_query = contents_query.filter(orm_filter)
+        for orm_filter in filters:
+            if orm_filter.filter_type == "orm":
+                contents_query = contents_query.filter(orm_filter.filter)
+
         contents_query = contents_query.order_by(*order_by)
 
         if limit is not None:
@@ -300,7 +331,7 @@ class HistoryContentsManager(containers.ContainerManagerMixin):
             columns.append(column)
         return columns
 
-    def _contents_common_query_for_contained(self, history_id):
+    def _contents_common_query_for_contained(self, history_id, user_id):
         component_class = self.contained_class
         # TODO: and now a join with Dataset - this is getting sad
         columns = self._contents_common_columns(component_class,
@@ -312,10 +343,17 @@ class HistoryContentsManager(containers.ContainerManagerMixin):
         subquery = self._session().query(*columns)
         # for the HDA's we need to join the Dataset since it has an actual state column
         subquery = subquery.join(model.Dataset, model.Dataset.id == component_class.dataset_id)
-        subquery = subquery.filter(component_class.history_id == history_id)
+        if history_id:
+            subquery = subquery.filter(component_class.history_id == history_id)
+        else:
+            # Make sure we only return items that are user-accessible by checking that they are in a history
+            # owned by the current user.
+            # TODO: move into filter mixin, and implement accessible logic as SQL query
+            subquery = subquery.filter(component_class.history_id == model.History.table.c.id,
+                                       model.History.table.c.user_id == user_id)
         return subquery
 
-    def _contents_common_query_for_subcontainer(self, history_id):
+    def _contents_common_query_for_subcontainer(self, history_id, user_id):
         component_class = self.subcontainer_class
         columns = self._contents_common_columns(component_class,
             history_content_type=literal('dataset_collection'),
@@ -324,6 +362,7 @@ class HistoryContentsManager(containers.ContainerManagerMixin):
             state=model.DatasetCollection.populated_state,
             # TODO: should be purgable? fix
             purged=literal(False),
+            extension=literal(None),
             # these are attached instead to the inner collection joined below
             create_time=model.DatasetCollection.create_time,
             update_time=model.DatasetCollection.update_time
@@ -332,7 +371,11 @@ class HistoryContentsManager(containers.ContainerManagerMixin):
         # for the HDCA's we need to join the DatasetCollection since it has update/create times
         subquery = subquery.join(model.DatasetCollection,
             model.DatasetCollection.id == component_class.collection_id)
-        subquery = subquery.filter(component_class.history_id == history_id)
+        if history_id:
+            subquery = subquery.filter(component_class.history_id == history_id)
+        else:
+            subquery = subquery.filter(component_class.history_id == model.History.table.c.id,
+                                       model.History.table.c.user_id == user_id)
         return subquery
 
     def _get_union_type(self, union):
@@ -415,56 +458,59 @@ class HistoryContentsSerializer(base.ModelSerializer, deletable.PurgableSerializ
         return self.serialize_id(content, key, **context)
 
 
-class HistoryContentsFilters(base.ModelFilterParser, deletable.PurgableFiltersMixin):
+class HistoryContentsFilters(base.ModelFilterParser,
+                             annotatable.AnnotatableFilterMixin,
+                             deletable.PurgableFiltersMixin,
+                             taggable.TaggableFilterMixin,
+                             tools.ToolFilterMixin):
     # surprisingly (but ominously), this works for both content classes in the union that's filtered
     model_class = model.HistoryDatasetAssociation
+    subcontainer_model_class = model.HistoryDatasetCollectionAssociation
 
-    # TODO: history_content_type filter doesn't work with psycopg2: column does not exist (even with hybrid props)
     def _parse_orm_filter(self, attr, op, val):
 
-        def raise_filter_err(attr, op, val, msg):
-            raise glx_exceptions.RequestParameterInvalidException(msg, column=attr, operation=op, val=val)
-
         # we need to use some manual/text/column fu here since some where clauses on the union don't work
         # using the model_class defined above - they need to be wrapped in their own .column()
         # (and some of these are *not* a normal columns (especially 'state') anyway)
         # TODO: genericize these - can probably extract a _get_column( attr, ... ) or something
         # special cases...special cases everywhere
-        if attr == 'history_content_type' and op == 'eq':
-            if val == 'dataset':
-                return sql.column('history_content_type') == 'dataset'
-            if val == 'dataset_collection':
-                return sql.column('history_content_type') == 'dataset_collection'
-            raise_filter_err(attr, op, val, 'bad op in filter')
+        def get_filter(attr, op, val):
+            if attr == 'history_content_type' and op == 'eq':
+                if val in ('dataset', 'dataset_collection'):
+                    return sql.column('history_content_type') == val
+                self.raise_filter_err(attr, op, val, 'bad op in filter')
 
-        if attr == 'type_id':
-            if op == 'eq':
-                return sql.column('type_id') == val
-            if op == 'in':
-                return sql.column('type_id').in_(self.parse_type_id_list(val))
-            raise_filter_err(attr, op, val, 'bad op in filter')
+            if attr == 'type_id':
+                if op == 'eq':
+                    return sql.column('type_id') == val
+                if op == 'in':
+                    return sql.column('type_id').in_(self.parse_type_id_list(val))
+                self.raise_filter_err(attr, op, val, 'bad op in filter')
 
-        if attr in ('update_time', 'create_time'):
-            if op == 'ge':
-                return sql.column(attr) >= self.parse_date(val)
-            if op == 'le':
-                return sql.column(attr) <= self.parse_date(val)
-            raise_filter_err(attr, op, val, 'bad op in filter')
+            if attr in ('update_time', 'create_time'):
+                if op == 'ge':
+                    return sql.column(attr) >= self.parse_date(val)
+                if op == 'le':
+                    return sql.column(attr) <= self.parse_date(val)
+                self.raise_filter_err(attr, op, val, 'bad op in filter')
 
-        if attr == 'state':
-            valid_states = model.Dataset.states.values()
-            if op == 'eq':
-                if val not in valid_states:
-                    raise_filter_err(attr, op, val, 'invalid state in filter')
-                return sql.column('state') == val
-            if op == 'in':
-                states = [s for s in val.split(',') if s]
-                for state in states:
-                    if state not in valid_states:
-                        raise_filter_err(attr, op, state, 'invalid state in filter')
-                return sql.column('state').in_(states)
-            raise_filter_err(attr, op, val, 'bad op in filter')
+            if attr == 'state':
+                valid_states = model.Dataset.states.values()
+                if op == 'eq':
+                    if val not in valid_states:
+                        self.raise_filter_err(attr, op, val, 'invalid state in filter')
+                    return sql.column('state') == val
+                if op == 'in':
+                    states = [s for s in val.split(',') if s]
+                    for state in states:
+                        if state not in valid_states:
+                            self.raise_filter_err(attr, op, state, 'invalid state in filter')
+                    return sql.column('state').in_(states)
+                self.raise_filter_err(attr, op, val, 'bad op in filter')
 
+        column_filter = get_filter(attr, op, val)
+        if column_filter is not None:
+            return self.parsed_filter(filter_type='orm', filter=column_filter)
         return super(HistoryContentsFilters, self)._parse_orm_filter(attr, op, val)
 
     def decode_type_id(self, type_id):
@@ -480,7 +526,10 @@ class HistoryContentsFilters(base.ModelFilterParser, deletable.PurgableFiltersMi
 
     def _add_parsers(self):
         super(HistoryContentsFilters, self)._add_parsers()
+        annotatable.AnnotatableFilterMixin._add_parsers(self)
         deletable.PurgableFiltersMixin._add_parsers(self)
+        taggable.TaggableFilterMixin._add_parsers(self)
+        tools.ToolFilterMixin._add_parsers(self)
         self.orm_filter_parsers.update({
             'history_content_type' : {'op': ('eq')},
             'type_id'       : {'op': ('eq', 'in'), 'val': self.parse_type_id_list},
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 4d56a7d02d1..3940e20c4eb 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -8,8 +8,13 @@ from sqlalchemy.orm import aliased
 from sqlalchemy.sql import select
 
 from galaxy import model
-from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import (
+    ItemAccessibilityException,
+    ObjectNotFound,
+    RequestParameterInvalidException,
+)
 from galaxy.managers.collections import DatasetCollectionManager
+from galaxy.managers.datasets import DatasetManager
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.lddas import LDDAManager
 from galaxy.util import (
@@ -39,6 +44,27 @@ def get_path_key(path_tuple):
     return path_key
 
 
+class JobManager(object):
+
+    def __init__(self, app):
+        self.app = app
+        self.dataset_manager = DatasetManager(app)
+
+    def get_accessible_job(self, trans, decoded_job_id):
+        job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
+        if job is None:
+            raise ObjectNotFound()
+        belongs_to_user = (job.user == trans.user) if job.user else (job.session_id == trans.get_galaxy_session().id)
+        if not trans.user_is_admin and not belongs_to_user:
+            # Check access granted via output datasets.
+            if not job.output_datasets:
+                raise ItemAccessibilityException("Job has no output datasets.")
+            for data_assoc in job.output_datasets:
+                if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user):
+                    raise ItemAccessibilityException("You are not allowed to rerun this job.")
+        return job
+
+
 class JobSearch(object):
     """Search for jobs using tool inputs or other jobs"""
     def __init__(self, app):
@@ -293,7 +319,7 @@ def fetch_job_states(app, sa_session, job_source_ids, job_source_types):
 
 
 def summarize_jobs_to_dict(sa_session, jobs_source):
-    """Proudce a summary of jobs for job summary endpoints.
+    """Produce a summary of jobs for job summary endpoints.
 
     :type   jobs_source: a Job or ImplicitCollectionJobs or None
     :param  jobs_source: the object to summarize
diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py
index 1dc1365a195..7021d1fe858 100644
--- a/lib/galaxy/managers/libraries.py
+++ b/lib/galaxy/managers/libraries.py
@@ -9,7 +9,10 @@ from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import exceptions
 from galaxy.managers import folders
-from galaxy.util import pretty_print_time_interval
+from galaxy.util import (
+    pretty_print_time_interval,
+    unicodify,
+)
 
 log = logging.getLogger(__name__)
 
@@ -42,7 +45,7 @@ class LibraryManager(object):
         except NoResultFound:
             raise exceptions.RequestParameterInvalidException('No library found with the id provided.')
         except Exception as e:
-            raise exceptions.InternalServerError('Error loading from the database.' + str(e))
+            raise exceptions.InternalServerError('Error loading from the database.' + unicodify(e))
         library = self.secure(trans, library, check_accessible)
         return library
 
diff --git a/lib/galaxy/managers/library_datasets.py b/lib/galaxy/managers/library_datasets.py
index 46c2c45a06a..6cdf791fd3a 100644
--- a/lib/galaxy/managers/library_datasets.py
+++ b/lib/galaxy/managers/library_datasets.py
@@ -43,7 +43,7 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         try:
             ld = trans.sa_session.query(trans.app.model.LibraryDataset).filter(trans.app.model.LibraryDataset.table.c.id == decoded_library_dataset_id).one()
         except Exception as e:
-            raise InternalServerError('Error loading from the database.' + str(e))
+            raise InternalServerError('Error loading from the database.' + util.unicodify(e))
         ld = self.secure(trans, ld, check_accessible)
         return ld
 
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index 08f2c9f46fc..8d2053acce3 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -6,14 +6,53 @@ Pages are markup created and saved by users that can contain Galaxy objects
 from within Galaxy.
 """
 import logging
+import re
 
-from galaxy import model
-from galaxy.managers import sharable
+from six.moves.html_entities import name2codepoint
+from six.moves.html_parser import HTMLParser
+
+from galaxy import exceptions, model
+from galaxy.managers import base, sharable
+from galaxy.managers.hdas import HDAManager
+from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.util import unicodify
+from galaxy.util.sanitize_html import sanitize_html
 
 log = logging.getLogger(__name__)
 
+# Copied from https://github.com/kurtmckee/feedparser
+_cp1252 = {
+    128: u'\u20ac',  # euro sign
+    130: u'\u201a',  # single low-9 quotation mark
+    131: u'\u0192',  # latin small letter f with hook
+    132: u'\u201e',  # double low-9 quotation mark
+    133: u'\u2026',  # horizontal ellipsis
+    134: u'\u2020',  # dagger
+    135: u'\u2021',  # double dagger
+    136: u'\u02c6',  # modifier letter circumflex accent
+    137: u'\u2030',  # per mille sign
+    138: u'\u0160',  # latin capital letter s with caron
+    139: u'\u2039',  # single left-pointing angle quotation mark
+    140: u'\u0152',  # latin capital ligature oe
+    142: u'\u017d',  # latin capital letter z with caron
+    145: u'\u2018',  # left single quotation mark
+    146: u'\u2019',  # right single quotation mark
+    147: u'\u201c',  # left double quotation mark
+    148: u'\u201d',  # right double quotation mark
+    149: u'\u2022',  # bullet
+    150: u'\u2013',  # en dash
+    151: u'\u2014',  # em dash
+    152: u'\u02dc',  # small tilde
+    153: u'\u2122',  # trade mark sign
+    154: u'\u0161',  # latin small letter s with caron
+    155: u'\u203a',  # single right-pointing angle quotation mark
+    156: u'\u0153',  # latin small ligature oe
+    158: u'\u017e',  # latin small letter z with caron
+    159: u'\u0178',  # latin capital letter y with diaeresis
+}
 
-class PageManager(sharable.SharableModelManager):
+
+class PageManager(sharable.SharableModelManager, UsesAnnotations):
     """
     """
 
@@ -35,6 +74,88 @@ class PageManager(sharable.SharableModelManager):
         """
         pass
 
+    def create(self, trans, payload):
+        user = trans.get_user()
+
+        if not payload.get("title", None):
+            raise exceptions.ObjectAttributeMissingException("Page name is required")
+        elif not payload.get("slug", None):
+            raise exceptions.ObjectAttributeMissingException("Page id is required")
+        elif not base.is_valid_slug(payload["slug"]):
+            raise exceptions.ObjectAttributeInvalidException("Page identifier must consist of only lowercase letters, numbers, and the '-' character")
+        elif trans.sa_session.query(trans.app.model.Page).filter_by(user=user, slug=payload["slug"], deleted=False).first():
+            raise exceptions.DuplicatedSlugException("Page identifier must be unique")
+
+        content = payload.get("content", "")
+        content = self.rewrite_content_for_import(trans, content)
+
+        # Create the new stored page
+        page = trans.app.model.Page()
+        page.title = payload['title']
+        page.slug = payload['slug']
+        page_annotation = payload.get("annotation", None)
+        if page_annotation is not None:
+            page_annotation = sanitize_html(page_annotation)
+            self.add_item_annotation(trans.sa_session, trans.get_user(), page, page_annotation)
+
+        page.user = user
+        # And the first (empty) page revision
+        page_revision = trans.app.model.PageRevision()
+        page_revision.title = payload['title']
+        page_revision.page = page
+        page.latest_revision = page_revision
+        page_revision.content = content
+        # Persist
+        session = trans.sa_session
+        session.add(page)
+        session.flush()
+        return page
+
+    def save_new_revision(self, trans, page, payload):
+        # Assumes security has already been checked by caller.
+        content = payload.get("content", None)
+        if not content:
+            raise exceptions.ObjectAttributeMissingException("content undefined or empty")
+
+        if 'title' in payload:
+            title = payload['title']
+        else:
+            title = page.title
+
+        content = self.rewrite_content_for_import(trans, content)
+
+        page_revision = trans.app.model.PageRevision()
+        page_revision.title = title
+        page_revision.page = page
+        page.latest_revision = page_revision
+        page_revision.content = content
+
+        # Persist
+        session = trans.sa_session
+        session.flush()
+        return page_revision
+
+    def rewrite_content_for_import(self, trans, content):
+        try:
+            content = sanitize_html(content)
+            processor = PageContentProcessor(trans, placeholderRenderForSave)
+            processor.feed(content)
+            # Output is string, so convert to unicode for saving.
+            content = unicodify(processor.output(), 'utf-8')
+        except exceptions.MessageException:
+            raise
+        except Exception:
+            raise exceptions.RequestParameterInvalidException("problem with embedded HTML content [%s]" % content)
+        return content
+
+    def rewrite_content_for_export(self, trans, as_dict):
+        content = as_dict["content"]
+        processor = PageContentProcessor(trans, placeholderRenderForEdit)
+        processor.feed(content)
+        content = unicodify(processor.output(), 'utf-8')
+        as_dict["content"] = content
+        return as_dict
+
 
 class PageSerializer(sharable.SharableModelSerializer):
     """
@@ -73,3 +194,230 @@ class PageDeserializer(sharable.SharableModelDeserializer):
         self.deserializers.update({
         })
         self.deserializable_keyset.update(self.deserializers.keys())
+
+
+class PageContentProcessor(HTMLParser, object):
+    """
+    Processes page content to produce HTML that is suitable for display.
+    For now, processor renders embedded objects.
+    """
+    bare_ampersand = re.compile(r"&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)")
+    elements_no_end_tag = set([
+        'area', 'base', 'basefont', 'br', 'col', 'command', 'embed', 'frame',
+        'hr', 'img', 'input', 'isindex', 'keygen', 'link', 'meta', 'param',
+        'source', 'track', 'wbr'
+    ])
+
+    def __init__(self, trans, render_embed_html_fn):
+        HTMLParser.__init__(self)
+        self.trans = trans
+        self.ignore_content = False
+        self.num_open_tags_for_ignore = 0
+        self.render_embed_html_fn = render_embed_html_fn
+
+    def reset(self):
+        self.pieces = []
+        HTMLParser.reset(self)
+
+    def _shorttag_replace(self, match):
+        tag = match.group(1)
+        if tag in self.elements_no_end_tag:
+            return '<' + tag + ' />'
+        else:
+            return '<' + tag + '></' + tag + '>'
+
+    def feed(self, data):
+        data = re.compile(r'<!((?!DOCTYPE|--|\[))', re.IGNORECASE).sub(r'&lt;!\1', data)
+        data = re.sub(r'<([^<>\s]+?)\s*/>', self._shorttag_replace, data)
+        data = data.replace('&#39;', "'")
+        data = data.replace('&#34;', '"')
+        HTMLParser.feed(self, data)
+        HTMLParser.close(self)
+
+    def handle_starttag(self, tag, attrs):
+        """
+        Called for each start tag
+
+        attrs is a list of (attr, value) tuples, e.g. for <pre class='screen'>,
+        tag='pre', attrs=[('class', 'screen')]
+        """
+
+        # If ignoring content, just increment tag count and ignore.
+        if self.ignore_content:
+            self.num_open_tags_for_ignore += 1
+            return
+
+        # Not ignoring tag; look for embedded content.
+        embedded_item = False
+        for attribute in attrs:
+            if (attribute[0] == "class") and ("embedded-item" in attribute[1].split(" ")):
+                embedded_item = True
+                break
+        # For embedded content, set ignore flag to ignore current content and add new content for embedded item.
+        if embedded_item:
+            # Set processing attributes to ignore content.
+            self.ignore_content = True
+            self.num_open_tags_for_ignore = 1
+
+            # Insert content for embedded element.
+            for attribute in attrs:
+                name = attribute[0]
+                if name == "id":
+                    # ID has form '<class_name>-<encoded_item_id>'
+                    item_class, item_id = attribute[1].split("-")
+                    embed_html = self.render_embed_html_fn(self.trans, item_class, item_id)
+                    self.pieces.append(embed_html)
+            return
+
+        # Default behavior: not ignoring and no embedded content.
+        uattrs = []
+        strattrs = ''
+        if attrs:
+            for key, value in attrs:
+                value = value.replace('>', '&gt;').replace('<', '&lt;').replace('"', '&quot;')
+                value = self.bare_ampersand.sub("&amp;", value)
+                uattrs.append((key, value))
+            strattrs = ''.join(' %s="%s"' % (k, v) for k, v in uattrs)
+        if tag in self.elements_no_end_tag:
+            self.pieces.append('<%s%s />' % (tag, strattrs))
+        else:
+            self.pieces.append('<%s%s>' % (tag, strattrs))
+
+    def handle_endtag(self, tag):
+        """
+        Called for each end tag
+
+        E.g. for </pre>, tag will be 'pre'
+        """
+        # If ignoring content, see if current tag is the end of content to ignore.
+        if self.ignore_content:
+            self.num_open_tags_for_ignore -= 1
+            if self.num_open_tags_for_ignore == 0:
+                # Done ignoring content.
+                self.ignore_content = False
+            return
+
+        # Default behavior: reconstruct the original end tag.
+        if tag not in self.elements_no_end_tag:
+            self.pieces.append("</%s>" % tag)
+
+    def handle_charref(self, ref):
+        # called for each character reference, e.g. for '&#160;', ref will be '160'
+        # Reconstruct the original character reference.
+        ref = ref.lower()
+        if ref.startswith('x'):
+            value = int(ref[1:], 16)
+        else:
+            value = int(ref)
+
+        if value in _cp1252:
+            self.pieces.append('&#%s;' % hex(ord(_cp1252[value]))[1:])
+        else:
+            self.pieces.append('&#%s;' % ref)
+
+    def handle_entityref(self, ref):
+        # called for each entity reference, e.g. for '&copy;', ref will be 'copy'
+        # Reconstruct the original entity reference.
+        if ref in name2codepoint or ref == 'apos':
+            self.pieces.append('&%s;' % ref)
+        else:
+            self.pieces.append('&amp;%s' % ref)
+
+    def handle_data(self, text):
+        """
+        Called for each block of plain text
+
+        Called outside of any tag and not containing any character or entity
+        references. Store the original text verbatim.
+        """
+        if self.ignore_content:
+            return
+        self.pieces.append(text)
+
+    def handle_comment(self, text):
+        # called for each HTML comment, e.g. <!-- insert Javascript code here -->
+        # Reconstruct the original comment.
+        self.pieces.append('<!--%s-->' % text)
+
+    def handle_decl(self, text):
+        # called for the DOCTYPE, if present, e.g.
+        # <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+        #     "http://www.w3.org/TR/html4/loose.dtd">
+        # Reconstruct original DOCTYPE
+        self.pieces.append('<!%s>' % text)
+
+    def handle_pi(self, text):
+        # called for each processing instruction, e.g. <?instruction>
+        # Reconstruct original processing instruction.
+        self.pieces.append('<?%s>' % text)
+
+    def output(self):
+        '''Return processed HTML as a single string'''
+        return ''.join(self.pieces)
+
+
+PAGE_MAXRAW = 10**15
+
+
+def get_page_identifiers(item_id, app):
+    # Assume if item id is integer and less than 10**15, it's unencoded.
+    try:
+        decoded_id = int(item_id)
+        if decoded_id >= PAGE_MAXRAW:
+            raise ValueError("Identifier larger than maximum expected raw int, must be already encoded.")
+        encoded_id = app.security.encode_id(item_id)
+    except ValueError:
+        # It's an encoded id.
+        encoded_id = item_id
+        decoded_id = base.decode_id(app, item_id)
+    return (encoded_id, decoded_id)
+
+
+# Utilities for encoding/decoding HTML content.
+PLACEHOLDER_TEMPLATE = '''<div class="embedded-item {class_shorthand_lower} placeholder" id="{item_class}-{item_id}"><p class="title">Embedded Galaxy {class_shorthand} - '{item_name}'</p><p class="content">[Do not edit this block; Galaxy will fill it in with the annotated {class_shorthand} when it is displayed]</p></div>'''
+
+# This is a mapping of the id portion of page contents to the cssclass/shortname.
+PAGE_CLASS_MAPPING = {
+    'History': 'History',
+    'HistoryDatasetAssociation': 'Dataset',
+    'StoredWorkflow': 'Workflow',
+    'Visualization': 'Visualization'
+}
+
+
+def placeholderRenderForEdit(trans, item_class, item_id):
+    return placeholderRenderForSave(trans, item_class, item_id, encode=True)
+
+
+def placeholderRenderForSave(trans, item_class, item_id, encode=False):
+    encoded_item_id, decoded_item_id = get_page_identifiers(item_id, trans.app)
+    item_name = ''
+    if item_class == 'History':
+        history = trans.sa_session.query(trans.model.History).get(decoded_item_id)
+        history = base.security_check(trans, history, False, True)
+        item_name = history.name
+    elif item_class == 'HistoryDatasetAssociation':
+        hda = trans.sa_session.query(trans.model.HistoryDatasetAssociation).get(decoded_item_id)
+        hda_manager = HDAManager(trans.app)
+        hda = hda_manager.get_accessible(decoded_item_id, trans.user)
+        item_name = hda.name
+    elif item_class == 'StoredWorkflow':
+        wf = trans.sa_session.query(trans.model.StoredWorkflow).get(decoded_item_id)
+        wf = base.security_check(trans, wf, False, True)
+        item_name = wf.name
+    elif item_class == 'Visualization':
+        visualization = trans.sa_session.query(trans.model.Visualization).get(decoded_item_id)
+        visualization = base.security_check(trans, visualization, False, True)
+        item_name = visualization.title
+    class_shorthand = PAGE_CLASS_MAPPING[item_class]
+    if encode:
+        item_id = encoded_item_id
+    else:
+        item_id = decoded_item_id
+    return PLACEHOLDER_TEMPLATE.format(
+        item_class=item_class,
+        class_shorthand=class_shorthand,
+        class_shorthand_lower=class_shorthand.lower(),
+        item_id=item_id,
+        item_name=item_name
+    )
diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index 0c6b3e58562..20e3c7ce511 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -8,6 +8,7 @@ from sqlalchemy.orm import exc as sqlalchemy_exceptions
 import galaxy.exceptions
 from galaxy import model
 from galaxy.managers import base
+from galaxy.util import unicodify
 
 log = logging.getLogger(__name__)
 
@@ -45,5 +46,5 @@ class RoleManager(base.ModelManager):
         except sqlalchemy_exceptions.NoResultFound:
             raise galaxy.exceptions.RequestParameterInvalidException('No role found with the id provided.')
         except Exception as e:
-            raise galaxy.exceptions.InternalServerError('Error loading from the database.' + str(e))
+            raise galaxy.exceptions.InternalServerError('Error loading from the database.' + unicodify(e))
         return role
diff --git a/lib/galaxy/managers/taggable.py b/lib/galaxy/managers/taggable.py
index 794ab41008d..da7de761428 100644
--- a/lib/galaxy/managers/taggable.py
+++ b/lib/galaxy/managers/taggable.py
@@ -6,6 +6,9 @@ Mixins for Taggable model managers and serializers.
 
 import logging
 
+from sqlalchemy import sql
+
+from galaxy import model
 from galaxy.util import unicodify
 
 log = logging.getLogger(__name__)
@@ -93,30 +96,38 @@ class TaggableDeserializerMixin(object):
 
 class TaggableFilterMixin(object):
 
-    def filter_has_partial_tag(self, item, val):
-        """
-        Return True if any tag partially contains `val`.
-        """
-        for tag_str in _tag_str_gen(item):
-            if val in tag_str:
-                return True
-        return False
+    valid_ops = ('eq', 'contains', 'has')
 
-    def filter_has_tag(self, item, val):
-        """
-        Return True if any tag exactly equals `val`.
-        """
-        for tag_str in _tag_str_gen(item):
-            if val == tag_str:
+    def create_tag_filter(self, attr, op, val):
+
+        def _create_tag_filter(model_class=None):
+            if op not in TaggableFilterMixin.valid_ops:
+                self.raise_filter_err(attr, op, val, 'bad op in filter')
+            if model_class is None:
                 return True
-        return False
+            class_name = model_class.__name__
+            if class_name == 'HistoryDatasetCollectionAssociation':
+                # Unfortunately we were a little inconsistent with out naming scheme
+                class_name = 'HistoryDatasetCollection'
+            target_model = getattr(model, "%sTagAssociation" % class_name)
+            id_column = "%s_id" % target_model.table.name.rsplit('_tag_association')[0]
+            column = target_model.table.c.user_tname + ":" + target_model.table.c.user_value
+            if op == 'eq':
+                if ':' not in val:
+                    # We require an exact match and the tag to look for has no user_value,
+                    # so we can't just concatenate user_tname, ':' and user_vale
+                    cond = target_model.table.c.user_tname == val
+                else:
+                    cond = column == val
+            else:
+                cond = column.contains(val, autoescape=True)
+            return sql.expression.and_(
+                model_class.table.c.id == getattr(target_model.table.c, id_column),
+                cond
+            )
+        return _create_tag_filter
 
     def _add_parsers(self):
-        self.fn_filter_parsers.update({
-            'tag': {
-                'op': {
-                    'eq'    : self.filter_has_tag,
-                    'has'   : self.filter_has_partial_tag,
-                }
-            }
+        self.orm_filter_parsers.update({
+            'tag': self.create_tag_filter
         })
diff --git a/lib/galaxy/managers/tools.py b/lib/galaxy/managers/tools.py
index d9f00a4f15a..03a849fbca6 100644
--- a/lib/galaxy/managers/tools.py
+++ b/lib/galaxy/managers/tools.py
@@ -1,6 +1,8 @@
 import logging
 from uuid import uuid4
 
+from sqlalchemy import sql
+
 from galaxy import exceptions
 from galaxy import model
 from galaxy.exceptions import DuplicatedIdentifierException
@@ -89,3 +91,37 @@ class DynamicToolManager(ModelManager):
     def deactivate(self, dynamic_tool):
         self.update(dynamic_tool, {"active": False})
         return dynamic_tool
+
+
+class ToolFilterMixin(object):
+
+    def create_tool_filter(self, attr, op, val):
+
+        def _create_tool_filter(model_class=None):
+            if op == 'eq':
+                cond = model.Job.table.c.tool_id == val
+            elif op == 'contains':
+                cond = model.Job.table.c.tool_id.contains(val, autoescape=True)
+            else:
+                self.raise_filter_err(attr, op, val, 'bad op in filter')
+            if model_class is model.HistoryDatasetAssociation:
+                return sql.expression.and_(
+                    model.Job.table.c.id == model.JobToOutputDatasetAssociation.table.c.job_id,
+                    model.HistoryDatasetAssociation.table.c.id == model.JobToOutputDatasetAssociation.table.c.dataset_id,
+                    cond
+                )
+            elif model_class is model.HistoryDatasetCollectionAssociation:
+                return sql.expression.and_(
+                    model.Job.id == model.JobToOutputDatasetAssociation.job_id,
+                    model.JobToOutputDatasetAssociation.dataset_id == model.DatasetCollectionElement.hda_id,
+                    model.DatasetCollectionElement.dataset_collection_id == model.HistoryDatasetCollectionAssociation.collection_id,
+                    cond,
+                )
+            else:
+                return True
+        return _create_tool_filter
+
+    def _add_parsers(self):
+        self.orm_filter_parsers.update({
+            'tool_id': self.create_tool_filter,
+        })
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 34004f6f85a..1c2cb729a90 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -51,7 +51,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         self.model_class = app.model.User
         super(UserManager, self).__init__(app)
 
-    def register(self, trans, email=None, username=None, password=None, confirm=None, subscribe=False, **kwd):
+    def register(self, trans, email=None, username=None, password=None, confirm=None, subscribe=False):
         """
         Register a new user.
         """
@@ -408,7 +408,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
                     trans.log_event('User reset password: %s' % email)
                 except Exception as e:
                     log.debug(body)
-                    return "Failed to submit email. Please contact the administrator: %s" % str(e)
+                    return "Failed to submit email. Please contact the administrator: %s" % util.unicodify(e)
             else:
                 return "Failed to produce password reset token. User not found."
 
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index d1fb3123d2b..586aa9eaf40 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -645,6 +645,10 @@ class WorkflowContentsManager(UsesAnnotations):
                         output_name=pja.output_name,
                         action_arguments=pja.action_arguments
                     )
+                    if pja.action_type == 'ChangeDatatypeAction':
+                        for output in step_dict['outputs']:
+                            if output['name'] == pja.output_name:
+                                output['force_datatype'] = [pja.action_arguments['newtype']]
                 step_dict['post_job_actions'] = pja_dict
 
             # workflow outputs
diff --git a/lib/galaxy/metadata/__init__.py b/lib/galaxy/metadata/__init__.py
index 5314c6dc3dd..6aa93062eab 100644
--- a/lib/galaxy/metadata/__init__.py
+++ b/lib/galaxy/metadata/__init__.py
@@ -13,15 +13,15 @@ from six.moves import cPickle
 
 import galaxy.model
 from galaxy.model.metadata import FileParameter, MetadataTempFile
-from galaxy.util import in_directory
+from galaxy.util import in_directory, safe_makedirs
 
 log = getLogger(__name__)
 
 SET_METADATA_SCRIPT = 'from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()'
 
 
-def get_metadata_compute_strategy(app, job_id):
-    metadata_strategy = app.config.metadata_strategy
+def get_metadata_compute_strategy(config, job_id):
+    metadata_strategy = config.metadata_strategy
     if metadata_strategy == "legacy":
         return JobExternalOutputMetadataWrapper(job_id)
     else:
@@ -46,7 +46,7 @@ class MetadataCollectionStrategy(object):
     @abc.abstractmethod
     def setup_external_metadata(self, datasets_dict, sa_session, exec_dir=None,
                                 tmp_dir=None, dataset_files_path=None,
-                                output_fnames=None, config_root=None,
+                                output_fnames=None, config_root=None, use_bin=False,
                                 config_file=None, datatypes_config=None,
                                 job_metadata=None, compute_tmp_dir=None,
                                 include_command=True, max_metadata_value_size=0,
@@ -73,14 +73,22 @@ class MetadataCollectionStrategy(object):
             normalized_remote_metadata_directory = remote_metadata_directory and os.path.normpath(remote_metadata_directory)
             normalized_path = os.path.normpath(path)
             if remote_metadata_directory and normalized_path.startswith(normalized_remote_metadata_directory):
-                return normalized_path.replace(normalized_remote_metadata_directory, working_directory, 1)
+                if self.portable:
+                    target_directory = os.path.join(working_directory, "metadata")
+                else:
+                    target_directory = working_directory
+                return normalized_path.replace(normalized_remote_metadata_directory, target_directory, 1)
             return path
 
         dataset.metadata.from_JSON_dict(metadata_output_path, path_rewriter=path_rewriter)
 
     def _metadata_results_from_file(self, dataset, filename_results_code):
-        with open(filename_results_code, "r") as f:
-            rval, rstring = json.load(f)
+        try:
+            with open(filename_results_code, "r") as f:
+                rval, rstring = json.load(f)
+        except (OSError, IOError):
+            rval = False
+            rstring = "Metadata results could not be read from '%s'" % filename_results_code
 
         if not rval:
             log.debug('setting metadata externally failed for %s %s: %s' % (dataset.__class__.__name__, dataset.id, rstring))
@@ -88,13 +96,14 @@ class MetadataCollectionStrategy(object):
 
 
 class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
+    portable = True
 
     def __init__(self, job_id):
         self.job_id = job_id
 
     def setup_external_metadata(self, datasets_dict, sa_session, exec_dir=None,
                                 tmp_dir=None, dataset_files_path=None,
-                                output_fnames=None, config_root=None,
+                                output_fnames=None, config_root=None, use_bin=False,
                                 config_file=None, datatypes_config=None,
                                 job_metadata=None, compute_tmp_dir=None,
                                 include_command=True, max_metadata_value_size=0,
@@ -104,7 +113,8 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
         tmp_dir = _init_tmp_dir(tmp_dir)
 
         metadata_dir = os.path.join(tmp_dir, "metadata")
-        os.mkdir(metadata_dir)
+        # may already exist (i.e. metadata collection in the job handler)
+        safe_makedirs(metadata_dir)
 
         def job_relative_path(path):
             path_relative = os.path.relpath(path, tmp_dir)
@@ -128,6 +138,7 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
             }
 
         metadata_params_path = os.path.join(metadata_dir, "params.json")
+        datatypes_config = os.path.relpath(datatypes_config, tmp_dir)
         metadata_params = {
             "job_metadata": job_relative_path(job_metadata),
             "datatypes_config": datatypes_config,
@@ -141,9 +152,12 @@ class PortableDirectoryMetadataGenerator(MetadataCollectionStrategy):
         if include_command:
             # return command required to build
             script_path = os.path.join(metadata_dir, "set.py")
-            with open(script_path, "w") as f:
-                f.write(SET_METADATA_SCRIPT)
-            return 'pwd; python "metadata/set.py"'
+            if use_bin:
+                return "galaxy-set-metadata"
+            else:
+                with open(script_path, "w") as f:
+                    f.write(SET_METADATA_SCRIPT)
+                return 'python "metadata/set.py"'
         else:
             # return args to galaxy_ext.metadata.set_metadata required to build
             return ''
@@ -171,6 +185,7 @@ class JobExternalOutputMetadataWrapper(MetadataCollectionStrategy):
     DatasetInstance object which will use pickle (in the future this could be
     JSONified as well)
     """
+    portable = False
 
     def __init__(self, job_id):
         self.job_id = job_id
@@ -207,7 +222,7 @@ class JobExternalOutputMetadataWrapper(MetadataCollectionStrategy):
 
     def setup_external_metadata(self, datasets_dict, sa_session, exec_dir=None,
                                 tmp_dir=None, dataset_files_path=None,
-                                output_fnames=None, config_root=None,
+                                output_fnames=None, config_root=None, use_bin=False,
                                 config_file=None, datatypes_config=None,
                                 job_metadata=None, compute_tmp_dir=None,
                                 include_command=True, max_metadata_value_size=0,
@@ -289,6 +304,7 @@ class JobExternalOutputMetadataWrapper(MetadataCollectionStrategy):
                                     job_metadata,
                                     " ".join(map(__metadata_files_list_to_cmd_line, metadata_files_list)),
                                     max_metadata_value_size)
+        assert not use_bin
         if include_command:
             # return command required to build
             fd, fp = tempfile.mkstemp(suffix='.py', dir=tmp_dir, prefix="set_metadata_")
@@ -393,8 +409,5 @@ def _get_filename_override(output_fnames, file_name):
 
 def _init_tmp_dir(tmp_dir):
     assert tmp_dir is not None
-
-    if not os.path.exists(tmp_dir):
-        os.makedirs(tmp_dir)
-
+    safe_makedirs(tmp_dir)
     return tmp_dir
diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
new file mode 100644
index 00000000000..52486966374
--- /dev/null
+++ b/lib/galaxy/metadata/set_metadata.py
@@ -0,0 +1,222 @@
+"""
+Execute an external process to set_meta() on a provided list of pickled datasets.
+
+This was formerly scripts/set_metadata.py and expects these arguments:
+
+    %prog datatypes_conf.xml job_metadata_file metadata_in,metadata_kwds,metadata_out,metadata_results_code,output_filename_override,metadata_override... max_metadata_value_size
+
+Galaxy should be importable on sys.path and output_filename_override should be
+set to the path of the dataset on which metadata is being set
+(output_filename_override could previously be left empty and the path would be
+constructed automatically).
+"""
+import json
+import logging
+import os
+import sys
+
+from six.moves import cPickle
+from sqlalchemy.orm import clear_mappers
+
+import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
+from galaxy.model.custom_types import total_size
+from galaxy.tool_util.provided_metadata import parse_tool_provided_metadata
+from galaxy.util import (
+    stringify_dictionary_keys,
+    unicodify,
+)
+
+logging.basicConfig()
+log = logging.getLogger(__name__)
+
+galaxy.model.Job()  # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
+
+
+def set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size):
+    # This method is somewhat odd, in that we set the metadata attributes from tool,
+    # then call set_meta, then set metadata attributes from tool again.
+    # This is intentional due to interplay of overwrite kwd, the fact that some metadata
+    # parameters may rely on the values of others, and that we are accepting the
+    # values provided by the tool as Truth.
+    extension = dataset_instance.extension
+    if extension == "_sniff_":
+        try:
+            from galaxy.datatypes import sniff
+            extension = sniff.handle_uploaded_dataset_file(dataset_instance.dataset.external_filename, datatypes_registry)
+            # We need to both set the extension so it is available to set_meta
+            # and record it in the metadata so it can be reloaded on the server
+            # side and the model updated (see MetadataCollection.{from,to}_JSON_dict)
+            dataset_instance.extension = extension
+            # Set special metadata property that will reload this on server side.
+            setattr(dataset_instance.metadata, "__extension__", extension)
+        except Exception:
+            log.exception("Problem sniffing datatype.")
+
+    for metadata_name, metadata_value in file_dict.get('metadata', {}).items():
+        setattr(dataset_instance.metadata, metadata_name, metadata_value)
+    dataset_instance.datatype.set_meta(dataset_instance, **set_meta_kwds)
+    for metadata_name, metadata_value in file_dict.get('metadata', {}).items():
+        setattr(dataset_instance.metadata, metadata_name, metadata_value)
+
+    if max_metadata_value_size:
+        for k, v in list(dataset_instance.metadata.items()):
+            if total_size(v) > max_metadata_value_size:
+                log.info("Key %s too large for metadata, discarding" % k)
+                dataset_instance.metadata.remove_key(k)
+
+
+def set_metadata():
+    if len(sys.argv) == 1:
+        set_metadata_portable()
+    else:
+        set_metadata_legacy()
+
+
+def set_metadata_portable():
+    import galaxy.model
+    galaxy.model.metadata.MetadataTempFile.tmp_dir = tool_job_working_directory = os.path.abspath(os.getcwd())
+
+    metadata_params_path = os.path.join("metadata", "params.json")
+    try:
+        with open(metadata_params_path, "r") as f:
+            metadata_params = json.load(f)
+    except IOError:
+        raise Exception("Failed to find metadata/params.json from cwd [%s]" % tool_job_working_directory)
+    datatypes_config = metadata_params["datatypes_config"]
+    job_metadata = metadata_params["job_metadata"]
+    max_metadata_value_size = metadata_params.get("max_metadata_value_size") or 0
+    outputs = metadata_params["outputs"]
+
+    datatypes_registry = validate_and_load_datatypes_config(datatypes_config)
+    tool_provided_metadata = load_job_metadata(job_metadata)
+
+    def set_meta(new_dataset_instance, file_dict):
+        set_meta_with_tool_provided(new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)
+
+    for output_name, output_dict in outputs.items():
+        filename_in = os.path.join("metadata/metadata_in_%s" % output_name)
+        filename_kwds = os.path.join("metadata/metadata_kwds_%s" % output_name)
+        filename_out = os.path.join("metadata/metadata_out_%s" % output_name)
+        filename_results_code = os.path.join("metadata/metadata_results_%s" % output_name)
+        override_metadata = os.path.join("metadata/metadata_override_%s" % output_name)
+        dataset_filename_override = output_dict["filename_override"]
+
+        # Same block as below...
+        set_meta_kwds = stringify_dictionary_keys(json.load(open(filename_kwds)))  # load kwds; need to ensure our keywords are not unicode
+        try:
+            dataset = cPickle.load(open(filename_in, 'rb'))  # load DatasetInstance
+            dataset.dataset.external_filename = dataset_filename_override
+            store_by = metadata_params.get("object_store_store_by", "id")
+            extra_files_dir_name = "dataset_%s_files" % getattr(dataset.dataset, store_by)
+            files_path = os.path.abspath(os.path.join(tool_job_working_directory, extra_files_dir_name))
+            dataset.dataset.external_extra_files_path = files_path
+            file_dict = tool_provided_metadata.get_dataset_meta(output_name, dataset.dataset.id)
+            if 'ext' in file_dict:
+                dataset.extension = file_dict['ext']
+            # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
+            override_metadata = json.load(open(override_metadata))
+            for metadata_name, metadata_file_override in override_metadata:
+                if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value(metadata_file_override):
+                    metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON(metadata_file_override)
+                setattr(dataset.metadata, metadata_name, metadata_file_override)
+            set_meta(dataset, file_dict)
+            dataset.metadata.to_JSON_dict(filename_out)  # write out results of set_meta
+            json.dump((True, 'Metadata has been set successfully'), open(filename_results_code, 'wt+'))  # setting metadata has succeeded
+        except Exception as e:
+            json.dump((False, unicodify(e)), open(filename_results_code, 'wt+'))  # setting metadata has failed somehow
+
+    write_job_metadata(tool_job_working_directory, job_metadata, set_meta, tool_provided_metadata)
+
+
+def set_metadata_legacy():
+    import galaxy.model
+    galaxy.model.metadata.MetadataTempFile.tmp_dir = tool_job_working_directory = os.path.abspath(os.getcwd())
+
+    # This is ugly, but to transition from existing jobs without this parameter
+    # to ones with, smoothly, it has to be the last optional parameter and we
+    # have to sniff it.
+    try:
+        max_metadata_value_size = int(sys.argv[-1])
+        sys.argv = sys.argv[:-1]
+    except ValueError:
+        max_metadata_value_size = 0
+        # max_metadata_value_size is unspecified and should be 0
+
+    # Set up datatypes registry
+    datatypes_config = sys.argv.pop(1)
+    datatypes_registry = validate_and_load_datatypes_config(datatypes_config)
+
+    job_metadata = sys.argv.pop(1)
+    tool_provided_metadata = load_job_metadata(job_metadata)
+
+    def set_meta(new_dataset_instance, file_dict):
+        set_meta_with_tool_provided(new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)
+
+    for filenames in sys.argv[1:]:
+        fields = filenames.split(',')
+        filename_in = fields.pop(0)
+        filename_kwds = fields.pop(0)
+        filename_out = fields.pop(0)
+        filename_results_code = fields.pop(0)
+        dataset_filename_override = fields.pop(0)
+        override_metadata = fields.pop(0)
+        set_meta_kwds = stringify_dictionary_keys(json.load(open(filename_kwds)))  # load kwds; need to ensure our keywords are not unicode
+        try:
+            dataset = cPickle.load(open(filename_in, 'rb'))  # load DatasetInstance
+            dataset.dataset.external_filename = dataset_filename_override
+            files_path = os.path.abspath(os.path.join(tool_job_working_directory, "dataset_%s_files" % (dataset.dataset.id)))
+            dataset.dataset.external_extra_files_path = files_path
+            file_dict = tool_provided_metadata.get_dataset_meta(None, dataset.dataset.id)
+            if 'ext' in file_dict:
+                dataset.extension = file_dict['ext']
+            # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
+            override_metadata = json.load(open(override_metadata))
+            for metadata_name, metadata_file_override in override_metadata:
+                if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value(metadata_file_override):
+                    metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON(metadata_file_override)
+                setattr(dataset.metadata, metadata_name, metadata_file_override)
+            set_meta(dataset, file_dict)
+            dataset.metadata.to_JSON_dict(filename_out)  # write out results of set_meta
+            json.dump((True, 'Metadata has been set successfully'), open(filename_results_code, 'wt+'))  # setting metadata has succeeded
+        except Exception as e:
+            json.dump((False, unicodify(e)), open(filename_results_code, 'wt+'))  # setting metadata has failed somehow
+
+    write_job_metadata(tool_job_working_directory, job_metadata, set_meta, tool_provided_metadata)
+
+
+def validate_and_load_datatypes_config(datatypes_config):
+    galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir))
+
+    if not os.path.exists(datatypes_config):
+        # Hack for Pulsar on usegalaxy.org, drop ASAP.
+        datatypes_config = "configs/registry.xml"
+
+    if not os.path.exists(datatypes_config):
+        print("Metadata setting failed because registry.xml [%s] could not be found. You may retry setting metadata." % datatypes_config)
+        sys.exit(1)
+    import galaxy.datatypes.registry
+    datatypes_registry = galaxy.datatypes.registry.Registry()
+    datatypes_registry.load_datatypes(root_dir=galaxy_root, config=datatypes_config, use_build_sites=False, use_converters=False, use_display_applications=False)
+    galaxy.model.set_datatypes_registry(datatypes_registry)
+    return datatypes_registry
+
+
+def load_job_metadata(job_metadata):
+    return parse_tool_provided_metadata(job_metadata)
+
+
+def write_job_metadata(tool_job_working_directory, job_metadata, set_meta, tool_provided_metadata):
+    for i, file_dict in enumerate(tool_provided_metadata.get_new_datasets_for_metadata_collection(), start=1):
+        filename = file_dict["filename"]
+        new_dataset_filename = os.path.join(tool_job_working_directory, "working", filename)
+        new_dataset = galaxy.model.Dataset(id=-i, external_filename=new_dataset_filename)
+        extra_files = file_dict.get('extra_files', None)
+        if extra_files is not None:
+            new_dataset._extra_files_path = os.path.join(tool_job_working_directory, "working", extra_files)
+        new_dataset.state = new_dataset.states.OK
+        new_dataset_instance = galaxy.model.HistoryDatasetAssociation(id=-i, dataset=new_dataset, extension=file_dict.get('ext', 'data'))
+        set_meta(new_dataset_instance, file_dict)
+        file_dict['metadata'] = json.loads(new_dataset_instance.metadata.to_JSON_dict())  # storing metadata in external form, need to turn back into dict, then later jsonify
+
+    tool_provided_metadata.rewrite()
+    clear_mappers()
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index fe26813a4e2..6ad851608f2 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -42,6 +42,7 @@ from sqlalchemy.orm import (
 )
 from sqlalchemy.schema import UniqueConstraint
 
+import galaxy.exceptions
 import galaxy.model.metadata
 import galaxy.model.orm.now
 import galaxy.model.tags
@@ -288,11 +289,13 @@ class JobLike(object):
 
     def set_streams(self, tool_stdout, tool_stderr, job_stdout=None, job_stderr=None, job_messages=None):
         def shrink_and_unicodify(what, stream):
-            stream = galaxy.util.unicodify(stream) or u''
-            if (len(stream) > galaxy.util.DATABASE_MAX_STRING_SIZE):
-                stream = galaxy.util.shrink_string_by_size(tool_stdout, galaxy.util.DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True)
-                log.info("%s for %s %d is greater than %s, only a portion will be logged to database", what, type(self), self.id, galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY)
-            return stream
+            if len(stream) > galaxy.util.DATABASE_MAX_STRING_SIZE:
+                log.info("%s for %s %d is greater than %s, only a portion will be logged to database",
+                         what,
+                         type(self),
+                         self.id,
+                         galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY)
+            return galaxy.util.shrink_and_unicodify(stream)
 
         self.tool_stdout = shrink_and_unicodify('tool_stdout', tool_stdout)
         self.tool_stderr = shrink_and_unicodify('tool_stderr', tool_stderr)
@@ -1633,13 +1636,10 @@ class History(HasTags, Dictifiable, UsesAnnotations, HasName, RepresentById):
         set_genome = genome_build not in [None, '?']
         for i, dataset in enumerate(datasets):
             dataset.hid = base_hid + i
-            # Don't let SA manage this.
-            delattr(dataset, "history")
+            dataset.history = self
             dataset.history_id = cached_id(self)
             if set_genome:
                 self.genome_build = genome_build
-        for dataset in datasets:
-            dataset.history_id = cached_id(self)
         return datasets
 
     def add_dataset_collection(self, history_dataset_collection, set_hid=True):
@@ -2156,8 +2156,10 @@ class Dataset(StorableObject, RepresentById):
     def get_file_name(self):
         if not self.external_filename:
             assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id
-            filename = self.object_store.get_filename(self)
-            return filename
+            if self.object_store.exists(self):
+                return self.object_store.get_filename(self)
+            else:
+                return ''
         else:
             filename = self.external_filename
         # Make filename absolute
@@ -2175,10 +2177,16 @@ class Dataset(StorableObject, RepresentById):
         # actual database column so if SA instantiates this object - the
         # attribute won't exist yet.
         if not getattr(self, "external_extra_files_path", None):
-            return self.object_store.get_filename(self, dir_only=True, extra_dir=self._extra_files_rel_path)
+            if self.object_store.exists(self, dir_only=True, extra_dir=self._extra_files_rel_path):
+                return self.object_store.get_filename(self, dir_only=True, extra_dir=self._extra_files_rel_path)
+            return ''
         else:
             return os.path.abspath(self.external_extra_files_path)
 
+    def create_extra_files_path(self):
+        if not self.extra_files_path_exists():
+            self.object_store.create(self, dir_only=True, extra_dir=self._extra_files_rel_path)
+
     def set_extra_files_path(self, extra_files_path):
         if not extra_files_path:
             self.external_extra_files_path = None
@@ -2266,11 +2274,12 @@ class Dataset(StorableObject, RepresentById):
     def full_delete(self):
         """Remove the file and extra files, marks deleted and purged"""
         # os.unlink( self.file_name )
-        self.object_store.delete(self)
+        try:
+            self.object_store.delete(self)
+        except galaxy.exceptions.ObjectNotFound:
+            pass
         if self.object_store.exists(self, extra_dir=self._extra_files_rel_path, dir_only=True):
             self.object_store.delete(self, entire_dir=True, extra_dir=self._extra_files_rel_path, dir_only=True)
-        # if os.path.exists( self.extra_files_path ):
-        #     shutil.rmtree( self.extra_files_path )
         # TODO: purge metadata files
         self.deleted = True
         self.purged = True
@@ -2390,6 +2399,14 @@ class DatasetInstance(object):
         self.parent_id = parent_id
         self.validation_errors = validation_errors
 
+    @property
+    def peek(self):
+        return self._peek
+
+    @peek.setter
+    def peek(self, peek):
+        self._peek = unicodify(peek, strip_null=True)
+
     def update(self):
         self.update_time = galaxy.model.orm.now.now()
 
@@ -2510,6 +2527,16 @@ class DatasetInstance(object):
         """Detects whether there is any data"""
         return self.dataset.has_data()
 
+    def get_created_from_basename(self):
+        return self.dataset.created_from_basename
+
+    def set_created_from_basename(self, created_from_basename):
+        if self.dataset.created_from_basename is not None:
+            raise Exception("Underlying dataset already has a created_from_basename set.")
+        self.dataset.created_from_basename = created_from_basename
+
+    created_from_basename = property(get_created_from_basename, set_created_from_basename)
+
     def get_raw_data(self):
         """Returns the full data. To stream it open the file_name and read/write as needed"""
         return self.datatype.get_raw_data(self)
@@ -3393,6 +3420,7 @@ class LibraryDataset(RepresentById):
                     state=ldda.state,
                     name=ldda.name,
                     file_name=ldda.file_name,
+                    created_from_basename=ldda.created_from_basename,
                     uploaded_by=ldda.user.email,
                     message=ldda.message,
                     date_uploaded=ldda.create_time.isoformat(),
@@ -3545,7 +3573,8 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, RepresentById):
                     data_type=ldda.datatype.__class__.__module__ + '.' + ldda.datatype.__class__.__name__,
                     genome_build=ldda.dbkey,
                     misc_info=ldda.info,
-                    misc_blurb=ldda.blurb)
+                    misc_blurb=ldda.blurb,
+                    created_from_basename=ldda.created_from_basename)
         if ldda.dataset.uuid is None:
             rval['uuid'] = None
         else:
@@ -3650,7 +3679,7 @@ class ImplicitlyConvertedDatasetAssociation(RepresentById):
             try:
                 os.unlink(self.file_name)
             except Exception as e:
-                log.error("Failed to purge associated file (%s) from disk: %s" % (self.file_name, e))
+                log.error("Failed to purge associated file (%s) from disk: %s" % (self.file_name, unicodify(e)))
 
 
 DEFAULT_COLLECTION_NAME = "Unnamed Collection"
@@ -4875,6 +4904,9 @@ class WorkflowInvocation(UsesCreateAndUpdateTime, Dictifiable, RepresentById):
         return [wid for wid in query.all()]
 
     def add_output(self, workflow_output, step, output_object):
+        if step.type == 'parameter_input':
+            # TODO: these should be properly tracked.
+            return
         if output_object.history_content_type == "dataset":
             output_assoc = WorkflowInvocationOutputDatasetAssociation()
             output_assoc.workflow_invocation = self
diff --git a/lib/galaxy/web/stack/database_heartbeat.py b/lib/galaxy/model/database_heartbeat.py
similarity index 100%
rename from lib/galaxy/web/stack/database_heartbeat.py
rename to lib/galaxy/model/database_heartbeat.py
diff --git a/lib/galaxy/model/item_attrs.py b/lib/galaxy/model/item_attrs.py
index bf32ed87a5a..d054c8bbc42 100644
--- a/lib/galaxy/model/item_attrs.py
+++ b/lib/galaxy/model/item_attrs.py
@@ -74,13 +74,10 @@ class UsesItemRatings(object):
         item_rating_assoc_class = '%sRatingAssociation' % item.__class__.__name__
         return getattr(webapp_model, item_rating_assoc_class, None)
 
-    def _get_item_id_filter_str(self, item, item_rating_assoc_class, webapp_model=None):
+    def _get_item_id_filter_str(self, item, item_rating_assoc_class):
         # Get foreign key in item-rating association table that references item table.
-        if webapp_model is None:
-            webapp_model = galaxy.model
         item_fk = get_foreign_key(item_rating_assoc_class, item)
-        # TODO: can we provide a better filter than a raw string?
-        return "%s=%i" % (item_fk.parent.name, item.id)
+        return item_fk.parent == item.id
 
 
 class UsesAnnotations(object):
@@ -122,7 +119,6 @@ def get_item_annotation_obj(db_session, user, item):
     # Get annotation association object.
     annotation_assoc = db_session.query(annotation_assoc_class).filter_by(user=user)
 
-    # TODO: use filtering like that in _get_item_id_filter_str()
     if item.__class__ == galaxy.model.History:
         annotation_assoc = annotation_assoc.filter_by(history=item)
     elif item.__class__ == galaxy.model.HistoryDatasetAssociation:
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index f7f563c54c8..251c2695d17 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -222,7 +222,7 @@ model.HistoryDatasetAssociation.table = Table(
     Column("name", TrimmedString(255)),
     Column("info", TrimmedString(255)),
     Column("blurb", TrimmedString(255)),
-    Column("peek", TEXT),
+    Column("peek", TEXT, key="_peek"),
     Column("tool_version", TEXT),
     Column("extension", TrimmedString(64)),
     Column("metadata", MetadataType(), key="_metadata"),
@@ -263,6 +263,7 @@ model.Dataset.table = Table(
     Column("object_store_id", TrimmedString(255), index=True),
     Column("external_filename", TEXT),
     Column("_extra_files_path", TEXT),
+    Column("created_from_basename", TEXT),
     Column('file_size', Numeric(15, 0)),
     Column('total_size', Numeric(15, 0)),
     Column('uuid', UUIDType()))
@@ -505,7 +506,7 @@ model.LibraryDatasetDatasetAssociation.table = Table(
     Column("name", TrimmedString(255), index=True),
     Column("info", TrimmedString(255)),
     Column("blurb", TrimmedString(255)),
-    Column("peek", TEXT),
+    Column("peek", TEXT, key="_peek"),
     Column("tool_version", TEXT),
     Column("extension", TrimmedString(64)),
     Column("metadata", MetadataType(), key="_metadata"),
@@ -2727,7 +2728,7 @@ def db_next_hid(self, n=1):
     trans = session.begin()
     try:
         if "postgres" not in session.bind.dialect.name:
-            next_hid = select([table.c.hid_counter], table.c.id == model.cached_id(self), for_update=True).scalar()
+            next_hid = select([table.c.hid_counter], table.c.id == model.cached_id(self)).with_for_update().scalar()
             table.update(table.c.id == self.id).execute(hid_counter=(next_hid + n))
         else:
             stmt = table.update().where(table.c.id == model.cached_id(self)).values(hid_counter=(table.c.hid_counter + n)).returning(table.c.hid_counter)
diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py
index 1cd05399320..3b5506e143a 100644
--- a/lib/galaxy/model/metadata.py
+++ b/lib/galaxy/model/metadata.py
@@ -17,8 +17,13 @@ from six import string_types
 from sqlalchemy.orm import object_session
 
 import galaxy.model
-from galaxy.util import (form_builder, listify, string_as_bool,
-                         stringify_dictionary_keys)
+from galaxy.util import (
+    form_builder,
+    listify,
+    string_as_bool,
+    stringify_dictionary_keys,
+    unicodify,
+)
 from galaxy.util.json import safe_dumps
 from galaxy.util.object_wrapper import sanitize_lists_to_string
 from galaxy.util.odict import odict
@@ -624,10 +629,10 @@ class MetadataTempFile(object):
                 if cls.is_JSONified_value(value):
                     value = cls.from_JSON(value)
                 if isinstance(value, cls) and os.path.exists(value.file_name):
-                    log.debug('Cleaning up abandoned MetadataTempFile file: %s' % value.file_name)
+                    log.debug('Cleaning up abandoned MetadataTempFile file: %s', value.file_name)
                     os.unlink(value.file_name)
         except Exception as e:
-            log.debug('Failed to cleanup MetadataTempFile temp files from %s: %s' % (filename, e))
+            log.debug('Failed to cleanup MetadataTempFile temp files from %s: %s', filename, unicodify(e))
 
 
 __all__ = (
diff --git a/lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py b/lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py
index f9d26724a37..0f25287393c 100644
--- a/lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py
+++ b/lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py
@@ -6,9 +6,10 @@ from __future__ import print_function
 
 import logging
 
-from sqlalchemy import Column, MetaData, Table
+from sqlalchemy import Column, MetaData
 
 from galaxy.model.custom_types import UUIDType
+from galaxy.model.migrate.versions.util import add_column, drop_column
 
 log = logging.getLogger(__name__)
 
@@ -19,14 +20,8 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    metadata_file_table = Table("metadata_file", metadata, autoload=True)
-
-    try:
-        uuid_column = Column('uuid', UUIDType())
-        uuid_column.create(metadata_file_table)
-        assert uuid_column is metadata_file_table.c.uuid
-    except Exception:
-        log.exception("Adding column 'uuid' to `MetadataFile` table failed.")
+    uuid_column = Column('uuid', UUIDType())
+    add_column(uuid_column, 'metadata_file', metadata)
 
 
 def downgrade(migrate_engine):
@@ -34,10 +29,4 @@ def downgrade(migrate_engine):
     metadata.bind = migrate_engine
     metadata.reflect()
 
-    metadata_file_table = Table("metadata_file", metadata, autoload=True)
-
-    try:
-        column = metadata_file_table.c.uuid
-        column.drop()
-    except Exception:
-        log.exception("Dropping 'uuid' column from `metadata_file` table failed.")
+    drop_column('uuid', 'metadata_file', metadata)
diff --git a/lib/galaxy/model/migrate/versions/0154_created_from_basename.py b/lib/galaxy/model/migrate/versions/0154_created_from_basename.py
new file mode 100644
index 00000000000..c4664b48e97
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0154_created_from_basename.py
@@ -0,0 +1,29 @@
+"""
+Adds created_from_basename to dataset.
+"""
+import datetime
+import logging
+
+from sqlalchemy import Column, MetaData, TEXT
+
+from galaxy.model.migrate.versions.util import add_column, drop_column
+
+now = datetime.datetime.utcnow
+log = logging.getLogger(__name__)
+metadata = MetaData()
+
+
+def upgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    print(__doc__)
+    metadata.reflect()
+
+    created_from_basename_column = Column("created_from_basename", TEXT, default=None)
+    add_column(created_from_basename_column, 'dataset', metadata)
+
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    drop_column('created_from_basename', 'dataset', metadata)
diff --git a/lib/galaxy/util/none_like.py b/lib/galaxy/model/none_like.py
similarity index 78%
rename from lib/galaxy/util/none_like.py
rename to lib/galaxy/model/none_like.py
index ff7c5de0475..293ecc5860c 100644
--- a/lib/galaxy/util/none_like.py
+++ b/lib/galaxy/model/none_like.py
@@ -2,7 +2,6 @@
 Objects with No values
 """
 
-from galaxy.datatypes.registry import Registry
 from galaxy.model.metadata import MetadataCollection
 
 
@@ -27,10 +26,7 @@ class NoneDataset(RecursiveNone):
     def __init__(self, datatypes_registry=None, ext='data', dbkey='?'):
         self.ext = self.extension = ext
         self.dbkey = dbkey
-        if datatypes_registry is None:
-            # Default Value Required for unit tests
-            datatypes_registry = Registry()
-            datatypes_registry.load_datatypes()
+        assert datatypes_registry is not None
         self.datatype = datatypes_registry.get_datatype_by_extension(ext)
         self._metadata = None
         self.metadata = MetadataCollection(self)
diff --git a/lib/galaxy/model/store/build_objects.py b/lib/galaxy/model/store/build_objects.py
index 1e3b2701d04..bc2c4fea4f6 100644
--- a/lib/galaxy/model/store/build_objects.py
+++ b/lib/galaxy/model/store/build_objects.py
@@ -91,7 +91,7 @@ def main(argv=None):
     mapping.init("/tmp", "sqlite:///:memory:", create_tables=True, object_store=object_store)
 
     with open(args.objects, "r") as f:
-        targets = yaml.load(f)
+        targets = yaml.safe_load(f)
         if not isinstance(targets, list):
             targets = [targets]
 
diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py
index 697aefc15b0..2f5964d4ed9 100644
--- a/lib/galaxy/model/store/discover.py
+++ b/lib/galaxy/model/store/discover.py
@@ -55,6 +55,7 @@ class ModelPersistenceContext(object):
         tag_list=[],
         sources=[],
         hashes=[],
+        created_from_basename=None,
     ):
         sa_session = self.sa_session
 
@@ -116,6 +117,9 @@ class ModelPersistenceContext(object):
             hash_object.hash_value = hash_dict["hash_value"]
             primary_data.dataset.hashes.append(hash_object)
 
+        if created_from_basename is not None:
+            primary_data.created_from_basename = created_from_basename
+
         self.flush()
 
         if tag_list:
@@ -204,6 +208,7 @@ class ModelPersistenceContext(object):
 
             sources = discovered_file.match.sources
             hashes = discovered_file.match.hashes
+            created_from_basename = discovered_file.match.created_from_basename
 
             dataset = self.create_dataset(
                 ext=ext,
@@ -217,6 +222,7 @@ class ModelPersistenceContext(object):
                 tag_list=tag_list,
                 sources=sources,
                 hashes=hashes,
+                created_from_basename=created_from_basename,
             )
             log.debug(
                 "(%s) Created dynamic collection dataset for path [%s] with element identifier [%s] for output [%s] %s",
@@ -475,6 +481,8 @@ def persist_elements_to_folder(model_persistence_context, elements, library_fold
 
             sources = fields_match.sources
             hashes = fields_match.hashes
+            created_from_basename = fields_match.created_from_basename
+
             model_persistence_context.create_dataset(
                 ext=ext,
                 designation=designation,
@@ -487,6 +495,7 @@ def persist_elements_to_folder(model_persistence_context, elements, library_fold
                 link_data=link_data,
                 sources=sources,
                 hashes=hashes,
+                created_from_basename=created_from_basename,
             )
 
 
@@ -517,6 +526,8 @@ def persist_hdas(elements, model_persistence_context):
 
                 sources = fields_match.sources
                 hashes = fields_match.hashes
+                created_from_basename = fields_match.created_from_basename
+
                 dataset = model_persistence_context.create_dataset(
                     ext=ext,
                     designation=designation,
@@ -529,6 +540,7 @@ def persist_hdas(elements, model_persistence_context):
                     primary_data=primary_dataset,
                     sources=sources,
                     hashes=hashes,
+                    created_from_basename=created_from_basename,
                 )
                 dataset.raw_set_dataset_state('ok')
                 if not hda_id:
@@ -701,6 +713,10 @@ class JsonCollectedDatasetMatch(object):
     def hashes(self):
         return self.as_dict.get("hashes", [])
 
+    @property
+    def created_from_basename(self):
+        return self.as_dict.get("created_from_basename")
+
 
 class RegexCollectedDatasetMatch(JsonCollectedDatasetMatch):
 
diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py
index 6192b25ba53..3b72f31a223 100644
--- a/lib/galaxy/model/tags.py
+++ b/lib/galaxy/model/tags.py
@@ -30,7 +30,7 @@ class TagHandler(object):
     def __init__(self, sa_session):
         self.sa_session = sa_session
         # Minimum tag length.
-        self.min_tag_len = 2
+        self.min_tag_len = 1
         # Maximum tag length.
         self.max_tag_len = 255
         # Tag separator.
@@ -311,6 +311,8 @@ class TagHandler(object):
     def _get_name_value_pair(self, tag_str):
         """Get name, value pair from a tag string."""
         # Use regular expression to parse name, value.
+        if tag_str.startswith('#'):
+            tag_str = "name:%s" % tag_str[1:]
         reg_exp = re.compile("[" + self.key_value_separators + "]")
         name_value_pair = reg_exp.split(tag_str, 1)
         # Add empty slot if tag does not have value.
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index b73a4a8ad56..a10b56e97ab 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -25,6 +25,7 @@ from galaxy.util import (
     force_symlink,
     umask_fix_perms,
 )
+from galaxy.util.bunch import Bunch
 from galaxy.util.odict import odict
 from galaxy.util.path import (
     safe_makedirs,
@@ -467,7 +468,10 @@ class DiskObjectStore(ObjectStore):
             # construct and return hashed path
             if os.path.exists(path):
                 return path
-        return self._construct_path(obj, **kwargs)
+        path = self._construct_path(obj, **kwargs)
+        if not os.path.exists(path):
+            raise ObjectNotFound
+        return path
 
     def update_from_file(self, obj, file_name=None, create=False, **kwargs):
         """`create` parameter is not used in this implementation."""
@@ -889,6 +893,12 @@ def build_object_store_from_config(config, fsmon=False, config_xml=None, config_
     """
     from_object = 'xml'
 
+    if config is None and config_dict is not None and 'config' in config_dict:
+        # Build a config object from to_dict of an ObjectStore.
+        config = Bunch(**config_dict["config"])
+    elif config is None:
+        raise Exception("build_object_store_from_config sent None as config parameter and one cannot be recovered from config_dict")
+
     if config_xml is None and config_dict is None:
         config_file = config.object_store_config_file
         if os.path.exists(config_file):
diff --git a/lib/galaxy/objectstore/s3_multipart_upload.py b/lib/galaxy/objectstore/s3_multipart_upload.py
index f564c1f8524..64b15ce76f9 100644
--- a/lib/galaxy/objectstore/s3_multipart_upload.py
+++ b/lib/galaxy/objectstore/s3_multipart_upload.py
@@ -5,13 +5,10 @@ This parallelizes the task over available cores using multiprocessing.
 Code mostly taken form CloudBioLinux.
 """
 
-import contextlib
-import functools
 import glob
-import multiprocessing
 import os
 import subprocess
-from multiprocessing.pool import IMapIterator
+import threading
 
 try:
     import boto
@@ -20,13 +17,6 @@ except ImportError:
     boto = None
 
 
-def map_wrap(f):
-    @functools.wraps(f)
-    def wrapper(args):
-        return f(*args)
-    return wrapper
-
-
 def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname):
     """Get the multipart upload from the bucket and multipart IDs.
 
@@ -51,7 +41,6 @@ def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname):
     return mp
 
 
-@map_wrap
 def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part):
     """Transfer a part of a multipart upload. Designed to be run in parallel.
     """
@@ -64,8 +53,6 @@ def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part):
 def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size):
     """Upload large files using Amazon's multipart upload functionality.
     """
-    cores = multiprocessing.cpu_count()
-
     def split_file(in_file, mb_size, split_num=5):
         prefix = os.path.join(os.path.dirname(in_file),
                               "%sS3PART" % (os.path.basename(s3_key_name)))
@@ -80,29 +67,11 @@ def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size):
     mp = bucket.initiate_multipart_upload(s3_key_name,
                                           reduced_redundancy=s3server['use_rr'])
 
-    with multimap(cores) as pmap:
-        for _ in pmap(transfer_part, ((s3server, mp.id, mp.key_name, mp.bucket_name, i, part)
-                                      for (i, part) in
-                                      enumerate(split_file(tarball, mb_size, cores)))):
-            pass
+    for (i, part) in enumerate(split_file(tarball, mb_size)):
+        t = threading.Thread(
+            target=transfer_part,
+            args=(s3server, mp.id, mp.key_name, mp.bucket_name, i, part))
+        t.start()
+        t.join()
+
     mp.complete_upload()
-
-
-@contextlib.contextmanager
-def multimap(cores=None):
-    """Provide multiprocessing imap like function.
-
-    The context manager handles setting up the pool, worked around interrupt issues
-    and terminating the pool on completion.
-    """
-    if cores is None:
-        cores = max(multiprocessing.cpu_count() - 1, 1)
-
-    def wrapper(func):
-        def wrap(self, timeout=None):
-            return func(self, timeout=timeout if timeout is not None else 1e100)
-        return wrap
-    IMapIterator.next = wrapper(IMapIterator.next)
-    pool = multiprocessing.Pool(cores)
-    yield pool.imap
-    pool.terminate()
diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py
index 7d5b3302858..23ac03f7597 100644
--- a/lib/galaxy/queue_worker.py
+++ b/lib/galaxy/queue_worker.py
@@ -16,7 +16,10 @@ from kombu import (
     uuid,
 )
 from kombu.mixins import ConsumerProducerMixin
-from kombu.pools import producers
+from kombu.pools import (
+    connections,
+    producers,
+)
 from six.moves import reload_module
 
 import galaxy.queues
@@ -308,6 +311,7 @@ class GalaxyQueueWorker(ConsumerProducerMixin, threading.Thread):
         # Force connection instead of lazy-connecting the first time it is required.
         # Fixes `'kombu.transport.sqlalchemy.Message' is not mapped` error.
         self.connection.connect()
+        self.connection.release()
         self.app = app
         self.task_mapping = task_mapping
         self.exchange_queue = None
@@ -325,8 +329,9 @@ class GalaxyQueueWorker(ConsumerProducerMixin, threading.Thread):
         self.exchange_queue, self.direct_queue = galaxy.queues.control_queues_from_config(self.app.config)
         self.control_queues = [self.exchange_queue, self.direct_queue]
         # Delete messages for the current workers' control queues on startup
-        for q in self.control_queues:
-            q(self.connection).delete()
+        with connections[self.connection].acquire(block=True) as conn:
+            for q in self.control_queues:
+                q(conn).delete()
         self.start()
 
     def get_consumers(self, Consumer, channel):
diff --git a/lib/galaxy/tool_util/__init__.py b/lib/galaxy/tool_util/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/lib/galaxy/tools/cwl/__init__.py b/lib/galaxy/tool_util/cwl/__init__.py
similarity index 100%
rename from lib/galaxy/tools/cwl/__init__.py
rename to lib/galaxy/tool_util/cwl/__init__.py
diff --git a/lib/galaxy/tools/cwl/cwltool_deps.py b/lib/galaxy/tool_util/cwl/cwltool_deps.py
similarity index 100%
rename from lib/galaxy/tools/cwl/cwltool_deps.py
rename to lib/galaxy/tool_util/cwl/cwltool_deps.py
diff --git a/lib/galaxy/tools/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
similarity index 100%
rename from lib/galaxy/tools/cwl/parser.py
rename to lib/galaxy/tool_util/cwl/parser.py
diff --git a/lib/galaxy/tools/cwl/representation.py b/lib/galaxy/tool_util/cwl/representation.py
similarity index 100%
rename from lib/galaxy/tools/cwl/representation.py
rename to lib/galaxy/tool_util/cwl/representation.py
diff --git a/lib/galaxy/tools/cwl/runtime_actions.py b/lib/galaxy/tool_util/cwl/runtime_actions.py
similarity index 100%
rename from lib/galaxy/tools/cwl/runtime_actions.py
rename to lib/galaxy/tool_util/cwl/runtime_actions.py
diff --git a/lib/galaxy/tools/cwl/schema.py b/lib/galaxy/tool_util/cwl/schema.py
similarity index 100%
rename from lib/galaxy/tools/cwl/schema.py
rename to lib/galaxy/tool_util/cwl/schema.py
diff --git a/lib/galaxy/tools/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
similarity index 100%
rename from lib/galaxy/tools/cwl/util.py
rename to lib/galaxy/tool_util/cwl/util.py
diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tool_util/deps/__init__.py
similarity index 83%
rename from lib/galaxy/tools/deps/__init__.py
rename to lib/galaxy/tool_util/deps/__init__.py
index 116193ddc7e..397a9a12faf 100644
--- a/lib/galaxy/tools/deps/__init__.py
+++ b/lib/galaxy/tool_util/deps/__init__.py
@@ -24,8 +24,6 @@ from .resolvers import (
     ContainerDependency,
     NullDependency,
 )
-from .resolvers.conda import CondaDependencyResolver
-from .resolvers.galaxy_packages import GalaxyPackageDependencyResolver
 from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver
 
 log = logging.getLogger(__name__)
@@ -34,13 +32,26 @@ CONFIG_VAL_NOT_FOUND = object()
 
 
 def build_dependency_manager(config):
-    if getattr(config, "use_tool_dependencies", False):
+    config_dict = {
+        "use_tool_dependencies": getattr(config, "use_tool_dependencies", False),
+        "default_base_path": getattr(config, "tool_dependency_dir", None),
+        "conf_file": getattr(config, "dependency_resolvers_config_file", None),
+        "cache": getattr(config, "use_cached_dependency_manager", False),
+        "app_config": config,
+        "dependency_resolvers": getattr(config, "dependency_resolvers", None),
+    }
+    return build_dependency_manager_from_dict(config_dict)
+
+
+def build_dependency_manager_from_dict(config_dict):
+    if config_dict.get("use_tool_dependencies", False):
         dependency_manager_kwds = {
-            'default_base_path': config.tool_dependency_dir,
-            'conf_file': config.dependency_resolvers_config_file,
-            'app_config': config,
+            'default_base_path': config_dict.get("default_base_path"),
+            'conf_file': config_dict.get("conf_file"),
+            'app_config': config_dict.get("app_config"),
+            "dependency_resolver_dicts": config_dict.get("dependency_resolvers"),
         }
-        if getattr(config, "use_cached_dependency_manager", False):
+        if config_dict.get("cache"):
             dependency_manager = CachedDependencyManager(**dependency_manager_kwds)
         else:
             dependency_manager = DependencyManager(**dependency_manager_kwds)
@@ -61,8 +72,9 @@ class DependencyManager(object):
     and should each contain a file 'env.sh' which can be sourced to make the
     dependency available in the current shell environment.
     """
+    cached = False
 
-    def __init__(self, default_base_path, conf_file=None, app_config={}):
+    def __init__(self, default_base_path, conf_file=None, app_config={}, dependency_resolver_dicts=None):
         """
         Create a new dependency manager looking for packages under the paths listed
         in `base_paths`.  The default base path is app.config.tool_dependency_dir.
@@ -74,7 +86,13 @@ class DependencyManager(object):
         self.__app_config = app_config
         self.default_base_path = os.path.abspath(default_base_path)
         self.resolver_classes = self.__resolvers_dict()
-        self.dependency_resolvers = self.__build_dependency_resolvers(conf_file)
+
+        plugin_source = None
+        if dependency_resolver_dicts is not None:
+            plugin_source = ('dict', dependency_resolver_dicts)
+        else:
+            plugin_source = self.__build_dependency_resolvers_plugin_source(conf_file)
+        self.dependency_resolvers = self.__parse_resolver_conf_plugins(plugin_source)
         self._enabled_container_types = []
         self._destination_for_container_type = {}
 
@@ -232,38 +250,50 @@ class DependencyManager(object):
         else:
             return NullDependency(name=name, version=version)
 
-    def __build_dependency_resolvers(self, conf_file):
+    def __build_dependency_resolvers_plugin_source(self, conf_file):
         if not conf_file:
-            return self.__default_dependency_resolvers()
+            return self.__default_dependency_resolvers_source()
         if not os.path.exists(conf_file):
             log.debug("Unable to find config file '%s'", conf_file)
-            return self.__default_dependency_resolvers()
+            return self.__default_dependency_resolvers_source()
         plugin_source = plugin_config.plugin_source_from_path(conf_file)
-        return self.__parse_resolver_conf_xml(plugin_source)
+        return plugin_source
 
-    def __default_dependency_resolvers(self):
-        return [
-            ToolShedPackageDependencyResolver(self),
-            GalaxyPackageDependencyResolver(self),
-            CondaDependencyResolver(self),
-            GalaxyPackageDependencyResolver(self, versionless=True),
-            CondaDependencyResolver(self, versionless=True),
-        ]
+    def __default_dependency_resolvers_source(self):
+        return ('dict', [
+            {"type": "tool_shed_packages"},
+            {"type": "galaxy_packages"},
+            {"type": "conda"},
+            {"type": "galaxy_packages", "versionless": True},
+            {"type": "conda", "versionless": True},
+        ])
 
-    def __parse_resolver_conf_xml(self, plugin_source):
+    def __parse_resolver_conf_plugins(self, plugin_source):
         """
         """
         extra_kwds = dict(dependency_manager=self)
-        return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds)
+        # Use either 'type' from YAML definition or 'resolver_type' from to_dict definition.
+        return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds, plugin_type_keys=['type', 'resolver_type'])
 
     def __resolvers_dict(self):
-        import galaxy.tools.deps.resolvers
-        return plugin_config.plugins_dict(galaxy.tools.deps.resolvers, 'resolver_type')
+        import galaxy.tool_util.deps.resolvers
+        return plugin_config.plugins_dict(galaxy.tool_util.deps.resolvers, 'resolver_type')
+
+    def to_dict(self):
+        return {
+            "cache": self.cached,
+            "use_tool_dependencies": True,
+            "default_base_path": self.default_base_path,
+            "dependency_resolvers": [m.to_dict() for m in self.dependency_resolvers],
+            "tool_dependency_cache_dir": getattr(self, "tool_dependency_cache_dir", None),
+        }
 
 
 class CachedDependencyManager(DependencyManager):
-    def __init__(self, default_base_path, conf_file=None, app_config={}, tool_dependency_cache_dir=None):
-        super(CachedDependencyManager, self).__init__(default_base_path=default_base_path, conf_file=conf_file, app_config=app_config)
+    cached = True
+
+    def __init__(self, default_base_path, **kwd):
+        super(CachedDependencyManager, self).__init__(default_base_path=default_base_path, **kwd)
         self.tool_dependency_cache_dir = self.get_app_option("tool_dependency_cache_dir")
 
     def build_cache(self, requirements, **kwds):
@@ -338,3 +368,6 @@ class NullDependencyManager(DependencyManager):
 
     def find_dep(self, name, version=None, type='package', **kwds):
         return NullDependency(version=version, name=name)
+
+    def to_dict(self):
+        return {"use_tool_dependencies": False}
diff --git a/lib/galaxy/tools/deps/brew_exts.py b/lib/galaxy/tool_util/deps/brew_exts.py
similarity index 100%
rename from lib/galaxy/tools/deps/brew_exts.py
rename to lib/galaxy/tool_util/deps/brew_exts.py
diff --git a/lib/galaxy/tools/deps/brew_util.py b/lib/galaxy/tool_util/deps/brew_util.py
similarity index 100%
rename from lib/galaxy/tools/deps/brew_util.py
rename to lib/galaxy/tool_util/deps/brew_util.py
diff --git a/lib/galaxy/tools/deps/commands.py b/lib/galaxy/tool_util/deps/commands.py
similarity index 100%
rename from lib/galaxy/tools/deps/commands.py
rename to lib/galaxy/tool_util/deps/commands.py
diff --git a/lib/galaxy/tools/deps/conda_compat.py b/lib/galaxy/tool_util/deps/conda_compat.py
similarity index 100%
rename from lib/galaxy/tools/deps/conda_compat.py
rename to lib/galaxy/tool_util/deps/conda_compat.py
diff --git a/lib/galaxy/tools/deps/conda_util.py b/lib/galaxy/tool_util/deps/conda_util.py
similarity index 98%
rename from lib/galaxy/tools/deps/conda_util.py
rename to lib/galaxy/tool_util/deps/conda_util.py
index 546bc487325..baa90a7eaf8 100644
--- a/lib/galaxy/tools/deps/conda_util.py
+++ b/lib/galaxy/tool_util/deps/conda_util.py
@@ -12,7 +12,7 @@ import packaging.version
 import six
 from six.moves import shlex_quote
 
-from galaxy.tools.deps.commands import CommandLineException
+from galaxy.tool_util.deps.commands import CommandLineException
 from galaxy.util import (
     smart_str,
     unicodify
@@ -35,19 +35,19 @@ CONDA_LICENSE = "http://docs.continuum.io/anaconda/eula"
 VERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@(.*)")
 UNVERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@_uv_")
 USE_PATH_EXEC_DEFAULT = False
-CONDA_VERSION = "4.3.33"
-CONDA_BUILD_VERSION = "2.1.18"
+CONDA_VERSION = "4.6.14"
+CONDA_BUILD_VERSION = "3.17.8"
 USE_LOCAL_DEFAULT = False
 
 
 def conda_link():
     if IS_OS_X:
-        url = "https://repo.continuum.io/miniconda/Miniconda3-4.3.31-MacOSX-x86_64.sh"
+        url = "https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-MacOSX-x86_64.sh"
     else:
         if sys.maxsize > 2**32:
-            url = "https://repo.continuum.io/miniconda/Miniconda3-4.3.31-Linux-x86_64.sh"
+            url = "https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh"
         else:
-            url = "https://repo.continuum.io/miniconda/Miniconda3-4.3.31-Linux-x86.sh"
+            url = "https://repo.anaconda.com/miniconda/Miniconda3-4.5.12-Linux-x86.sh"
     return url
 
 
diff --git a/lib/galaxy/tools/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
similarity index 100%
rename from lib/galaxy/tools/deps/container_classes.py
rename to lib/galaxy/tool_util/deps/container_classes.py
diff --git a/lib/galaxy/tools/deps/container_resolvers/__init__.py b/lib/galaxy/tool_util/deps/container_resolvers/__init__.py
similarity index 94%
rename from lib/galaxy/tools/deps/container_resolvers/__init__.py
rename to lib/galaxy/tool_util/deps/container_resolvers/__init__.py
index 337b0328a4d..8a6dd286ad1 100644
--- a/lib/galaxy/tools/deps/container_resolvers/__init__.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/__init__.py
@@ -37,7 +37,7 @@ class ContainerResolver(Dictifiable):
     def resolve(self, enabled_container_types, tool_info, **kwds):
         """Find a container matching all supplied requirements for tool.
 
-        The supplied argument is a :class:`galaxy.tools.deps.containers.ToolInfo` description
+        The supplied argument is a :class:`galaxy.tool_util.deps.containers.ToolInfo` description
         of the tool and its requirements.
         """
 
diff --git a/lib/galaxy/tools/deps/container_resolvers/explicit.py b/lib/galaxy/tool_util/deps/container_resolvers/explicit.py
similarity index 100%
rename from lib/galaxy/tools/deps/container_resolvers/explicit.py
rename to lib/galaxy/tool_util/deps/container_resolvers/explicit.py
diff --git a/lib/galaxy/tools/deps/container_resolvers/mulled.py b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
similarity index 100%
rename from lib/galaxy/tools/deps/container_resolvers/mulled.py
rename to lib/galaxy/tool_util/deps/container_resolvers/mulled.py
diff --git a/lib/galaxy/tools/deps/containers.py b/lib/galaxy/tool_util/deps/containers.py
similarity index 95%
rename from lib/galaxy/tools/deps/containers.py
rename to lib/galaxy/tool_util/deps/containers.py
index 5a8234f84db..55a994ec78c 100644
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tool_util/deps/containers.py
@@ -148,7 +148,7 @@ class ContainerFinder(object):
             key = "%s_image" % container_type
         if key in destination_info:
             return destination_info.get(key)
-        elif "%s_image_default" in destination_info:
+        elif "%s_image_default" % container_type in destination_info:
             return self.__build_container_id_from_parts(container_type, destination_info, mode="default")
         return None
 
@@ -159,7 +159,7 @@ class ContainerFinder(object):
 
         # TODO: Right now this assumes all containers available when a
         # container type is - there should be more thought put into this.
-        # Checking which are availalbe - settings policies for what can be
+        # Checking which are available - settings policies for what can be
         # auto-fetched, etc....
         return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info, container_description)
 
@@ -206,7 +206,9 @@ class ContainerRegistry(object):
         if self.enable_beta_mulled_containers:
             default_resolvers.extend([
                 CachedMulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
+                CachedMulledDockerContainerResolver(self.app_info, namespace="local"),
                 CachedMulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
+                CachedMulledSingularityContainerResolver(self.app_info, namespace="local"),
                 MulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
                 MulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
                 BuildMulledDockerContainerResolver(self.app_info),
@@ -215,8 +217,8 @@ class ContainerRegistry(object):
         return default_resolvers
 
     def __resolvers_dict(self):
-        import galaxy.tools.deps.container_resolvers
-        return plugin_config.plugins_dict(galaxy.tools.deps.container_resolvers, 'resolver_type')
+        import galaxy.tool_util.deps.container_resolvers
+        return plugin_config.plugins_dict(galaxy.tool_util.deps.container_resolvers, 'resolver_type')
 
     def find_best_container_description(self, enabled_container_types, tool_info):
         """Yield best container description of supplied types matching tool info."""
diff --git a/lib/galaxy/tools/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py
similarity index 98%
rename from lib/galaxy/tools/deps/dependencies.py
rename to lib/galaxy/tool_util/deps/dependencies.py
index bc1820cf52c..dc1ffcee146 100644
--- a/lib/galaxy/tools/deps/dependencies.py
+++ b/lib/galaxy/tool_util/deps/dependencies.py
@@ -1,4 +1,4 @@
-from galaxy.tools.deps.requirements import ToolRequirements
+from galaxy.tool_util.deps.requirements import ToolRequirements
 from galaxy.util import bunch
 from .mulled.mulled_build import DEFAULT_CHANNELS
 
diff --git a/lib/galaxy/tools/deps/docker_util.py b/lib/galaxy/tool_util/deps/docker_util.py
similarity index 100%
rename from lib/galaxy/tools/deps/docker_util.py
rename to lib/galaxy/tool_util/deps/docker_util.py
diff --git a/lib/galaxy/tools/deps/dockerfiles.py b/lib/galaxy/tool_util/deps/dockerfiles.py
similarity index 100%
rename from lib/galaxy/tools/deps/dockerfiles.py
rename to lib/galaxy/tool_util/deps/dockerfiles.py
diff --git a/lib/galaxy/tools/deps/installable.py b/lib/galaxy/tool_util/deps/installable.py
similarity index 100%
rename from lib/galaxy/tools/deps/installable.py
rename to lib/galaxy/tool_util/deps/installable.py
diff --git a/lib/galaxy/tool_util/deps/mulled/__init__.py b/lib/galaxy/tool_util/deps/mulled/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/lib/galaxy/tools/deps/mulled/_cli.py b/lib/galaxy/tool_util/deps/mulled/_cli.py
similarity index 100%
rename from lib/galaxy/tools/deps/mulled/_cli.py
rename to lib/galaxy/tool_util/deps/mulled/_cli.py
diff --git a/lib/galaxy/tools/deps/mulled/invfile.lua b/lib/galaxy/tool_util/deps/mulled/invfile.lua
similarity index 100%
rename from lib/galaxy/tools/deps/mulled/invfile.lua
rename to lib/galaxy/tool_util/deps/mulled/invfile.lua
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
similarity index 99%
rename from lib/galaxy/tools/deps/mulled/mulled_build.py
rename to lib/galaxy/tool_util/deps/mulled/mulled_build.py
index c3c84f5a586..e08c5d53d93 100644
--- a/lib/galaxy/tools/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -24,7 +24,7 @@ try:
 except ImportError:
     yaml = None
 
-from galaxy.tools.deps import commands, installable
+from galaxy.tool_util.deps import commands, installable
 from galaxy.util import safe_makedirs
 from ._cli import arg_parser
 from .util import (
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_channel.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_channel.py
similarity index 100%
rename from lib/galaxy/tools/deps/mulled/mulled_build_channel.py
rename to lib/galaxy/tool_util/deps/mulled/mulled_build_channel.py
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_files.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_files.py
similarity index 100%
rename from lib/galaxy/tools/deps/mulled/mulled_build_files.py
rename to lib/galaxy/tool_util/deps/mulled/mulled_build_files.py
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
similarity index 96%
rename from lib/galaxy/tools/deps/mulled/mulled_build_tool.py
rename to lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
index a46cb06da57..682c6755830 100644
--- a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
@@ -9,7 +9,7 @@ Build mulled images for requirements defined in a tool:
 
 """
 
-from galaxy.tools.parser import get_tool_source
+from galaxy.tool_util.parser import get_tool_source
 from ._cli import arg_parser
 from .mulled_build import (
     add_build_arguments,
diff --git a/lib/galaxy/tools/deps/mulled/mulled_search.py b/lib/galaxy/tool_util/deps/mulled/mulled_search.py
similarity index 100%
rename from lib/galaxy/tools/deps/mulled/mulled_search.py
rename to lib/galaxy/tool_util/deps/mulled/mulled_search.py
diff --git a/lib/galaxy/tools/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py
similarity index 100%
rename from lib/galaxy/tools/deps/mulled/util.py
rename to lib/galaxy/tool_util/deps/mulled/util.py
diff --git a/lib/galaxy/tools/deps/requirements.py b/lib/galaxy/tool_util/deps/requirements.py
similarity index 100%
rename from lib/galaxy/tools/deps/requirements.py
rename to lib/galaxy/tool_util/deps/requirements.py
diff --git a/lib/galaxy/tools/deps/resolvers/__init__.py b/lib/galaxy/tool_util/deps/resolvers/__init__.py
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/__init__.py
rename to lib/galaxy/tool_util/deps/resolvers/__init__.py
diff --git a/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py b/lib/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
rename to lib/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.py
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tool_util/deps/resolvers/conda.py
similarity index 95%
rename from lib/galaxy/tools/deps/resolvers/conda.py
rename to lib/galaxy/tool_util/deps/resolvers/conda.py
index 58037239ab0..e7f4d3a25f0 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tool_util/deps/resolvers/conda.py
@@ -7,8 +7,8 @@ import logging
 import os
 import re
 
-import galaxy.tools.deps.installable
-import galaxy.tools.deps.requirements
+import galaxy.tool_util.deps.installable
+import galaxy.tool_util.deps.requirements
 from . import (
     Dependency,
     DependencyException,
@@ -42,11 +42,11 @@ DEFAULT_CONDARC_OVERRIDE = "_condarc"
 # https://github.com/bioconda/bioconda-recipes/blob/master/config.yml , but
 # adding `iuc` as first channel (for Galaxy-specific packages)
 DEFAULT_ENSURE_CHANNELS = "iuc,conda-forge,bioconda,defaults"
-CONDA_SOURCE_CMD = """[ "$CONDA_DEFAULT_ENV" = "%s" ] ||
+CONDA_SOURCE_CMD = """[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '{environment_path}')" ] ||
 MAX_TRIES=3
 COUNT=0
 while [ $COUNT -lt $MAX_TRIES ]; do
-    . %s '%s' > conda_activate.log 2>&1
+    . '{activate_path}' '{environment_path}' > conda_activate.log 2>&1
     if [ $? -eq 0 ];then
         break
     else
@@ -65,7 +65,7 @@ log = logging.getLogger(__name__)
 
 
 class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, ListableDependencyResolver, InstallableDependencyResolver, SpecificationPatternDependencyResolver, MappableDependencyResolver):
-    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['conda_prefix', 'versionless', 'ensure_channels', 'auto_install']
+    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['conda_prefix', 'versionless', 'ensure_channels', 'auto_install', 'auto_init']
     resolver_type = "conda"
     config_options = {
         'prefix': None,
@@ -133,7 +133,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
         auto_install = _string_as_bool(get_option("auto_install"))
         self.auto_init = _string_as_bool(get_option("auto_init"))
         self.conda_context = conda_context
-        self.disabled = not galaxy.tools.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init)
+        self.disabled = not galaxy.tool_util.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init)
         if self.auto_init and not self.disabled:
             self.conda_context.ensure_conda_build_installed_if_needed()
         self.auto_install = auto_install
@@ -206,7 +206,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
             if requirement.type != "package":
                 return []
 
-        ToolRequirements = galaxy.tools.deps.requirements.ToolRequirements
+        ToolRequirements = galaxy.tool_util.deps.requirements.ToolRequirements
         expanded_requirements = ToolRequirements([self._expand_requirement(r) for r in requirements])
         if self.versionless:
             conda_targets = [CondaTarget(r.name, version=None) for r in expanded_requirements]
@@ -405,10 +405,9 @@ class MergedCondaDependency(Dependency):
                 self.environment_path,
             )
         else:
-            return CONDA_SOURCE_CMD % (
-                self.environment_path,
-                self.activate,
-                self.environment_path
+            return CONDA_SOURCE_CMD.format(
+                activate_path=self.activate,
+                environment_path=self.environment_path
             )
 
 
@@ -474,10 +473,9 @@ class CondaDependency(Dependency):
                 self.environment_path,
             )
         else:
-            return CONDA_SOURCE_CMD % (
-                self.environment_path,
-                self.activate,
-                self.environment_path
+            return CONDA_SOURCE_CMD.format(
+                activate_path=self.activate,
+                environment_path=self.environment_path
             )
 
 
diff --git a/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml b/lib/galaxy/tool_util/deps/resolvers/default_conda_mapping.yml
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
rename to lib/galaxy/tool_util/deps/resolvers/default_conda_mapping.yml
diff --git a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py b/lib/galaxy/tool_util/deps/resolvers/galaxy_packages.py
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/galaxy_packages.py
rename to lib/galaxy/tool_util/deps/resolvers/galaxy_packages.py
diff --git a/lib/galaxy/tools/deps/resolvers/homebrew.py b/lib/galaxy/tool_util/deps/resolvers/homebrew.py
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/homebrew.py
rename to lib/galaxy/tool_util/deps/resolvers/homebrew.py
diff --git a/lib/galaxy/tools/deps/resolvers/lmod.py b/lib/galaxy/tool_util/deps/resolvers/lmod.py
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/lmod.py
rename to lib/galaxy/tool_util/deps/resolvers/lmod.py
diff --git a/lib/galaxy/tools/deps/resolvers/modules.py b/lib/galaxy/tool_util/deps/resolvers/modules.py
similarity index 98%
rename from lib/galaxy/tools/deps/resolvers/modules.py
rename to lib/galaxy/tool_util/deps/resolvers/modules.py
index fc7e17b62da..37ac3d70b8b 100644
--- a/lib/galaxy/tools/deps/resolvers/modules.py
+++ b/lib/galaxy/tool_util/deps/resolvers/modules.py
@@ -41,7 +41,7 @@ UNKNOWN_FIND_BY_MESSAGE = "ModuleDependencyResolver does not know how to find mo
 
 
 class ModuleDependencyResolver(DependencyResolver, MappableDependencyResolver):
-    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['base_path', 'modulepath']
+    dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['base_path', 'modulepath', 'modulecmd', 'prefetch', 'default_indicator', 'find_by']
     resolver_type = "modules"
 
     def __init__(self, dependency_manager, **kwds):
@@ -50,6 +50,7 @@ class ModuleDependencyResolver(DependencyResolver, MappableDependencyResolver):
         self._setup_mapping(dependency_manager, **kwds)
         self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
         find_by = kwds.get('find_by', 'avail')
+        self.find_by = find_by
         prefetch = _string_as_bool(kwds.get('prefetch', DEFAULT_MODULE_PREFETCH))
         self.modulecmd = kwds.get('modulecmd', DEFAULT_MODULECMD_PATH)
         self.modulepath = kwds.get('modulepath', self.__default_modulespath())
diff --git a/lib/galaxy/tools/deps/resolvers/resolver_mixins.py b/lib/galaxy/tool_util/deps/resolvers/resolver_mixins.py
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/resolver_mixins.py
rename to lib/galaxy/tool_util/deps/resolvers/resolver_mixins.py
diff --git a/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py b/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
rename to lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py
diff --git a/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py b/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py
similarity index 100%
rename from lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
rename to lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py
diff --git a/lib/galaxy/tools/deps/singularity_util.py b/lib/galaxy/tool_util/deps/singularity_util.py
similarity index 100%
rename from lib/galaxy/tools/deps/singularity_util.py
rename to lib/galaxy/tool_util/deps/singularity_util.py
diff --git a/lib/galaxy/tools/deps/views.py b/lib/galaxy/tool_util/deps/views.py
similarity index 99%
rename from lib/galaxy/tools/deps/views.py
rename to lib/galaxy/tool_util/deps/views.py
index 0ce83a3d121..bd78aa54cf5 100644
--- a/lib/galaxy/tools/deps/views.py
+++ b/lib/galaxy/tool_util/deps/views.py
@@ -2,7 +2,7 @@ from galaxy import exceptions
 
 
 class DependencyResolversView(object):
-    """ Provide a RESTfulish/JSONy interface to a galaxy.tools.deps.DependencyResolver
+    """ Provide a RESTfulish/JSONy interface to a galaxy.tool_util.deps.DependencyResolver
     object. This can be adapted by the Galaxy web framework or other web apps.
     """
 
diff --git a/lib/galaxy/tools/fetcher.py b/lib/galaxy/tool_util/fetcher.py
similarity index 86%
rename from lib/galaxy/tools/fetcher.py
rename to lib/galaxy/tool_util/fetcher.py
index 686de383fb9..a0b01dbd956 100644
--- a/lib/galaxy/tools/fetcher.py
+++ b/lib/galaxy/tool_util/fetcher.py
@@ -7,8 +7,8 @@ class ToolLocationFetcher(object):
         self.resolver_classes = self.__resolvers_dict()
 
     def __resolvers_dict(self):
-        import galaxy.tools.locations
-        return plugin_config.plugins_dict(galaxy.tools.locations, 'scheme')
+        import galaxy.tool_util.locations
+        return plugin_config.plugins_dict(galaxy.tool_util.locations, 'scheme')
 
     def to_tool_path(self, path_or_uri_like, **kwds):
         if "://" not in path_or_uri_like:
diff --git a/lib/galaxy/tools/loader.py b/lib/galaxy/tool_util/loader.py
similarity index 100%
rename from lib/galaxy/tools/loader.py
rename to lib/galaxy/tool_util/loader.py
diff --git a/lib/galaxy/tools/locations/__init__.py b/lib/galaxy/tool_util/locations/__init__.py
similarity index 100%
rename from lib/galaxy/tools/locations/__init__.py
rename to lib/galaxy/tool_util/locations/__init__.py
diff --git a/lib/galaxy/tools/locations/dockstore.py b/lib/galaxy/tool_util/locations/dockstore.py
similarity index 100%
rename from lib/galaxy/tools/locations/dockstore.py
rename to lib/galaxy/tool_util/locations/dockstore.py
diff --git a/lib/galaxy/tools/locations/file.py b/lib/galaxy/tool_util/locations/file.py
similarity index 100%
rename from lib/galaxy/tools/locations/file.py
rename to lib/galaxy/tool_util/locations/file.py
diff --git a/lib/galaxy/tools/locations/http.py b/lib/galaxy/tool_util/locations/http.py
similarity index 100%
rename from lib/galaxy/tools/locations/http.py
rename to lib/galaxy/tool_util/locations/http.py
diff --git a/lib/galaxy/jobs/output_checker.py b/lib/galaxy/tool_util/output_checker.py
similarity index 96%
rename from lib/galaxy/jobs/output_checker.py
rename to lib/galaxy/tool_util/output_checker.py
index a5fb26ba0e5..807c5d87c1f 100644
--- a/lib/galaxy/jobs/output_checker.py
+++ b/lib/galaxy/tool_util/output_checker.py
@@ -1,7 +1,7 @@
 import re
 from logging import getLogger
 
-from galaxy.tools.parser.error_level import StdioErrorLevel
+from galaxy.tool_util.parser.error_level import StdioErrorLevel
 from galaxy.util import unicodify
 from galaxy.util.bunch import Bunch
 
@@ -146,10 +146,9 @@ def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code
             if stderr:
                 state = DETECTED_JOB_STATE.GENERIC_ERROR
 
-        if DETECTED_JOB_STATE != DETECTED_JOB_STATE.OK and stderr:
-            if stderr:
-                peak = stderr[0:ERROR_PEAK]
-                log.debug("job failed, standard error is - [%s]" % peak)
+        if state != DETECTED_JOB_STATE.OK:
+            peak = stderr[0:ERROR_PEAK] if stderr else ""
+            log.debug("job failed, detected state %s, standard error is - [%s]" % (state, peak))
     except Exception:
         log.exception("Job state check encountered unexpected exception; assuming execution successful")
 
diff --git a/lib/galaxy/tools/parser/__init__.py b/lib/galaxy/tool_util/parser/__init__.py
similarity index 100%
rename from lib/galaxy/tools/parser/__init__.py
rename to lib/galaxy/tool_util/parser/__init__.py
diff --git a/lib/galaxy/tools/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
similarity index 97%
rename from lib/galaxy/tools/parser/cwl.py
rename to lib/galaxy/tool_util/parser/cwl.py
index 576023848b5..bdec03eb641 100644
--- a/lib/galaxy/tools/parser/cwl.py
+++ b/lib/galaxy/tool_util/parser/cwl.py
@@ -1,8 +1,8 @@
 import logging
 import os
 
-from galaxy.tools.cwl import tool_proxy
-from galaxy.tools.deps import requirements
+from galaxy.tool_util.cwl import tool_proxy
+from galaxy.tool_util.deps import requirements
 from galaxy.util.odict import odict
 from .error_level import StdioErrorLevel
 from .interface import (
@@ -150,6 +150,9 @@ class CwlToolSource(ToolSource):
     def parse_profile(self):
         return "16.04"
 
+    def parse_python_template_version(self):
+        return '3.5'
+
 
 class CwlPageSource(PageSource):
 
diff --git a/lib/galaxy/tools/parser/error_level.py b/lib/galaxy/tool_util/parser/error_level.py
similarity index 100%
rename from lib/galaxy/tools/parser/error_level.py
rename to lib/galaxy/tool_util/parser/error_level.py
diff --git a/lib/galaxy/tools/parser/factory.py b/lib/galaxy/tool_util/parser/factory.py
similarity index 98%
rename from lib/galaxy/tools/parser/factory.py
rename to lib/galaxy/tool_util/parser/factory.py
index 10ab5587063..63a65fea3c8 100644
--- a/lib/galaxy/tools/parser/factory.py
+++ b/lib/galaxy/tool_util/parser/factory.py
@@ -5,7 +5,7 @@ import logging
 
 import yaml
 
-from galaxy.tools.loader import load_tool_with_refereces
+from galaxy.tool_util.loader import load_tool_with_refereces
 from galaxy.util.odict import odict
 from .cwl import CwlToolSource
 from .interface import InputSource
diff --git a/lib/galaxy/tools/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py
similarity index 98%
rename from lib/galaxy/tools/parser/interface.py
rename to lib/galaxy/tool_util/parser/interface.py
index aa6ade42b69..f63e51ce8e5 100644
--- a/lib/galaxy/tools/parser/interface.py
+++ b/lib/galaxy/tool_util/parser/interface.py
@@ -218,6 +218,12 @@ class ToolSource(object):
         """ Return tool profile version as Galaxy major e.g. 16.01 or 16.04.
         """
 
+    @abstractmethod
+    def parse_python_template_version(self):
+        """
+        Return minimum python version that the tool template has been developed against.
+        """
+
     def macro_paths(self):
         return []
 
diff --git a/lib/galaxy/tools/parser/output_actions.py b/lib/galaxy/tool_util/parser/output_actions.py
similarity index 100%
rename from lib/galaxy/tools/parser/output_actions.py
rename to lib/galaxy/tool_util/parser/output_actions.py
diff --git a/lib/galaxy/tools/parser/output_collection_def.py b/lib/galaxy/tool_util/parser/output_collection_def.py
similarity index 100%
rename from lib/galaxy/tools/parser/output_collection_def.py
rename to lib/galaxy/tool_util/parser/output_collection_def.py
diff --git a/lib/galaxy/tools/parser/output_objects.py b/lib/galaxy/tool_util/parser/output_objects.py
similarity index 100%
rename from lib/galaxy/tools/parser/output_objects.py
rename to lib/galaxy/tool_util/parser/output_objects.py
diff --git a/lib/galaxy/tools/parser/util.py b/lib/galaxy/tool_util/parser/util.py
similarity index 100%
rename from lib/galaxy/tools/parser/util.py
rename to lib/galaxy/tool_util/parser/util.py
diff --git a/lib/galaxy/tools/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
similarity index 98%
rename from lib/galaxy/tools/parser/xml.py
rename to lib/galaxy/tool_util/parser/xml.py
index c142c97745d..24eca5a78a4 100644
--- a/lib/galaxy/tools/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -5,7 +5,9 @@ import traceback
 import uuid
 from math import isinf
 
-from galaxy.tools.deps import requirements
+import packaging.version
+
+from galaxy.tool_util.deps import requirements
 from galaxy.util import string_as_bool, xml_text, xml_to_string
 from galaxy.util.odict import odict
 from .error_level import StdioErrorLevel
@@ -113,7 +115,7 @@ class XmlToolSource(ToolSource):
         return ((command_el is not None) and command_el.text) or None
 
     def parse_expression(self):
-        """ Return string contianing command to run.
+        """ Return string containing command to run.
         """
         expression_el = self.root.find("expression")
         if expression_el is not None:
@@ -270,6 +272,7 @@ class XmlToolSource(ToolSource):
 
         def _parse_expression(output_elem, **kwds):
             output_def = self._parse_expression_output(output_elem, tool, **kwds)
+            output_def.filters = output_elem.findall('filter')
             data_dict[output_def.name] = output_def
             return output_def
 
@@ -329,7 +332,7 @@ class XmlToolSource(ToolSource):
                 output_collection.outputs[output_name] = data
             output_collections[name] = output_collection
 
-        for out_child in out_elem.getchildren():
+        for out_child in out_elem:
             if out_child.tag == "data":
                 _parse(out_child)
             elif out_child.tag == "collection":
@@ -345,7 +348,7 @@ class XmlToolSource(ToolSource):
                 else:
                     _parse_expression(out_child)
             else:
-                log.warn("Unknown output tag encountered [%s]" % out_child.tag)
+                log.warning("Unknown output tag encountered [%s]" % out_child.tag)
 
         for output_def in data_dict.values():
             outputs[output_def.name] = output_def
@@ -482,6 +485,12 @@ class XmlToolSource(ToolSource):
         # - Enable buggy interpreter attribute.
         return self.root.get("profile", "16.01")
 
+    def parse_python_template_version(self):
+        python_template_version = self.root.get("python_template_version", None)
+        if python_template_version is not None:
+            python_template_version = packaging.version.parse(python_template_version)
+        return python_template_version
+
 
 def _test_elem_to_dict(test_elem, i):
     rval = dict(
diff --git a/lib/galaxy/tools/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
similarity index 96%
rename from lib/galaxy/tools/parser/yaml.py
rename to lib/galaxy/tool_util/parser/yaml.py
index 65ce7747644..d13331cd768 100644
--- a/lib/galaxy/tools/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -1,4 +1,6 @@
-from galaxy.tools.deps import requirements
+import packaging.version
+
+from galaxy.tool_util.deps import requirements
 from galaxy.util.odict import odict
 from .interface import InputSource
 from .interface import PageSource
@@ -162,6 +164,12 @@ class YamlToolSource(ToolSource):
     def parse_profile(self):
         return self.root_dict.get("profile", "16.04")
 
+    def parse_python_template_version(self):
+        python_template_version = self.root_dict.get("python_template_version", None)
+        if python_template_version is not None:
+            python_template_version = packaging.version.parse(python_template_version)
+        return python_template_version
+
 
 def _parse_test(i, test_dict):
     inputs = test_dict["inputs"]
diff --git a/lib/galaxy/tools/provided_metadata.py b/lib/galaxy/tool_util/provided_metadata.py
similarity index 100%
rename from lib/galaxy/tools/provided_metadata.py
rename to lib/galaxy/tool_util/provided_metadata.py
diff --git a/lib/galaxy/tools/xsd/LICENSE b/lib/galaxy/tool_util/xsd/LICENSE
similarity index 100%
rename from lib/galaxy/tools/xsd/LICENSE
rename to lib/galaxy/tool_util/xsd/LICENSE
diff --git a/lib/galaxy/tools/xsd/README.md b/lib/galaxy/tool_util/xsd/README.md
similarity index 100%
rename from lib/galaxy/tools/xsd/README.md
rename to lib/galaxy/tool_util/xsd/README.md
diff --git a/lib/galaxy/tools/xsd/galaxy.jxb b/lib/galaxy/tool_util/xsd/galaxy.jxb
similarity index 100%
rename from lib/galaxy/tools/xsd/galaxy.jxb
rename to lib/galaxy/tool_util/xsd/galaxy.jxb
diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
similarity index 99%
rename from lib/galaxy/tools/xsd/galaxy.xsd
rename to lib/galaxy/tool_util/xsd/galaxy.xsd
index 7713c7bb614..a9c208e62ca 100644
--- a/lib/galaxy/tools/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -175,13 +175,22 @@ set this to have values such as ``data_source`` or ``manage_data``.</xs:document
       </xs:attribute>
       <xs:attribute name="profile" type="xs:string">
         <xs:annotation>
-          <xs:documentation xml:lang="en">This string specified the minimum Galaxy
+          <xs:documentation xml:lang="en">This string specifies the minimum Galaxy
 version that should be required to run this tool. Certain legacy behaviors such
 as using standard error content to detect errors instead of exit code are disabled
 automatically if profile is set to any version newer than ``16.01``, such as
 ``16.04``.</xs:documentation>
         </xs:annotation>
       </xs:attribute>
+      <xs:attribute name="python_template_version" type="xs:float">
+        <xs:annotation>
+          <xs:documentation xml:lang="en">This string specifies the minimum Python
+version that is able to fill the Cheetah sections of the tool. If unset defaults
+to 2.7 if the profile is older than 19.01, otherwise defaults to 3.5. Galaxy will 
+attempt to convert Python statements in Cheetah sections using [future](http://python-future.org/)
+if Galaxy is run on Python 3 and ``python_template_version`` is below 3.</xs:documentation>
+        </xs:annotation>
+      </xs:attribute>
       <xs:attribute name="workflow_compatible" type="xs:boolean" default="true">
         <xs:annotation>
           <xs:documentation xml:lang="en">This attribute indicates if
@@ -1660,7 +1669,7 @@ module.
   </xs:group>
   <xs:complexType name="AssertHasH5Keys">
     <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[Asserts HDF5 output has a set of attributes (``keys``), specified as a comma-separated list (e.g. ``<has_h5_keys keys="bins,chroms,indexes,pixels" />``).]]></xs:documentation>
+      <xs:documentation xml:lang="en"><![CDATA[Asserts HDF5 output has a set of attributes (``keys``), specified as a comma-separated list (e.g. ``<has_h5_keys keys="bins,chroms,indexes,pixels,chroms/lengths" />``).]]></xs:documentation>
     </xs:annotation>
     <xs:attribute name="keys" type="xs:string">
       <xs:annotation>
@@ -2098,7 +2107,7 @@ parameter being described. All the attributes for the ``param`` element are
 documented below for completeness, but here are the common ones for each
 type are as follows:
 
-$attribute_list:name,type,optional,label,help,argument,refresh_on_change:4
+$attribute_list:name,type,optional,label,help,argument,load_contents,refresh_on_change:4
 
 ### Parameter Types
 
@@ -2364,6 +2373,13 @@ tool form just below the associated field to provide information about the
 field.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
+        <xs:attribute name="load_contents" type="xs:integer">
+          <xs:annotation>
+            <xs:documentation xml:lang="en">Number of bytes that should be
+loaded into the `contents` attribute of the jobs dictionary provided to Expression
+Tools. Applies only to type="data" inputs.</xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
         <xs:attribute name="value" type="xs:string">
           <xs:annotation>
             <xs:documentation xml:lang="en">The default value for this
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 7e22d209b4d..a6c9581a3be 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -25,19 +25,31 @@ from galaxy import (
     exceptions,
     model
 )
+from galaxy.job_execution import output_collect
 from galaxy.managers.jobs import JobSearch
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.model.tags import GalaxyTagHandler
-from galaxy.queue_worker import send_control_task
+from galaxy.tool_util.deps import (
+    CachedDependencyManager,
+)
+from galaxy.tool_util.fetcher import ToolLocationFetcher
+from galaxy.tool_util.loader import (
+    imported_macro_paths,
+    raw_tool_xml_tree,
+    template_macro_params
+)
+from galaxy.tool_util.parser import (
+    get_tool_source,
+    get_tool_source_from_representation,
+    ToolOutputCollectionPart
+)
+from galaxy.tool_util.parser.xml import XmlPageSource
+from galaxy.tool_util.provided_metadata import parse_tool_provided_metadata
 from galaxy.tools import expressions
 from galaxy.tools.actions import DefaultToolAction
 from galaxy.tools.actions.data_manager import DataManagerToolAction
 from galaxy.tools.actions.data_source import DataSourceToolAction
 from galaxy.tools.actions.model_operations import ModelOperationToolAction
-from galaxy.tools.deps import (
-    CachedDependencyManager,
-)
-from galaxy.tools.fetcher import ToolLocationFetcher
 from galaxy.tools.parameters import (
     check_param,
     params_from_strings,
@@ -46,7 +58,6 @@ from galaxy.tools.parameters import (
     populate_state,
     visit_input_values
 )
-from galaxy.tools.parameters import output_collect
 from galaxy.tools.parameters.basic import (
     BaseURLToolParameter,
     DataCollectionToolParameter,
@@ -64,12 +75,6 @@ from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repea
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.meta import expand_meta_parameters
 from galaxy.tools.parameters.wrapped_json import json_wrap
-from galaxy.tools.parser import (
-    get_tool_source,
-    get_tool_source_from_representation,
-    ToolOutputCollectionPart
-)
-from galaxy.tools.parser.xml import XmlPageSource
 from galaxy.tools.test import parse_tests
 from galaxy.tools.toolbox import BaseGalaxyToolBox
 from galaxy.util import (
@@ -96,12 +101,6 @@ from .execute import (
     execute as execute_job,
     MappingParameters,
 )
-from .loader import (
-    imported_macro_paths,
-    raw_tool_xml_tree,
-    template_macro_params
-)
-from .provided_metadata import parse_tool_provided_metadata
 
 log = logging.getLogger(__name__)
 
@@ -158,6 +157,7 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "sam_pileup",
     "find_diag_hits",
     "cufflinks",
+    "gops_intersect_1",
     # Tools improperly migrated to the tool shed (iuc)
     "tabular_to_dbnsfp",
     # Tools improperly migrated using Galaxy (from shed other)
@@ -192,7 +192,7 @@ class ToolErrorLog(object):
             "file": file,
             "time": str(datetime.now()),
             "phase": phase,
-            "error": str(exception)
+            "error": unicodify(exception)
         })
         if len(self.error_stack) > self.max_errors:
             self.error_stack.pop()
@@ -241,16 +241,6 @@ class ToolBox(BaseGalaxyToolBox):
             app=app,
         )
 
-    def handle_panel_update(self, section_dict):
-        """
-        Sends a panel update to all threads/processes.
-        """
-        send_control_task(self.app, 'create_panel_section', kwargs=section_dict)
-        # The following local call to self.create_section should be unnecessary
-        # but occasionally the local ToolPanelElements instance appears to not
-        # get updated.
-        self.create_section(section_dict)
-
     def has_reloaded(self, other_toolbox):
         return self._reload_count != other_toolbox._reload_count
 
@@ -463,6 +453,7 @@ class Tool(Dictifiable):
         self.guid = guid
         self.old_id = None
         self.version = None
+        self.python_template_version = None
         self._lineage = None
         self.dependencies = []
         # populate toolshed repository info, if available
@@ -642,6 +633,14 @@ class Tool(Dictifiable):
             message = template % (self.id, self.profile)
             raise Exception(message)
 
+        self.python_template_version = tool_source.parse_python_template_version()
+        if self.python_template_version is None:
+            # If python_template_version not specified we assume tools with profile versions >= 19.05 are python 3 ready
+            if self.profile >= 19.05:
+                self.python_template_version = '3.5'
+            else:
+                self.python_template_version = '2.7'
+
         # Get the (user visible) name of the tool
         self.name = tool_source.parse_name()
         if not self.name and dynamic:
@@ -1064,7 +1063,7 @@ class Tool(Dictifiable):
             if citation_elem.tag != "citation":
                 pass
             if hasattr(self.app, 'citations_manager'):
-                citation = self.app.citations_manager.parse_citation(citation_elem, self.tool_dir)
+                citation = self.app.citations_manager.parse_citation(citation_elem)
                 if citation:
                     citations.append(citation)
         return citations
@@ -1476,7 +1475,7 @@ class Tool(Dictifiable):
             return False, e
         except Exception as e:
             log.exception('Exception caught while attempting tool execution:')
-            message = 'Error executing tool: %s' % str(e)
+            message = 'Error executing tool: %s' % unicodify(e)
             return False, message
         if isinstance(out_data, odict):
             return job, list(out_data.items())
@@ -1727,6 +1726,8 @@ class Tool(Dictifiable):
         Find any additional datasets generated by a tool and attach (for
         cases where number of outputs is not known in advance).
         """
+        # given the job_execution import is the only one, probably makes sense to refactor this out
+        # into job_wrapper.
         tool = self
         permission_provider = output_collect.PermissionProvider(inp_data, tool.app.security_agent, job)
         metadata_source_provider = output_collect.MetadataSourceProvider(inp_data)
@@ -1923,7 +1924,7 @@ class Tool(Dictifiable):
                 if history is None:
                     raise exceptions.MessageException('History unavailable. Please specify a valid history id')
             except Exception as e:
-                raise exceptions.MessageException('[history_id=%s] Failed to retrieve history. %s.' % (history_id, str(e)))
+                raise exceptions.MessageException('[history_id=%s] Failed to retrieve history. %s.' % (history_id, unicodify(e)))
 
         # build request context
         request_context = WorkRequestContext(app=trans.app, user=trans.user, history=history, workflow_building_mode=workflow_building_mode)
@@ -1939,7 +1940,7 @@ class Tool(Dictifiable):
                 tool_message = self._compare_tool_version(job)
                 params_to_incoming(kwd, self.inputs, job_params, self.app)
             except Exception as e:
-                raise exceptions.MessageException(str(e))
+                raise exceptions.MessageException(unicodify(e))
 
         # create parameter object
         params = Params(kwd, sanitize=False)
@@ -2139,7 +2140,7 @@ class Tool(Dictifiable):
             if len(self.tool_versions) > 1 and tool_version != self.tool_versions[-1]:
                 message += 'There is a newer version of this tool available.'
         except Exception as e:
-            raise exceptions.MessageException(str(e))
+            raise exceptions.MessageException(unicodify(e))
         return message
 
     def get_default_history_by_trans(self, trans, create=False):
@@ -2382,7 +2383,7 @@ class SetMetadataTool(Tool):
             job, base_dir='job_work', dir_only=True, obj_dir=True
         )
         for name, dataset in inp_data.items():
-            external_metadata = get_metadata_compute_strategy(app, job.id)
+            external_metadata = get_metadata_compute_strategy(app.config, job.id)
             sa_session = app.model.context
             if external_metadata.external_metadata_set_successfully(dataset, name, sa_session, working_directory=working_directory):
                 external_metadata.load_metadata(dataset, name, sa_session, working_directory=working_directory)
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 7f4ecd03c92..def2be977ee 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -1,5 +1,6 @@
 import json
 import logging
+import os
 import re
 from json import dumps
 
@@ -9,12 +10,12 @@ from galaxy import model
 from galaxy.jobs.actions.post import ActionBox
 from galaxy.model import LibraryDatasetDatasetAssociation, WorkflowRequestInputParameter
 from galaxy.model.dataset_collections.builder import CollectionBuilder
+from galaxy.model.none_like import NoneDataset
 from galaxy.objectstore import ObjectStorePopulator
 from galaxy.tools.parameters import update_dataset_ids
 from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter, RuntimeValue
 from galaxy.tools.parameters.wrapped import WrappedParameters
 from galaxy.util import ExecutionTimer
-from galaxy.util.none_like import NoneDataset
 from galaxy.util.odict import odict
 from galaxy.util.template import fill_template
 from galaxy.web import url_for
@@ -260,7 +261,6 @@ class DefaultToolAction(object):
         for data in inp_data.values():
             if not data:
                 continue
-
             for tag in data.auto_propagated_tags:
                 preserved_tags[tag.value] = tag
 
@@ -378,7 +378,8 @@ class DefaultToolAction(object):
                     wrapped_params.params,
                     inp_data,
                     inp_dataset_collections,
-                    input_ext
+                    input_ext,
+                    python_template_version=tool.python_template_version,
                 )
                 create_datasets = True
                 dataset = None
@@ -392,6 +393,10 @@ class DefaultToolAction(object):
                             break
 
                 data = app.model.HistoryDatasetAssociation(extension=ext, dataset=dataset, create_dataset=create_datasets, flush=False)
+                if create_datasets:
+                    from_work_dir = output.from_work_dir
+                    if from_work_dir is not None:
+                        data.dataset.created_from_basename = os.path.basename(from_work_dir)
                 if hidden is None:
                     hidden = output.hidden
                 if not hidden and dataset_collection_elements is not None:  # Mapping over a collection - hide datasets
@@ -513,9 +518,8 @@ class DefaultToolAction(object):
         add_datasets_timer = ExecutionTimer()
         # Add all the top-level (non-child) datasets to the history unless otherwise specified
         datasets_to_persist = []
-        for name in out_data.keys():
+        for name, data in out_data.items():
             if name not in child_dataset_names and name not in incoming:  # don't add children; or already existing datasets, i.e. async created
-                data = out_data[name]
                 datasets_to_persist.append(data)
         # Set HID and add to history.
         # This is brand new and certainly empty so don't worry about quota.
@@ -745,7 +749,7 @@ class DefaultToolAction(object):
         if output.label:
             params['tool'] = tool
             params['on_string'] = on_text
-            return fill_template(output.label, context=params)
+            return fill_template(output.label, context=params, python_template_version=tool.python_template_version)
         else:
             return self._get_default_data_name(dataset, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params)
 
@@ -762,7 +766,7 @@ class DefaultToolAction(object):
         if output.actions:
             for action in output.actions.actions:
                 if action.tag == "metadata" and action.default:
-                    metadata_new_value = fill_template(action.default, context=params).split(",")
+                    metadata_new_value = fill_template(action.default, context=params, python_template_version=tool.python_template_version).split(",")
                     dataset.metadata.__setattr__(str(action.name), metadata_new_value)
 
     def _get_default_data_name(self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd):
@@ -925,9 +929,9 @@ def get_ext_or_implicit_ext(hda):
     return hda.ext
 
 
-def determine_output_format(output, parameter_context, input_datasets, input_dataset_collections, random_input_ext):
+def determine_output_format(output, parameter_context, input_datasets, input_dataset_collections, random_input_ext, python_template_version='3'):
     """ Determines the output format for a dataset based on an abstract
-    description of the output (galaxy.tools.parser.ToolOutput), the parameter
+    description of the output (galaxy.tool_util.parser.ToolOutput), the parameter
     wrappers, a map of the input datasets (name => HDA), and the last input
     extensions in the tool form.
 
@@ -987,7 +991,7 @@ def determine_output_format(output, parameter_context, input_datasets, input_dat
                         if '$' not in check:
                             # allow a simple name or more complex specifications
                             check = '${%s}' % check
-                        if str(fill_template(check, context=parameter_context)) == when_elem.get('value', None):
+                        if fill_template(check, context=parameter_context, python_template_version=python_template_version) == when_elem.get('value', None):
                             ext = when_elem.get('format', ext)
                     except Exception:  # bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct
                         continue
diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py
index f82206a8249..c15439cb706 100644
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -2,7 +2,7 @@ import logging
 import os
 from json import dumps
 
-from galaxy.jobs.datasets import DatasetPath
+from galaxy.job_execution.datasets import DatasetPath
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.util.odict import odict
 from . import ToolAction
@@ -78,7 +78,7 @@ class SetMetadataToolAction(ToolAction):
         job_working_dir = app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
         datatypes_config = os.path.join(job_working_dir, 'registry.xml')
         app.datatypes_registry.to_xml_file(path=datatypes_config)
-        external_metadata_wrapper = get_metadata_compute_strategy(app, job.id)
+        external_metadata_wrapper = get_metadata_compute_strategy(app.config, job.id)
         output_datatasets_dict = {
             dataset_name: dataset,
         }
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index f24f11cf868..1ec3953f754 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -308,7 +308,7 @@ def create_paramfile(trans, uploaded_datasets):
             stdout, stderr = p.communicate()
             assert p.returncode == 0, stderr
         except Exception as e:
-            log.warning('Changing ownership of uploaded file %s failed: %s' % (path, str(e)))
+            log.warning('Changing ownership of uploaded file %s failed: %s', path, unicodify(e))
 
     tool_params = []
     json_file_path = None
diff --git a/lib/galaxy/tools/cache.py b/lib/galaxy/tools/cache.py
index d03445c43da..70366ed54f3 100644
--- a/lib/galaxy/tools/cache.py
+++ b/lib/galaxy/tools/cache.py
@@ -5,8 +5,10 @@ from threading import (
     Lock,
 )
 
+from sqlalchemy import inspect
 from sqlalchemy.orm.exc import DetachedInstanceError
 
+from galaxy.util import unicodify
 from galaxy.util.hash_util import md5_hash_file
 
 log = logging.getLogger(__name__)
@@ -55,7 +57,7 @@ class ToolCache(object):
                     if tool_id in self._new_tool_ids:
                         self._new_tool_ids.remove(tool_id)
         except Exception as e:
-            log.debug("Exception while checking tools to remove from cache: %s" % e)
+            log.debug("Exception while checking tools to remove from cache: %s", unicodify(e))
             # If by chance the file is being removed while calculating the hash or modtime
             # we don't want the thread to die.
             pass
@@ -147,7 +149,8 @@ class ToolShedRepositoryCache(object):
         except AttributeError:
             self.rebuild()
             repositories = self.cache.repositories
-        if repositories and not repositories[0]._sa_instance_state._attached:
+        tool_shed_repositories = [repo for repo in repositories if isinstance(repo, self.app.install_model.ToolShedRepository)]
+        if tool_shed_repositories and inspect(tool_shed_repositories[0]).detached:
             self.rebuild()
             repositories = self.cache.repositories
         return repositories
diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py
index e4a13d0e207..1c8b036eb23 100644
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -150,7 +150,7 @@ class ToolDataTableManager(object):
                                                      tool_data_path=tool_data_path,
                                                      from_shed_config=True)
         except Exception as e:
-            error_message = 'Error attempting to parse file %s: %s' % (str(os.path.split(config_filename)[1]), str(e))
+            error_message = 'Error attempting to parse file %s: %s' % (str(os.path.split(config_filename)[1]), util.unicodify(e))
             log.debug(error_message)
             table_elems = []
         if persist:
diff --git a/lib/galaxy/tools/data_fetch.py b/lib/galaxy/tools/data_fetch.py
index 75eaa204d48..90b35f64c69 100644
--- a/lib/galaxy/tools/data_fetch.py
+++ b/lib/galaxy/tools/data_fetch.py
@@ -108,6 +108,7 @@ def _fetch_target(upload_config, target):
         dbkey = item.get("dbkey", "?")
         requested_ext = item.get("ext", "auto")
         info = item.get("info", None)
+        created_from_basename = item.get("created_from_basename", None)
         tags = item.get("tags", [])
         object_id = item.get("object_id", None)
         link_data_only = upload_config.link_data_only
@@ -162,6 +163,8 @@ def _fetch_target(upload_config, target):
             rval["object_id"] = object_id
         if tags:
             rval["tags"] = tags
+        if created_from_basename:
+            rval["created_from_basename"] = created_from_basename
         return rval
 
     elements = elements_tree_map(_resolve_src, items)
diff --git a/lib/galaxy/tools/error_reports/plugins/email.py b/lib/galaxy/tools/error_reports/plugins/email.py
index fa939e0f4c2..ef00b0b383e 100644
--- a/lib/galaxy/tools/error_reports/plugins/email.py
+++ b/lib/galaxy/tools/error_reports/plugins/email.py
@@ -4,7 +4,10 @@ from __future__ import absolute_import
 import logging
 
 from galaxy.tools.errors import EmailErrorReporter
-from galaxy.util import string_as_bool
+from galaxy.util import (
+    string_as_bool,
+    unicodify,
+)
 from . import ErrorPlugin
 
 log = logging.getLogger(__name__)
@@ -29,7 +32,7 @@ class EmailPlugin(ErrorPlugin):
             error_reporter.send_report(user=job.get_user(), email=kwargs.get('email', None), message=kwargs.get('message', None), redact_user_details_in_bugreport=self.redact_user_details_in_bugreport)
             return ("Your error report has been sent", "success")
         except Exception as e:
-            return ("An error occurred sending the report by email: %s" % str(e), "danger")
+            return ("An error occurred sending the report by email: %s" % unicodify(e), "danger")
 
 
 __all__ = ('EmailPlugin', )
diff --git a/lib/galaxy/tools/errors.py b/lib/galaxy/tools/errors.py
index 2ccb00cdfb3..af939a9a020 100644
--- a/lib/galaxy/tools/errors.py
+++ b/lib/galaxy/tools/errors.py
@@ -1,9 +1,10 @@
 """
 Functionality for dealing with tool errors.
 """
-import cgi
 import string
 
+import markupsafe
+
 from galaxy import (
     model,
     util,
@@ -219,7 +220,7 @@ class ErrorReporter(object):
         # Escape all of the content  for use in the HTML report
         for parameter in report_variables.keys():
             if report_variables[parameter] is not None:
-                report_variables[parameter] = cgi.escape(unicodify(report_variables[parameter]))
+                report_variables[parameter] = markupsafe.escape(unicodify(report_variables[parameter]))
 
         self.html_report = string.Template(error_report_template_html).safe_substitute(report_variables)
 
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 1b741b7dc97..9d95987e8cf 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -7,7 +7,8 @@ import tempfile
 from six import string_types
 
 from galaxy import model
-from galaxy.jobs.datasets import dataset_path_rewrites
+from galaxy.job_execution.datasets import dataset_path_rewrites
+from galaxy.model.none_like import NoneDataset
 from galaxy.tools import global_tool_errors
 from galaxy.tools.parameters import (
     visit_input_values,
@@ -38,7 +39,6 @@ from galaxy.util import (
     unicodify,
 )
 from galaxy.util.bunch import Bunch
-from galaxy.util.none_like import NoneDataset
 from galaxy.util.object_wrapper import wrap_with_safe_string
 from galaxy.util.template import fill_template
 from galaxy.work.context import WorkRequestContext
@@ -469,7 +469,7 @@ class ToolEvaluator(object):
             return
         try:
             # Substituting parameters into the command
-            command_line = fill_template(command, context=param_dict)
+            command_line = fill_template(command, context=param_dict, python_template_version=self.tool.python_template_version)
             cleaned_command_line = []
             # Remove leading and trailing whitespace from each line for readability.
             for line in command_line.split('\n'):
@@ -575,7 +575,7 @@ class ToolEvaluator(object):
 
     def __write_workdir_file(self, config_filename, content, context, is_template=True):
         if is_template:
-            value = fill_template(content, context=context)
+            value = fill_template(content, context=context, python_template_version=self.tool.python_template_version)
         else:
             value = unicodify(content)
         with io.open(config_filename, "w", encoding='utf-8') as f:
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index 16012e25e49..e5a10d7c18e 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -11,8 +11,8 @@ import six.moves
 
 from galaxy import model
 from galaxy.model.dataset_collections.structure import get_structure, tool_output_to_structure
+from galaxy.tool_util.parser import ToolOutputCollectionPart
 from galaxy.tools.actions import filter_output, on_text_for_names, ToolExecutionCache
-from galaxy.tools.parser import ToolOutputCollectionPart
 from galaxy.util import ExecutionTimer
 
 log = logging.getLogger(__name__)
diff --git a/lib/galaxy/tools/expressions/util.py b/lib/galaxy/tools/expressions/util.py
index 082ed3c916f..e2d969e84f9 100644
--- a/lib/galaxy/tools/expressions/util.py
+++ b/lib/galaxy/tools/expressions/util.py
@@ -1,4 +1,4 @@
-from galaxy.tools.deps.commands import which
+from galaxy.tool_util.deps.commands import which
 
 
 def find_engine(config):
diff --git a/lib/galaxy/tools/imp_exp/export_history.py b/lib/galaxy/tools/imp_exp/export_history.py
index e01911fb4cf..24afcf619b9 100644
--- a/lib/galaxy/tools/imp_exp/export_history.py
+++ b/lib/galaxy/tools/imp_exp/export_history.py
@@ -13,6 +13,7 @@ import shutil
 import sys
 
 from galaxy.model.store import tar_export_directory
+from galaxy.util import unicodify
 
 
 def create_archive(export_directory, out_file, gzip=False):
@@ -23,7 +24,7 @@ def create_archive(export_directory, out_file, gzip=False):
         print('Created history archive.')
         return 0
     except Exception as e:
-        print('Error creating history archive: %s' % str(e), file=sys.stderr)
+        print('Error creating history archive: %s' % unicodify(e), file=sys.stderr)
         return 1
 
 
diff --git a/lib/galaxy/tools/lint.py b/lib/galaxy/tools/lint.py
index 237b6ab2925..7a808dad744 100644
--- a/lib/galaxy/tools/lint.py
+++ b/lib/galaxy/tools/lint.py
@@ -3,8 +3,9 @@ from __future__ import print_function
 
 import inspect
 
+from galaxy.tool_util.parser import get_tool_source
 from galaxy.util import submodules
-from .parser import get_tool_source
+from galaxy.util.getargspec import getfullargspec
 
 
 LEVEL_ALL = "all"
@@ -42,7 +43,7 @@ def lint_tool_source_with(lint_context, tool_source, extra_modules=[]):
                 # Look at the first argument to the linter to decide
                 # if we should lint the XML description or the abstract
                 # tool parser object.
-                first_arg = inspect.getargspec(value).args[0]
+                first_arg = getfullargspec(value).args[0]
                 if first_arg == "tool_xml":
                     if tool_xml is None:
                         # XML linter and non-XML tool, skip for now
diff --git a/lib/galaxy/tools/linters/citations.py b/lib/galaxy/tools/linters/citations.py
index 95c03d078ab..23d8b63cdcb 100644
--- a/lib/galaxy/tools/linters/citations.py
+++ b/lib/galaxy/tools/linters/citations.py
@@ -21,12 +21,15 @@ def lint_citations(tool_xml, lint_ctx):
     for citation in citations[0]:
         if citation.tag != "citation":
             lint_ctx.warn("Unknown tag discovered in citations block [%s], will be ignored." % citation.tag)
-        if "type" in citation.attrib:
-            citation_type = citation.attrib.get("type")
-            if citation_type not in ["doi", "bibtex"]:
-                lint_ctx.warn("Unknown citation type discovered [%s], will be ignored.", citation_type)
-            else:
-                valid_citations += 1
+            continue
+        citation_type = citation.attrib.get("type")
+        if citation_type not in ('bibtex', 'doi'):
+            lint_ctx.warn("Unknown citation type discovered [%s], will be ignored.", citation_type)
+            continue
+        if citation.text is None or not citation.text.strip():
+            lint_ctx.error('Empty %s citation.' % citation_type)
+            continue
+        valid_citations += 1
 
     if valid_citations > 0:
         lint_ctx.valid("Found %d likely valid citations.", valid_citations)
diff --git a/lib/galaxy/tools/linters/cwl.py b/lib/galaxy/tools/linters/cwl.py
new file mode 100644
index 00000000000..58390b5ddd4
--- /dev/null
+++ b/lib/galaxy/tools/linters/cwl.py
@@ -0,0 +1,48 @@
+"""Linter for CWL tools."""
+
+lint_tool_types = ["cwl"]
+
+from galaxy.tool_util.cwl.schema import schema_loader
+
+
+def lint_cwl_validation(tool_source, lint_ctx):
+    """Determine in CWL tool validates against spec."""
+    raw_reference = schema_loader.raw_process_reference(tool_source._source_path)
+    validation_exception = None
+    try:
+        schema_loader.process_definition(raw_reference)
+    except Exception as e:
+        validation_exception = e
+    if validation_exception:
+        lint_ctx.error("Failed to valdiate CWL artifact [%s]", validation_exception)
+    else:
+        lint_ctx.info("CWL appears to be valid.")
+
+
+def lint_new_draft(tool_source, lint_ctx):
+    """Determine in CWL tool is valid, modern draft."""
+    raw_reference = schema_loader.raw_process_reference(tool_source._source_path)
+    cwl_version = raw_reference.process_object.get("cwlVersion", None)
+    if cwl_version is None:
+        lint_ctx.error("CWL file does not contain a 'cwlVersion'")
+    if cwl_version not in ["v1.0"]:
+        lint_ctx.warn("CWL version [%s] is unknown, we recommend the v1.0 the stable release." % cwl_version)
+    else:
+        lint_ctx.info("Modern CWL version [%s]", cwl_version)
+
+
+def lint_docker_image(tool_source, lint_ctx):
+    _, containers = tool_source.parse_requirements_and_containers()
+    if len(containers) == 0:
+        lint_ctx.warn("Tool does not specify a DockerPull source.")
+    else:
+        identifier = containers[0].identifier
+        lint_ctx.info("Tool will run in Docker image [%s]." % identifier)
+
+
+def lint_description(tool_source, lint_ctx):
+    help = tool_source.parse_help()
+    if not help:
+        lint_ctx.warn("Description of tool is empty or absent.")
+    elif "TODO" in help:
+        lint_ctx.warn("Help contains TODO text.")
diff --git a/lib/galaxy/tools/linters/help.py b/lib/galaxy/tools/linters/help.py
index 503d43942e8..e5717ca9805 100644
--- a/lib/galaxy/tools/linters/help.py
+++ b/lib/galaxy/tools/linters/help.py
@@ -1,5 +1,8 @@
 """This module contains a linting function for a tool's help."""
-from galaxy.util import rst_to_html
+from galaxy.util import (
+    rst_to_html,
+    unicodify,
+)
 
 
 def lint_help(tool_xml, lint_ctx):
@@ -41,5 +44,5 @@ def rst_invalid(text):
     try:
         rst_to_html(text, error=True)
     except Exception as e:
-        invalid_rst = str(e)
+        invalid_rst = unicodify(e)
     return invalid_rst
diff --git a/lib/galaxy/tools/loader_directory.py b/lib/galaxy/tools/loader_directory.py
index 1cdbc7d6b35..c21937987b7 100644
--- a/lib/galaxy/tools/loader_directory.py
+++ b/lib/galaxy/tools/loader_directory.py
@@ -8,9 +8,9 @@ import sys
 
 import yaml
 
+from galaxy.tool_util import loader
+from galaxy.tool_util.parser import get_tool_source
 from galaxy.util import checkers
-from .parser import get_tool_source
-from ..tools import loader
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index 006b7c783fb..00ad022df89 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -7,6 +7,7 @@ from json import dumps
 
 from boltons.iterutils import remap
 
+from galaxy.util import unicodify
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.json import safe_loads
 from .basic import DataCollectionToolParameter, DataToolParameter, is_runtime_value, runtime_to_json, SelectToolParameter
@@ -184,7 +185,7 @@ def check_param(trans, param, incoming_value, param_values):
         value = param.from_json(value, trans, param_values)
         param.validate(value, trans)
     except ValueError as e:
-        error = str(e)
+        error = unicodify(e)
     return value, error
 
 
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index e5330b09c3e..e87c9542b2b 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -14,8 +14,8 @@ from six import string_types
 from webob.compat import cgi_FieldStorage
 
 import galaxy.model
-import galaxy.tools.parser
 from galaxy import util
+from galaxy.tool_util.parser import get_input_source as ensure_input_source
 from galaxy.util import (
     sanitize_param,
     string_as_bool,
@@ -35,7 +35,6 @@ from .dataset_matcher import (
     get_dataset_matcher_factory,
 )
 from .sanitize import ToolParameterSanitizer
-from ..parser import get_input_source as ensure_input_source
 
 log = logging.getLogger(__name__)
 
@@ -95,6 +94,7 @@ class ToolParameter(Dictifiable):
         self.name = self.__class__.parse_name(input_source)
         self.type = input_source.get("type")
         self.hidden = input_source.get_bool("hidden", False)
+        self.load_contents = int(input_source.get("load_contents", 0))
         self.refresh_on_change = input_source.get_bool("refresh_on_change", False)
         self.optional = input_source.parse_optional()
         self.is_dynamic = False
@@ -238,9 +238,9 @@ class ToolParameter(Dictifiable):
         param_name = cls.parse_name(param)
         param_type = param.get('type')
         if not param_type:
-            raise ValueError("Tool parameter '%s' requires a 'type'" % (param_name))
+            raise ValueError("parameter '%s' requires a 'type'" % (param_name))
         elif param_type not in parameter_types:
-            raise ValueError("Tool parameter '%s' uses an unknown type '%s'" % (param_name, param_type))
+            raise ValueError("parameter '%s' uses an unknown type '%s'" % (param_name, param_type))
         else:
             return parameter_types[param_type](tool, param)
 
@@ -252,7 +252,7 @@ class ToolParameter(Dictifiable):
             if argument:
                 name = argument.lstrip('-')
             else:
-                raise ValueError("Tool parameter must specify a name.")
+                raise ValueError("parameter must specify a name.")
         return name
 
 
@@ -314,7 +314,7 @@ class IntegerToolParameter(TextToolParameter):
     >>> type(p.from_json("_string", trans))
     Traceback (most recent call last):
         ...
-    ValueError: An integer or workflow parameter e.g. ${name} is required
+    ValueError: parameter '_name': an integer or workflow parameter is required
     """
 
     dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ['min', 'max']
@@ -325,21 +325,21 @@ class IntegerToolParameter(TextToolParameter):
             try:
                 int(self.value)
             except ValueError:
-                raise ValueError("An integer is required")
+                raise ValueError("parameter '%s': the attribute 'value' must be an integer" % self.name)
         elif self.value is None and not self.optional:
-            raise ValueError("The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name)
+            raise ValueError("parameter '%s': the attribute 'value' must be set for non optional parameters" % self.name)
         self.min = input_source.get('min')
         self.max = input_source.get('max')
         if self.min:
             try:
                 self.min = int(self.min)
             except ValueError:
-                raise ValueError("An integer is required")
+                raise ValueError("parameter '%s': attribute 'min' must be an integer" % self.name)
         if self.max:
             try:
                 self.max = int(self.max)
             except ValueError:
-                raise ValueError("An integer is required")
+                raise ValueError("parameter '%s': attribute 'max' must be an integer" % self.name)
         if self.min is not None or self.max is not None:
             self.validators.append(validation.InRangeValidator(None, self.min, self.max))
 
@@ -352,9 +352,9 @@ class IntegerToolParameter(TextToolParameter):
             if not value and self.optional:
                 return ""
             if trans.workflow_building_mode is workflow_building_modes.ENABLED:
-                raise ValueError("An integer or workflow parameter e.g. ${name} is required")
+                raise ValueError("parameter '%s': an integer or workflow parameter is required" % self.name)
             else:
-                raise ValueError("An integer is required")
+                raise ValueError("parameter '%s': the attribute 'value' must be set for non optional parameters" % self.name)
 
     def to_python(self, value, app):
         try:
@@ -387,7 +387,7 @@ class FloatToolParameter(TextToolParameter):
     >>> type(p.from_json("_string", trans))
     Traceback (most recent call last):
         ...
-    ValueError: A real number or workflow parameter e.g. ${name} is required
+    ValueError: parameter '_name': an integer or workflow parameter is required
     """
 
     dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ['min', 'max']
@@ -400,19 +400,19 @@ class FloatToolParameter(TextToolParameter):
             try:
                 float(self.value)
             except ValueError:
-                raise ValueError("A real number is required")
+                raise ValueError("parameter '%s': the attribute 'value' must be a real number" % self.name)
         elif self.value is None and not self.optional:
-            raise ValueError("The settings for this field require a 'value' setting and optionally a default value which must be a real number")
+            raise ValueError("parameter '%s': the attribute 'value' must be set for non optional parameters" % self.name)
         if self.min:
             try:
                 self.min = float(self.min)
             except ValueError:
-                raise ValueError("A real number is required")
+                raise ValueError("parameter '%s': attribute 'min' must be a real number" % self.name)
         if self.max:
             try:
                 self.max = float(self.max)
             except ValueError:
-                raise ValueError("A real number is required")
+                raise ValueError("parameter '%s': attribute 'max' must be a real number" % self.name)
         if self.min is not None or self.max is not None:
             self.validators.append(validation.InRangeValidator(None, self.min, self.max))
 
@@ -424,10 +424,10 @@ class FloatToolParameter(TextToolParameter):
                 return value
             if not value and self.optional:
                 return ""
-            if trans and trans.workflow_building_mode is workflow_building_modes.ENABLED:
-                raise ValueError("A real number or workflow parameter e.g. ${name} is required")
+            if trans.workflow_building_mode is workflow_building_modes.ENABLED:
+                raise ValueError("parameter '%s': an integer or workflow parameter is required" % self.name)
             else:
-                raise ValueError("A real number is required")
+                raise ValueError("parameter '%s': the attribute 'value' must be set for non optional parameters" % self.name)
 
     def to_python(self, value, app):
         try:
@@ -751,7 +751,7 @@ class BaseURLToolParameter(HiddenToolParameter):
         try:
             return url_for(self.value, qualified=True)
         except Exception as e:
-            log.debug('Url creation failed for "%s": %s', self.name, e)
+            log.debug('Url creation failed for "%s": %s', self.name, unicodify(e))
             return self.value
 
     def to_dict(self, trans, other_values={}):
@@ -841,7 +841,7 @@ class SelectToolParameter(ToolParameter):
                 call_other_values = self._get_dynamic_options_call_other_values(trans, other_values)
                 return set(v for _, v, _ in eval(self.dynamic_options, self.tool.code_namespace, call_other_values))
             except Exception as e:
-                log.debug("Determining legal values failed for '%s': %s", self.name, e)
+                log.debug("Determining legal values failed for '%s': %s", self.name, unicodify(e))
                 return set()
         else:
             return self.legal_values
@@ -866,20 +866,20 @@ class SelectToolParameter(ToolParameter):
         elif value is None:
             if self.optional:
                 return None
-            raise ValueError("An invalid option was selected for %s, please verify." % (self.name))
+            raise ValueError("parameter '%s': an invalid option (None) was selected, please verify" % self.name)
         elif not legal_values:
             if self.optional and self.tool.profile < 18.09:
                 # Covers optional parameters with default values that reference other optional parameters.
                 # These will have a value but no legal_values.
                 return None
-            raise ValueError("Parameter %s requires a value, but has no legal values defined." % self.name)
+            raise ValueError("parameter '%s': requires a value, but no legal values defined" % self.name)
         if isinstance(value, list):
             if not self.multiple:
-                raise ValueError("Multiple values provided but parameter %s is not expecting multiple values." % self.name)
+                raise ValueError("parameter '%s': multiple values provided but parameter is not expecting multiple values" % (self.name))
             rval = []
             for v in value:
                 if v not in legal_values:
-                    raise ValueError("An invalid option was selected for %s, %r, please verify." % (self.name, v))
+                    raise ValueError("parameter '%s': an invalid option (%r) was selected (valid options: %s)" % (self.name, v, ",".join(legal_values)))
                 rval.append(v)
             return rval
         else:
@@ -889,9 +889,9 @@ class SelectToolParameter(ToolParameter):
                     if self.optional:
                         return []
                     else:
-                        raise ValueError("No option was selected for %s but input is not optional." % self.name)
+                        raise ValueError("parameter '%s': no option was selected for non optional parameter" % (self.name))
             if value not in legal_values and require_legal_value:
-                raise ValueError("An invalid option was selected for %s, %r, please verify." % (self.name, value))
+                raise ValueError("parameter '%s': an invalid option (%r) was selected (valid options: %s)" % (self.name, value, ",".join(legal_values)))
             return value
 
     def to_param_dict_string(self, value, other_values={}):
@@ -899,7 +899,7 @@ class SelectToolParameter(ToolParameter):
             return "None"
         if isinstance(value, list):
             if not self.multiple:
-                raise ValueError("Multiple values provided but parameter %s is not expecting multiple values." % self.name)
+                raise ValueError("parameter '%s': multiple values provided but parameter is not expecting multiple values" % (self.name))
             value = list(map(str, value))
         else:
             value = str(value)
@@ -1426,17 +1426,17 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         elif value is None:
             if self.optional:
                 return None
-            raise ValueError("An invalid option was selected for %s, please verify." % (self.name))
+            raise ValueError("parameter '%s': an invalid option (%r) was selected" % (self.name, value))
         elif not legal_values:
-            raise ValueError("Parameter %s requires a value, but has no legal values defined." % self.name)
+            raise ValueError("parameter '%s': requires a value, but no legal values defined" % (self.name))
         if not isinstance(value, list):
             value = [value]
         if len(value) > 1 and not self.multiple:
-            raise ValueError("Multiple values provided but parameter %s is not expecting multiple values." % self.name)
+            raise ValueError("parameter '%s': multiple values provided but parameter is not expecting multiple values" % (self.name))
         rval = []
         for val in value:
             if val not in legal_values:
-                raise ValueError("An invalid option was selected for %s, %r, please verify" % (self.name, val))
+                raise ValueError("parameter '%s': an invalid option (%r) was selected (valid options: %s)" % (self.name, val, ",".join(legal_values)))
             rval.append(val)
         return rval
 
@@ -1471,7 +1471,7 @@ class DrillDownSelectToolParameter(SelectToolParameter):
                 options = get_options_list(val)
                 rval.extend(options)
         if len(rval) > 1 and not self.multiple:
-            raise ValueError("Multiple values provided but parameter %s is not expecting multiple values." % self.name)
+            raise ValueError("parameter '%s': multiple values provided but parameter is not expecting multiple values" % (self.name))
         rval = self.separator.join(rval)
         if self.tool is None or self.tool.options.sanitize:
             if self.sanitizer:
@@ -1618,6 +1618,8 @@ class BaseDataToolParameter(ToolParameter):
                 src = 'dce'
             elif isinstance(value, app.model.HistoryDatasetCollectionAssociation):
                 src = 'hdca'
+            elif isinstance(value, app.model.LibraryDatasetDatasetAssociation):
+                src = 'ldda'
             elif isinstance(value, app.model.HistoryDatasetAssociation) or hasattr(value, 'id'):
                 # hasattr 'id' fires a query on persistent objects after a flush so better
                 # to do the isinstance check. Not sure we need the hasattr check anymore - it'd be
@@ -1643,6 +1645,8 @@ class BaseDataToolParameter(ToolParameter):
                     return app.model.context.query(app.model.DatasetCollectionElement).get(id)
                 elif value['src'] == 'hdca':
                     return app.model.context.query(app.model.HistoryDatasetCollectionAssociation).get(id)
+                elif value['src'] == 'ldda':
+                    return app.model.context.query(app.model.LibraryDatasetDatasetAssociation).get(id)
                 else:
                     return app.model.context.query(app.model.HistoryDatasetAssociation).get(id)
 
@@ -1699,16 +1703,16 @@ class DataToolParameter(BaseDataToolParameter):
             try:
                 self.min = int(self.min)
             except ValueError:
-                raise ValueError("An integer is required for min property.")
+                raise ValueError("parameter '%s': attribute 'min' must be an integer" % self.name)
         if self.max:
             try:
                 self.max = int(self.max)
             except ValueError:
-                raise ValueError("An integer is required for max property.")
+                raise ValueError("parameter '%s': attribute 'max' must be an integer" % self.name)
         if not self.multiple and (self.min is not None):
-            raise ValueError("Cannot specify min property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name)
+            raise ValueError("parameter '%s': cannot specify 'min' property on single data parameter '%s'. Set multiple=\"true\" to enable this option" % self.name)
         if not self.multiple and (self.max is not None):
-            raise ValueError("Cannot specify max property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name)
+            raise ValueError("parameter '%s': cannot specify 'max' property on single data parameter '%s'. Set multiple=\"true\" to enable this option" % self.name)
         self.is_dynamic = True
         self._parse_options(input_source)
         # Load conversions required for the dataset input
@@ -1718,14 +1722,14 @@ class DataToolParameter(BaseDataToolParameter):
             if self.datatypes_registry:
                 conv_type = self.datatypes_registry.get_datatype_by_extension(conv_extension.lower())
                 if conv_type is None:
-                    raise ValueError("Datatype class not found for extension '%s', which is used as 'type' attribute in conversion of data parameter '%s'" % (conv_type, self.name))
+                    raise ValueError("parameter '%s': datatype class not found for extension '%s', which is used as 'type' attribute in conversion of data parameter" % (self.name, conv_type))
                 self.conversions.append((name, conv_extension, [conv_type]))
 
     def from_json(self, value, trans, other_values={}):
         if trans.workflow_building_mode is workflow_building_modes.ENABLED or is_runtime_value(value):
             return None
         if not value and not self.optional:
-            raise ValueError("Specify a dataset of the required format / build for parameter %s." % self.name)
+            raise ValueError("parameter '%s': specify a dataset of the required format / build for parameter" % self.name)
         if value in [None, "None", '']:
             return None
         if isinstance(value, dict) and 'values' in value:
@@ -1738,11 +1742,15 @@ class DataToolParameter(BaseDataToolParameter):
             for single_value in value:
                 if isinstance(single_value, dict) and 'src' in single_value and 'id' in single_value:
                     if single_value['src'] == 'hda':
-                        rval.append(trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(trans.security.decode_id(single_value['id'])))
+                        decoded_id = trans.security.decode_id(single_value['id'])
+                        rval.append(trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(decoded_id))
                     elif single_value['src'] == 'hdca':
                         found_hdca = True
                         decoded_id = trans.security.decode_id(single_value['id'])
                         rval.append(trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(decoded_id))
+                    elif single_value['src'] == 'ldda':
+                        decoded_id = trans.security.decode_id(single_value['id'])
+                        rval.append(trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(decoded_id))
                     else:
                         raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
                 elif isinstance(single_value, trans.app.model.HistoryDatasetCollectionAssociation):
@@ -1751,6 +1759,8 @@ class DataToolParameter(BaseDataToolParameter):
                     rval.append(single_value)
                 elif isinstance(single_value, trans.app.model.HistoryDatasetAssociation):
                     rval.append(single_value)
+                elif isinstance(single_value, trans.app.model.LibraryDatasetDatasetAssociation):
+                    rval.append(single_value)
                 else:
                     if len(str(single_value)) == 16:
                         # Could never really have an ID this big anyway - postgres doesn't
@@ -1761,12 +1771,13 @@ class DataToolParameter(BaseDataToolParameter):
             if found_hdca:
                 for val in rval:
                     if not isinstance(val, trans.app.model.HistoryDatasetCollectionAssociation):
-                        raise ValueError("If collections are supplied to multiple data input parameter, only collections may be used.")
+                        raise ValueError("parameter '%s': if collections are supplied to multiple data input parameter, only collections may be used" % self.name)
         elif isinstance(value, trans.app.model.HistoryDatasetAssociation):
             rval = value
         elif isinstance(value, dict) and 'src' in value and 'id' in value:
             if value['src'] == 'hda':
-                rval = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(trans.security.decode_id(value['id']))
+                decoded_id = trans.security.decode_id(value['id'])
+                rval = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(decoded_id)
             elif value['src'] == 'hdca':
                 decoded_id = trans.security.decode_id(value['id'])
                 rval = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(decoded_id)
@@ -1789,20 +1800,20 @@ class DataToolParameter(BaseDataToolParameter):
         for v in values:
             if v:
                 if hasattr(v, "deleted") and v.deleted:
-                    raise ValueError("The previously selected dataset has been deleted.")
+                    raise ValueError("parameter '%s': the previously selected dataset has been deleted." % self.name)
                 elif hasattr(v, "dataset") and v.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED]:
-                    raise ValueError("The previously selected dataset has entered an unusable state")
+                    raise ValueError("parameter '%s': the previously selected dataset has entered an unusable state" % self.name)
                 elif hasattr(v, "dataset"):
                     match = dataset_matcher.hda_match(v)
                     if match and match.implicit_conversion:
                         v.implicit_conversion = True
         if not self.multiple:
             if len(values) > 1:
-                raise ValueError("More than one dataset supplied to single input dataset parameter.")
+                raise ValueError("parameter '%s': more than one dataset supplied to single input dataset parameter" % self.name)
             if len(values) > 0:
                 rval = values[0]
             else:
-                raise ValueError("Invalid dataset supplied to single input dataset parameter.")
+                raise ValueError("parameter '%s': invalid dataset supplied to single input dataset parameter" % self.name)
         return rval
 
     def to_param_dict_string(self, value, other_values={}):
@@ -1851,10 +1862,10 @@ class DataToolParameter(BaseDataToolParameter):
 
         if self.min is not None:
             if self.min > dataset_count:
-                raise ValueError("At least %d datasets are required." % self.min)
+                raise ValueError("At least %d datasets are required for %s" % (self.min, self.name))
         if self.max is not None:
             if self.max < dataset_count:
-                raise ValueError("At most %d datasets are required." % self.max)
+                raise ValueError("At most %d datasets are required for %s" % (self.max, self.name))
 
     def get_dependencies(self):
         """
@@ -2040,7 +2051,7 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         if trans.workflow_building_mode is workflow_building_modes.ENABLED:
             return None
         if not value and not self.optional:
-            raise ValueError("Specify a dataset collection of the correct type.")
+            raise ValueError("parameter '%s': specify a dataset collection of the correct type" % self.name)
         if value in [None, "None"]:
             return None
         if isinstance(value, dict) and 'values' in value:
@@ -2072,7 +2083,7 @@ class DataCollectionToolParameter(BaseDataToolParameter):
                 rval = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(value)
         if rval and isinstance(rval, trans.app.model.HistoryDatasetCollectionAssociation):
             if rval.deleted:
-                raise ValueError("The previously selected dataset collection has been deleted")
+                raise ValueError("parameter '%s': the previously selected dataset collection has been deleted" % self.name)
             # TODO: Handle error states, implement error states ...
         return rval
 
@@ -2230,10 +2241,10 @@ class LibraryDatasetToolParameter(ToolParameter):
                 if lda is not None:
                     lst.append(lda)
                 elif validate:
-                    raise ValueError("One of the selected library datasets is invalid or not available anymore.")
+                    raise ValueError("parameter '%s': one of the selected library datasets is invalid or not available anymore" % self.name)
         if len(lst) == 0:
             if not self.optional and validate:
-                raise ValueError("Please select a valid library dataset.")
+                raise ValueError("parameter '%s': invalid library dataset selected" % self.name)
             return None
         else:
             return lst
diff --git a/lib/galaxy/tools/parameters/wrapped_json.py b/lib/galaxy/tools/parameters/wrapped_json.py
index f9c90d4abe1..73d019cdedc 100644
--- a/lib/galaxy/tools/parameters/wrapped_json.py
+++ b/lib/galaxy/tools/parameters/wrapped_json.py
@@ -66,7 +66,11 @@ def _json_wrap_input(input, value, handle_files="skip"):
             if value:
                 if isinstance(value, list):
                     value = value[0]
-                return _hda_to_object(value)
+                json_value = _hda_to_object(value)
+                if input.load_contents:
+                    with open(str(value), mode='rb') as fh:
+                        json_value['contents'] = fh.read(input.load_contents).decode('utf-8', errors='replace')
+                return json_value
             else:
                 return None
         else:
diff --git a/lib/galaxy/tools/relabel_from_file.xml b/lib/galaxy/tools/relabel_from_file.xml
index e60457b90ea..c35cb51de74 100644
--- a/lib/galaxy/tools/relabel_from_file.xml
+++ b/lib/galaxy/tools/relabel_from_file.xml
@@ -147,6 +147,9 @@
         in the collection. In that case only matching list identifiers will be
         relabeled.
 
+        Valid identifiers must contain only characters (a-z, A-Z), numbers (0-9), 
+        dash and underscore (-, _). Punctuation or whitespace are not allowed. 
+
         This tool will create new history datasets from your collection
         but your quota usage will not increase.
     ]]></help>
diff --git a/lib/galaxy/tools/tag_collection_from_file.xml b/lib/galaxy/tools/tag_collection_from_file.xml
index 1427fb504c5..2abad0f5452 100644
--- a/lib/galaxy/tools/tag_collection_from_file.xml
+++ b/lib/galaxy/tools/tag_collection_from_file.xml
@@ -34,13 +34,13 @@
                     <assert_contents>
                         <has_text_matching expression="^This is a line of text.\n$" />
                     </assert_contents>
-                    <metadata name="tags" value="alias:f,alias:r1,orientation:forward,zoo" />
+                    <metadata name="tags" value="alias:f,alias:r1,name:forward,orientation:forward,zoo" />
                 </element>
                 <element name="reverse">
                     <assert_contents>
                         <has_text_matching expression="^This is a different line of text.\n$" />
                     </assert_contents>
-                    <metadata name="tags" value="alias:r,alias:r2,orientation:reverse" />
+                    <metadata name="tags" value="alias:r,alias:r2,name:reverse,orientation:reverse" />
                 </element>
             </output_collection>
         </test>
@@ -63,13 +63,13 @@
                         <assert_contents>
                             <has_text_matching expression="^This is a line of text.\n$" />
                         </assert_contents>
-                        <metadata name="tags" value="alias:f,alias:r1,orientation:forward" />
+                        <metadata name="tags" value="alias:f,alias:r1,name:forward,orientation:forward" />
                     </element>
                     <element name="reverse">
                         <assert_contents>
                             <has_text_matching expression="^This is a different line of text.\n$" />
                         </assert_contents>
-                        <metadata name="tags" value="alias:r,alias:r2,orientation:reverse" />
+                        <metadata name="tags" value="alias:r,alias:r2,name:reverse,orientation:reverse" />
                     </element>
                 </element>
             </output_collection>
diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index a4acd0f5ee2..03ddd53df46 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -7,7 +7,10 @@ from six import string_types
 import galaxy.tools.parameters.basic
 import galaxy.tools.parameters.grouping
 from galaxy.tools.verify.interactor import ToolTestDescription
-from galaxy.util import string_as_bool
+from galaxy.util import (
+    string_as_bool,
+    unicodify,
+)
 
 try:
     from nose.tools import nottest
@@ -21,7 +24,7 @@ log = logging.getLogger(__name__)
 @nottest
 def parse_tests(tool, tests_source):
     """
-    Build ToolTestBuilder objects for each "<test>" elements and
+    Build ToolTestDescription objects for each "<test>" elements and
     return default interactor (if any).
     """
     raw_tests_dict = tests_source.parse_tests_to_dict()
@@ -63,7 +66,7 @@ def description_from_tool_object(tool, test_index, raw_test_dict):
             "test_index": test_index,
             "inputs": {},
             "error": True,
-            "exception": str(e),
+            "exception": unicodify(e),
         }
 
     return ToolTestDescription(processed_test_dict)
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 9e2ae51a2dc..df38375939d 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -11,13 +11,14 @@ from six import iteritems
 from six.moves.urllib.parse import urlparse
 
 from galaxy.exceptions import MessageException, ObjectNotFound
-from galaxy.tools.deps import build_dependency_manager
+from galaxy.tool_util.deps import build_dependency_manager
 from galaxy.tools.loader_directory import looks_like_a_tool
 from galaxy.util import (
     ExecutionTimer,
     listify,
     parse_xml,
-    string_as_bool
+    string_as_bool,
+    unicodify,
 )
 from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
@@ -98,13 +99,6 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             self._load_tool_panel()
         self._save_integrated_tool_panel()
 
-    def handle_panel_update(self, section_dict):
-        """Extension-point for Galaxy-app specific reload logic.
-
-        This abstract representation of the toolbox shouldn't have details about
-        interacting with the rest of the Galaxy app or message queues, etc....
-        """
-
     def create_tool(self, config_file, tool_shed_repository=None, guid=None, **kwds):
         raise NotImplementedError()
 
@@ -254,6 +248,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             # Appending a tool to an existing section in toolbox._tool_panel
             tool_section = self._tool_panel[tool_panel_section_key]
             log.debug("Appending to tool panel section: %s" % str(tool_section.name))
+        elif new_label and self._tool_panel.get_label(new_label):
+            tool_section = self._tool_panel.get_label(new_label)
+            tool_panel_section_key = tool_section.id
         elif create_if_needed:
             # Appending a new section to toolbox._tool_panel
             if new_label is None:
@@ -264,7 +261,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 'id': section_id,
                 'version': '',
             }
-            self.handle_panel_update(section_dict)
+            self.create_section(section_dict)
             tool_section = self._tool_panel[tool_panel_section_key]
             self._save_integrated_tool_panel()
         else:
@@ -633,7 +630,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             if labels is not None:
                 tool.labels = labels
         except (IOError, OSError) as exc:
-            log.error("Error reading tool configuration file from path '%s': %s", path, exc)
+            log.error("Error reading tool configuration file from path '%s': %s", path, unicodify(exc))
         except Exception:
             log.exception("Error reading tool from path: %s", path)
 
@@ -1066,7 +1063,7 @@ def _filter_for_panel(item, item_type, filters, context):
                 if not filter_method(context, filter_item):
                     return False
             except Exception as e:
-                raise MessageException("Toolbox filter exception from '%s': %s." % (filter_method.__name__, e))
+                raise MessageException("Toolbox filter exception from '%s': %s." % (filter_method.__name__, unicodify(e)))
         return True
     if item_type == panel_item_types.TOOL:
         if _apply_filter(item, filters['tool']):
diff --git a/lib/galaxy/tools/toolbox/panel.py b/lib/galaxy/tools/toolbox/panel.py
index f2eb6dec3dd..30eceae64b6 100644
--- a/lib/galaxy/tools/toolbox/panel.py
+++ b/lib/galaxy/tools/toolbox/panel.py
@@ -123,6 +123,11 @@ class ToolPanelElements(odict, HasPanelItems):
         else:
             self.insert(index, key, value)
 
+    def get_label(self, label):
+        for element in self.values():
+            if isinstance(element, ToolSection) and element.name == label:
+                return element
+
     def has_tool_with_id(self, tool_id):
         key = 'tool_%s' % tool_id
         return key in self
diff --git a/lib/galaxy/tools/toolbox/watcher.py b/lib/galaxy/tools/toolbox/watcher.py
index 23f8d2423ee..f395b0a035f 100644
--- a/lib/galaxy/tools/toolbox/watcher.py
+++ b/lib/galaxy/tools/toolbox/watcher.py
@@ -15,7 +15,7 @@ except ImportError:
     can_watch = False
 
 from galaxy.util.hash_util import md5_hash_file
-from galaxy.web.stack import register_postfork_function
+from galaxy.web_stack import register_postfork_function
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/tools/unzip_collection.xml b/lib/galaxy/tools/unzip_collection.xml
index decfd1f30de..917204ad2c0 100644
--- a/lib/galaxy/tools/unzip_collection.xml
+++ b/lib/galaxy/tools/unzip_collection.xml
@@ -9,8 +9,8 @@
     <param type="data_collection" collection_type="paired" name="input" label="Input Paired Dataset" />
   </inputs>
   <outputs>
-    <data name="forward" label="${on_string} (forward)" />
-    <data name="reverse" label="${on_string} (reverse)" />
+    <data name="forward" label="${on_string} (forward)" format_source="input"/>
+    <data name="reverse" label="${on_string} (reverse)" format_source="input"/>
   </outputs>
   <help><![CDATA[
 
diff --git a/lib/galaxy/tools/util/galaxyops/__init__.py b/lib/galaxy/tools/util/galaxyops/__init__.py
index 9cb5d1d96ab..a52ed9a2ad5 100644
--- a/lib/galaxy/tools/util/galaxyops/__init__.py
+++ b/lib/galaxy/tools/util/galaxyops/__init__.py
@@ -3,6 +3,8 @@ from __future__ import print_function
 
 import sys
 
+from galaxy.util import unicodify
+
 
 def warn(msg):
     # TODO: since everything printed to stderr results in job.state = error, we
@@ -35,7 +37,7 @@ def parse_cols_arg(cols):
 
 def default_printer(stream, exc, obj):
     print("%d: %s" % (obj.linenum, obj.current_line), file=stream)
-    print("\tError: %s" % (str(exc)), file=stream)
+    print("\tError: %s" % unicodify(exc), file=stream)
 
 
 def skipped(reader, filedesc=""):
diff --git a/lib/galaxy/tools/verify/__init__.py b/lib/galaxy/tools/verify/__init__.py
index f78d43b7f4f..e842004c54e 100644
--- a/lib/galaxy/tools/verify/__init__.py
+++ b/lib/galaxy/tools/verify/__init__.py
@@ -16,6 +16,7 @@ try:
 except ImportError:
     pysam = None
 
+from galaxy.util import unicodify
 from galaxy.util.compression_utils import get_fileobj
 from .asserts import verify_assertions
 from .test_data import TestDataResolver
@@ -58,7 +59,7 @@ def verify(
             verify_assertions(output_content, attributes["assert_list"])
         except AssertionError as err:
             errmsg = '%s different than expected\n' % (item_label)
-            errmsg += str(err)
+            errmsg += unicodify(err)
             raise AssertionError(errmsg)
 
     # Verify checksum attributes...
@@ -78,7 +79,7 @@ def verify(
             _verify_checksum(output_content, expected_checksum_type, expected_checksum)
         except AssertionError as err:
             errmsg = '%s different than expected\n' % (item_label)
-            errmsg += str(err)
+            errmsg += unicodify(err)
             raise AssertionError(errmsg)
 
     if attributes is None:
@@ -104,20 +105,18 @@ def verify(
             log.debug('keep_outputs_dir: %s, ofn: %s', keep_outputs_dir, ofn)
             try:
                 shutil.copy(temp_name, ofn)
-            except Exception as exc:
-                error_log_msg = 'Could not save output file %s to %s: ' % (temp_name, ofn)
-                error_log_msg += str(exc)
-                log.error(error_log_msg, exc_info=True)
+            except Exception:
+                log.exception('Could not save output file %s to %s', temp_name, ofn)
             else:
-                log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % (keep_outputs_dir, ofn))
+                log.debug('## GALAXY_TEST_SAVE=%s. saved %s', keep_outputs_dir, ofn)
+        compare = attributes.get('compare', 'diff')
         try:
-            compare = attributes.get('compare', 'diff')
-            if attributes.get('ftype', None) in ['bam', 'qname_sorted.bam', 'qname_input_sorted.bam', 'unsorted.bam']:
+            if attributes.get('ftype', None) in ['bam', 'qname_sorted.bam', 'qname_input_sorted.bam', 'unsorted.bam', 'cram']:
                 try:
                     local_fh, temp_name = _bam_to_sam(local_name, temp_name)
                     local_name = local_fh.name
                 except Exception as e:
-                    log.warning("%s. Will compare BAM files" % e)
+                    log.warning("%s. Will compare BAM files", unicodify(e))
             if compare == 'diff':
                 files_diff(local_name, temp_name, attributes=attributes)
             elif compare == 're_match':
@@ -137,7 +136,7 @@ def verify(
         except AssertionError as err:
             errmsg = '%s different than expected, difference (using %s):\n' % (item_label, compare)
             errmsg += "( %s v. %s )\n" % (local_name, temp_name)
-            errmsg += str(err)
+            errmsg += unicodify(err)
             raise AssertionError(errmsg)
         finally:
             if 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
@@ -163,12 +162,12 @@ def _bam_to_sam(local_name, temp_name):
     try:
         pysam.view('-h', '-o%s' % temp_local.name, local_name)
     except Exception as e:
-        msg = "Converting local (test-data) BAM to SAM failed: %s" % e
+        msg = "Converting local (test-data) BAM to SAM failed: %s" % unicodify(e)
         raise Exception(msg)
     try:
         pysam.view('-h', '-o%s' % temp_temp, temp_name)
     except Exception as e:
-        msg = "Converting history BAM to SAM failed: %s" % e
+        msg = "Converting history BAM to SAM failed: %s" % unicodify(e)
         raise Exception(msg)
     os.remove(temp_name)
     return temp_local, temp_temp
@@ -196,7 +195,7 @@ def files_diff(file1, file2, attributes=None):
                 count += 1
         return count
 
-    if not filecmp.cmp(file1, file2):
+    if not filecmp.cmp(file1, file2, shallow=False):
         if attributes is None:
             attributes = {}
         decompress = attributes.get("decompress", None)
@@ -207,13 +206,17 @@ def files_diff(file1, file2, attributes=None):
             compressed_formats = []
         is_pdf = False
         try:
-            local_file = get_fileobj(file1, compressed_formats=compressed_formats).readlines()
-            history_data = get_fileobj(file2, compressed_formats=compressed_formats).readlines()
+            with get_fileobj(file2, compressed_formats=compressed_formats) as fh:
+                history_data = fh.readlines()
+            with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
+                local_file = fh.readlines()
         except UnicodeDecodeError:
             if file1.endswith('.pdf') or file2.endswith('.pdf'):
                 is_pdf = True
-                local_file = open(file1, 'rb').readlines()
-                history_data = open(file2, 'rb').readlines()
+                # Replace non-Unicode characters using unicodify(),
+                # difflib.unified_diff doesn't work on list of bytes
+                history_data = [unicodify(l) for l in get_fileobj(file2, mode='rb', compressed_formats=compressed_formats)]
+                local_file = [unicodify(l) for l in get_fileobj(file1, mode='rb', compressed_formats=compressed_formats)]
             else:
                 raise AssertionError("Binary data detected, not displaying diff")
         if attributes.get('sort', False):
@@ -268,9 +271,21 @@ def files_diff(file1, file2, attributes=None):
 
 def files_re_match(file1, file2, attributes=None):
     """Check the contents of 2 files for differences using re.match."""
-    local_file = io.open(file1, encoding='utf-8').readlines()  # regex file
-    history_data = io.open(file2, encoding='utf-8').readlines()
-    assert len(local_file) == len(history_data), 'Data File and Regular Expression File contain a different number of lines (%d != %d)\nHistory Data (first 40 lines):\n%s' % (len(local_file), len(history_data), ''.join(history_data[:40]))
+    join_char = ''
+    to_strip = os.linesep
+    try:
+        with io.open(file2, encoding='utf-8') as fh:
+            history_data = fh.readlines()
+        with io.open(file1, encoding='utf-8') as fh:
+            local_file = fh.readlines()
+    except UnicodeDecodeError:
+        join_char = b''
+        to_strip = os.linesep.encode('utf-8')
+        with open(file2, 'rb') as fh:
+            history_data = fh.readlines()
+        with open(file1, 'rb') as fh:
+            local_file = fh.readlines()
+    assert len(local_file) == len(history_data), 'Data File and Regular Expression File contain a different number of lines (%d != %d)\nHistory Data (first 40 lines):\n%s' % (len(local_file), len(history_data), join_char.join(history_data[:40]))
     if attributes is None:
         attributes = {}
     if attributes.get('sort', False):
@@ -278,38 +293,60 @@ def files_re_match(file1, file2, attributes=None):
     lines_diff = int(attributes.get('lines_diff', 0))
     line_diff_count = 0
     diffs = []
-    for i in range(len(history_data)):
-        if not re.match(local_file[i].rstrip('\r\n'), history_data[i].rstrip('\r\n')):
+    for regex_line, data_line in zip(local_file, history_data):
+        regex_line = regex_line.rstrip(to_strip)
+        data_line = data_line.rstrip(to_strip)
+        if not re.match(regex_line, data_line):
             line_diff_count += 1
-            diffs.append('Regular Expression: %s\nData file         : %s' % (local_file[i].rstrip('\r\n'), history_data[i].rstrip('\r\n')))
-        if line_diff_count > lines_diff:
-            raise AssertionError("Regular expression did not match data file (allowed variants=%i):\n%s" % (lines_diff, "".join(diffs)))
+            diffs.append('Regular Expression: %s, Data file: %s\n' % (regex_line, data_line))
+    if line_diff_count > lines_diff:
+        raise AssertionError("Regular expression did not match data file (allowed variants=%i):\n%s" % (lines_diff, "".join(diffs)))
 
 
 def files_re_match_multiline(file1, file2, attributes=None):
     """Check the contents of 2 files for differences using re.match in multiline mode."""
-    local_file = io.open(file1, encoding='utf-8').read()  # regex file
+    join_char = ''
+    try:
+        with io.open(file2, encoding='utf-8') as fh:
+            history_data = fh.readlines()
+        with io.open(file1, encoding='utf-8') as fh:
+            local_file = fh.read()
+    except UnicodeDecodeError:
+        join_char = b''
+        with open(file2, 'rb') as fh:
+            history_data = fh.readlines()
+        with open(file1, 'rb') as fh:
+            local_file = fh.read()
     if attributes is None:
         attributes = {}
     if attributes.get('sort', False):
-        history_data = io.open(file2, encoding='utf-8').readlines()
         history_data.sort()
-        history_data = ''.join(history_data)
-    else:
-        history_data = io.open(file2, encoding='utf-8').read()
+    history_data = join_char.join(history_data)
     # lines_diff not applicable to multiline matching
     assert re.match(local_file, history_data, re.MULTILINE), "Multiline Regular expression did not match data file"
 
 
 def files_contains(file1, file2, attributes=None):
     """Check the contents of file2 for substrings found in file1, on a per-line basis."""
-    local_file = io.open(file1, encoding='utf-8').readlines()  # regex file
     # TODO: allow forcing ordering of contains
-    history_data = io.open(file2, encoding='utf-8').read()
+    to_strip = os.linesep
+    try:
+        with io.open(file2, encoding='utf-8') as fh:
+            history_data = fh.read()
+        with io.open(file1, encoding='utf-8') as fh:
+            local_file = fh.readlines()
+    except UnicodeDecodeError:
+        to_strip = os.linesep.encode('utf-8')
+        with open(file2, 'rb') as fh:
+            history_data = fh.read()
+        with open(file1, 'rb') as fh:
+            local_file = fh.readlines()
+    if attributes is None:
+        attributes = {}
     lines_diff = int(attributes.get('lines_diff', 0))
     line_diff_count = 0
-    while local_file:
-        contains = local_file.pop(0).rstrip('\n\r')
+    for contains in local_file:
+        contains = contains.rstrip(to_strip)
         if contains not in history_data:
             line_diff_count += 1
         if line_diff_count > lines_diff:
diff --git a/lib/galaxy/tools/verify/asserts/__init__.py b/lib/galaxy/tools/verify/asserts/__init__.py
index 8810a032c44..ccdadb057e1 100644
--- a/lib/galaxy/tools/verify/asserts/__init__.py
+++ b/lib/galaxy/tools/verify/asserts/__init__.py
@@ -1,8 +1,8 @@
-import inspect
 import logging
 import sys
 
 from galaxy.util import unicodify
+from galaxy.util.getargspec import getfullargspec
 
 log = logging.getLogger(__name__)
 
@@ -43,7 +43,7 @@ def verify_assertion(data, assertion_description):
         errmsg = "Unable to find test function associated with XML tag '%s'. Check your tool file syntax." % tag
         raise AssertionError(errmsg)
 
-    assert_function_args = inspect.getargspec(assert_function).args
+    assert_function_args = getfullargspec(assert_function).args
     args = {}
     for attribute, value in assertion_description["attributes"].items():
         if attribute in assert_function_args:
diff --git a/lib/galaxy/tools/verify/asserts/hdf5.py b/lib/galaxy/tools/verify/asserts/hdf5.py
index f64314fe1ea..c4aae057c9e 100644
--- a/lib/galaxy/tools/verify/asserts/hdf5.py
+++ b/lib/galaxy/tools/verify/asserts/hdf5.py
@@ -24,10 +24,19 @@ def assert_has_h5_attribute(output_bytes, key, value):
 
 
 def assert_has_h5_keys(output_bytes, keys):
-    """ Asserts the specified HDF5 output has exactly the given keys."""
+    """ Asserts the specified HDF5 output has the given keys."""
     _assert_h5py()
     keys = [k.strip() for k in keys.strip().split(',')]
     h5_keys = sorted(keys)
     output_temp = io.BytesIO(output_bytes)
-    local_keys = sorted(list(h5py.File(output_temp, 'r').keys()))
-    assert local_keys == h5_keys, "Not a HDF5 file or H5 keys do not match:\n\t%s\n\t%s" % (local_keys, h5_keys)
+    local_keys = []
+
+    def append_keys(key):
+        local_keys.append(key)
+        return None
+    h5py.File(output_temp, 'r').visit(append_keys)
+    missing = 0
+    for key in h5_keys:
+        if key not in local_keys:
+            missing += 1
+    assert missing == 0, "Not a HDF5 file or H5 keys missing:\n\t%s\n\t%s" % (local_keys, h5_keys)
diff --git a/lib/galaxy/tools/verify/asserts/xml.py b/lib/galaxy/tools/verify/asserts/xml.py
index dc98a050cd2..8e31f9fd264 100644
--- a/lib/galaxy/tools/verify/asserts/xml.py
+++ b/lib/galaxy/tools/verify/asserts/xml.py
@@ -3,6 +3,8 @@ from __future__ import absolute_import
 import re
 import xml.etree
 
+from galaxy.util import unicodify
+
 
 # Helper functions used to work with XML output.
 def to_xml(output):
@@ -27,7 +29,7 @@ def assert_is_valid_xml(output):
         to_xml(output)
     except Exception as e:
         # TODO: Narrow caught exception to just parsing failure
-        raise AssertionError("Expected valid XML, but could not parse output. %s" % str(e))
+        raise AssertionError("Expected valid XML, but could not parse output. %s" % unicodify(e))
 
 
 def assert_has_element_with_path(output, path):
diff --git a/lib/galaxy/tools/verify/interactor.py b/lib/galaxy/tools/verify/interactor.py
index 81435bcf2d9..72ddd5b4ac4 100644
--- a/lib/galaxy/tools/verify/interactor.py
+++ b/lib/galaxy/tools/verify/interactor.py
@@ -29,7 +29,7 @@ from six import (
 )
 
 from galaxy import util
-from galaxy.tools.parser.interface import TestCollectionDef, TestCollectionOutputDef
+from galaxy.tool_util.parser.interface import TestCollectionDef, TestCollectionOutputDef
 from galaxy.util.bunch import Bunch
 from . import verify
 from .asserts import verify_assertions
@@ -42,13 +42,12 @@ log = getLogger(__name__)
 VERBOSE_ERRORS = util.asbool(os.environ.get("GALAXY_TEST_VERBOSE_ERRORS", False))
 UPLOAD_ASYNC = util.asbool(os.environ.get("GALAXY_TEST_UPLOAD_ASYNC", True))
 ERROR_MESSAGE_DATASET_SEP = "--------------------------------------"
-DEFAULT_TOOL_TEST_WAIT = os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 86400)
+DEFAULT_TOOL_TEST_WAIT = int(os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 86400))
 
 DEFAULT_FTYPE = 'auto'
 # This following default dbkey was traditionally hg17 before Galaxy 18.05,
 # restore this behavior by setting GALAXY_TEST_DEFAULT_DBKEY to hg17.
 DEFAULT_DBKEY = os.environ.get("GALAXY_TEST_DEFAULT_DBKEY", "?")
-DEFAULT_MAX_SECS = DEFAULT_TOOL_TEST_WAIT
 
 
 class OutputsDict(OrderedDict):
@@ -73,7 +72,7 @@ class OutputsDict(OrderedDict):
             return item
 
 
-def stage_data_in_history(galaxy_interactor, tool_id, all_test_data, history=None, force_path_paste=False):
+def stage_data_in_history(galaxy_interactor, tool_id, all_test_data, history=None, force_path_paste=False, maxseconds=DEFAULT_TOOL_TEST_WAIT):
     # Upload any needed files
     upload_waits = []
 
@@ -81,12 +80,20 @@ def stage_data_in_history(galaxy_interactor, tool_id, all_test_data, history=Non
 
     if UPLOAD_ASYNC:
         for test_data in all_test_data:
-            upload_waits.append(galaxy_interactor.stage_data_async(test_data, history, tool_id, force_path_paste=force_path_paste))
+            upload_waits.append(galaxy_interactor.stage_data_async(test_data,
+                                                                   history,
+                                                                   tool_id,
+                                                                   force_path_paste=force_path_paste,
+                                                                   maxseconds=maxseconds))
         for upload_wait in upload_waits:
             upload_wait()
     else:
         for test_data in all_test_data:
-            upload_wait = galaxy_interactor.stage_data_async(test_data, history, tool_id, force_path_paste=force_path_paste)
+            upload_wait = galaxy_interactor.stage_data_async(test_data,
+                                                             history,
+                                                             tool_id,
+                                                             force_path_paste=force_path_paste,
+                                                             maxseconds=maxseconds)
             upload_wait()
 
 
@@ -194,7 +201,7 @@ class GalaxyInteractorApi(object):
         """
         metadata = attributes.get('metadata', {}).copy()
         for key, value in metadata.copy().items():
-            if key not in ['name', 'info', 'tags']:
+            if key not in ['name', 'info', 'tags', 'created_from_basename']:
                 new_key = "metadata_%s" % key
                 metadata[new_key] = metadata[key]
                 del metadata[key]
@@ -240,7 +247,7 @@ class GalaxyInteractorApi(object):
     def wait_for(self, func, **kwd):
         sleep_amount = 0.2
         slept = 0
-        walltime_exceeded = kwd.get("maxseconds", DEFAULT_TOOL_TEST_WAIT)
+        walltime_exceeded = int(kwd.get("maxseconds", DEFAULT_TOOL_TEST_WAIT))
 
         while slept <= walltime_exceeded:
             result = func()
@@ -307,7 +314,7 @@ class GalaxyInteractorApi(object):
             output_id = output_data
         return output_id
 
-    def stage_data_async(self, test_data, history_id, tool_id, force_path_paste=False):
+    def stage_data_async(self, test_data, history_id, tool_id, force_path_paste=False, maxseconds=DEFAULT_TOOL_TEST_WAIT):
         fname = test_data['fname']
         tool_input = {
             "file_type": test_data['ftype'],
@@ -336,7 +343,7 @@ class GalaxyInteractorApi(object):
                 })
             name = test_data['name']
         else:
-            name = fname
+            name = os.path.basename(fname)
             tool_input.update({
                 "files_0|NAME": name,
                 "files_0|type": "upload_dataset",
@@ -365,7 +372,7 @@ class GalaxyInteractorApi(object):
         assert "jobs" in submit_response, "Invalid response from server [%s], expecting jobs in response." % submit_response
         jobs = submit_response["jobs"]
         assert len(jobs) > 0, "Invalid response from server [%s], expecting a job." % submit_response
-        return lambda: self.wait_for_job(jobs[0]["id"], history_id, DEFAULT_TOOL_TEST_WAIT)
+        return lambda: self.wait_for_job(jobs[0]["id"], history_id, maxseconds=maxseconds)
 
     def run_tool(self, testdef, history_id, resource_parameters={}):
         # We need to handle the case where we've uploaded a valid compressed file since the upload
@@ -684,7 +691,7 @@ def _verify_composite_datatype_file_content(file_name, hda_id, base_name=None, a
         )
     except AssertionError as err:
         errmsg = 'Composite file (%s) of %s different than expected, difference:\n' % (base_name, item_label)
-        errmsg += str(err)
+        errmsg += util.unicodify(err)
         raise AssertionError(errmsg)
 
 
@@ -717,19 +724,34 @@ def _verify_extra_files_content(extra_files, hda_id, dataset_fetcher, test_data_
             shutil.rmtree(path)
 
 
-def verify_tool(tool_id, galaxy_interactor, resource_parameters=None, register_job_data=None, test_index=0, tool_version=None, quiet=False, test_history=None, force_path_paste=False):
+def verify_tool(tool_id,
+                galaxy_interactor,
+                resource_parameters=None,
+                register_job_data=None,
+                test_index=0,
+                tool_version=None,
+                quiet=False,
+                test_history=None,
+                force_path_paste=False,
+                maxseconds=DEFAULT_TOOL_TEST_WAIT,
+                tool_test_dicts=None):
     if resource_parameters is None:
         resource_parameters = {}
-    tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
+    tool_test_dicts = tool_test_dicts or galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
     tool_test_dict = tool_test_dicts[test_index]
+    tool_test_dict.setdefault('maxseconds', maxseconds)
     testdef = ToolTestDescription(tool_test_dict)
-
     _handle_def_errors(testdef)
 
     if test_history is None:
         test_history = galaxy_interactor.new_history()
 
-    stage_data_in_history(galaxy_interactor, tool_id, testdef.test_data(), history=test_history, force_path_paste=force_path_paste)
+    stage_data_in_history(galaxy_interactor,
+                          tool_id,
+                          testdef.test_data(),
+                          history=test_history,
+                          force_path_paste=force_path_paste,
+                          maxseconds=maxseconds)
 
     # Once data is ready, run the tool and check the outputs - record API
     # input, job info, tool run exception, as well as exceptions related to
@@ -784,10 +806,10 @@ def verify_tool(tool_id, galaxy_interactor, resource_parameters=None, register_j
                 job_data["job"] = job_stdio
             status = "success"
             if job_output_exceptions:
-                job_data["output_problems"] = [str(_) for _ in job_output_exceptions]
+                job_data["output_problems"] = [util.unicodify(_) for _ in job_output_exceptions]
                 status = "failure"
             if tool_execution_exception:
-                job_data["execution_problem"] = str(tool_execution_exception)
+                job_data["execution_problem"] = util.unicodify(tool_execution_exception)
                 status = "error"
             job_data["status"] = status
             register_job_data(job_data)
@@ -915,7 +937,7 @@ def _verify_outputs(testdef, history, jobs, tool_id, data_list, data_collection_
                 verify_assertions(data, assertions)
             except AssertionError as err:
                 errmsg = '%s different than expected\n' % description
-                errmsg += str(err)
+                errmsg += util.unicodify(err)
                 register_exception(AssertionError(errmsg))
 
     for output_collection_def in testdef.output_collections:
@@ -1000,7 +1022,7 @@ def _format_stream(output, stream, format):
 class JobOutputsError(AssertionError):
 
     def __init__(self, output_exceptions, job_stdio):
-        big_message = "\n".join(map(str, output_exceptions))
+        big_message = "\n".join(map(util.unicodify, output_exceptions))
         super(JobOutputsError, self).__init__(big_message)
         self.job_stdio = job_stdio
         self.output_exceptions = output_exceptions
@@ -1016,7 +1038,7 @@ class ToolTestDescription(object):
     def __init__(self, processed_test_dict):
         test_index = processed_test_dict["test_index"]
         name = processed_test_dict.get('name', 'Test-%d' % (test_index + 1))
-        maxseconds = processed_test_dict.get('maxseconds', DEFAULT_MAX_SECS)
+        maxseconds = processed_test_dict.get('maxseconds', DEFAULT_TOOL_TEST_WAIT)
         if maxseconds is not None:
             maxseconds = int(maxseconds)
 
diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index 79f3883c70c..9952f301308 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -1,12 +1,13 @@
 import logging
 import tempfile
+from functools import total_ordering
 
 from six import string_types, text_type
 from six.moves import shlex_quote
 
 from galaxy import exceptions
+from galaxy.model.none_like import NoneDataset
 from galaxy.util import odict
-from galaxy.util.none_like import NoneDataset
 from galaxy.util.object_wrapper import wrap_with_safe_string
 
 log = logging.getLogger(__name__)
@@ -67,6 +68,7 @@ class RawObjectWrapper(ToolParameterValueWrapper):
         return getattr(self.obj, key)
 
 
+@total_ordering
 class InputValueWrapper(ToolParameterValueWrapper):
     """
     Wraps an input so that __str__ gives the "param_dict" representation.
@@ -107,6 +109,16 @@ class InputValueWrapper(ToolParameterValueWrapper):
     def __getattr__(self, key):
         return getattr(self.value, key)
 
+    def __gt__(self, other):
+        if isinstance(other, string_types):
+            return str(self) > other
+        elif isinstance(other, int):
+            return int(self) > other
+        elif isinstance(other, float):
+            return float(self) > other
+        else:
+            super(InputValueWrapper, self).__gt__(other)
+
     def __int__(self):
         return int(float(self))
 
@@ -310,7 +322,7 @@ class HasDatasets(object):
 
     def _dataset_wrapper(self, dataset, dataset_paths, **kwargs):
         wrapper_kwds = kwargs.copy()
-        if dataset:
+        if dataset and dataset_paths:
             real_path = dataset.file_name
             if real_path in dataset_paths:
                 wrapper_kwds["dataset_path"] = dataset_paths[real_path]
diff --git a/lib/galaxy/tools/zip_collection.xml b/lib/galaxy/tools/zip_collection.xml
index 70ce0841a45..0a047d71b1a 100644
--- a/lib/galaxy/tools/zip_collection.xml
+++ b/lib/galaxy/tools/zip_collection.xml
@@ -11,8 +11,8 @@
   </inputs>
   <outputs>
     <collection name="output" type="paired" label="${on_string} (zipped)">
-      <data name="forward" />
-      <data name="reverse" />
+      <data name="forward" format_source="input_forward" />
+      <data name="reverse" format_source="input_reverse" />
     </collection>
   </outputs>
   <help><![CDATA[
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index cfc9657be0e..cf5125a6af9 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -24,6 +24,8 @@ import time
 import unicodedata
 import xml.dom.minidom
 from datetime import datetime
+from email.mime.multipart import MIMEMultipart
+from email.mime.text import MIMEText
 from hashlib import md5
 from os.path import relpath
 from xml.etree import ElementInclude, ElementTree
@@ -40,7 +42,10 @@ from boltons.iterutils import (
     remap,
 )
 from six import binary_type, iteritems, PY2, string_types, text_type
-from six.moves import email_mime_multipart, email_mime_text, xrange, zip
+from six.moves import (
+    xrange,
+    zip
+)
 from six.moves.urllib import (
     parse as urlparse,
     request as urlrequest
@@ -63,6 +68,8 @@ inflector = Inflector(English)
 log = get_logger(__name__)
 _lock = threading.RLock()
 
+namedtuple = collections.namedtuple
+
 CHUNK_SIZE = 65536  # 64k
 
 DATABASE_MAX_STRING_SIZE = 32768
@@ -395,6 +402,17 @@ def shrink_stream_by_size(value, size, join_by=b"..", left_larger=True, beginnin
     return unicodify(rval)
 
 
+def shrink_and_unicodify(stream):
+    stream = unicodify(stream, strip_null=True) or u''
+    if (len(stream) > DATABASE_MAX_STRING_SIZE):
+        stream = shrink_string_by_size(stream,
+                                       DATABASE_MAX_STRING_SIZE,
+                                       join_by="\n..\n",
+                                       left_larger=True,
+                                       beginning_on_size_error=True)
+    return stream
+
+
 def shrink_string_by_size(value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False):
     if len(value) > size:
         len_join_by = len(join_by)
@@ -986,7 +1004,7 @@ def roundify(amount, sfs=2):
         return amount[0:sfs] + '0' * (len(amount) - sfs)
 
 
-def unicodify(value, encoding=DEFAULT_ENCODING, error='replace'):
+def unicodify(value, encoding=DEFAULT_ENCODING, error='replace', strip_null=False):
     u"""
     Returns a Unicode string or None.
 
@@ -994,22 +1012,22 @@ def unicodify(value, encoding=DEFAULT_ENCODING, error='replace'):
     >>> assert unicodify('simple string') == u'simple string'
     >>> assert unicodify(3) == u'3'
     >>> assert unicodify(bytearray([115, 116, 114, 196, 169, 195, 177, 103])) == u'strĩñg'
-    >>> assert unicodify(Exception('message')) == u'message'
+    >>> assert unicodify(Exception(u'strĩñg')) == u'strĩñg'
     >>> assert unicodify('cómpl�c�tëd strĩñg') == u'cómpl�c�tëd strĩñg'
     >>> s = u'cómpl�c�tëd strĩñg'; assert unicodify(s) == s
     >>> s = u'lâtín strìñg'; assert unicodify(s.encode('latin-1'), 'latin-1') == s
     >>> s = u'lâtín strìñg'; assert unicodify(s.encode('latin-1')) == u'l\ufffdt\ufffdn str\ufffd\ufffdg'
     >>> s = u'lâtín strìñg'; assert unicodify(s.encode('latin-1'), error='ignore') == u'ltn strg'
     """
-    if value is None or isinstance(value, text_type):
+    if value is None:
         return value
     try:
         if isinstance(value, bytearray):
             value = bytes(value)
         elif not isinstance(value, string_types) and not isinstance(value, binary_type):
-            # In Python 2, value is not an instance of basestring
+            # In Python 2, value is not an instance of basestring (i.e. str or unicode)
             # In Python 3, value is not an instance of bytes or str
-            value = str(value)
+            value = text_type(value)
         # Now in Python 2, value is an instance of basestring, but may be not unicode
         # Now in Python 3, value is an instance of bytes or str
         if not isinstance(value, text_type):
@@ -1018,6 +1036,8 @@ def unicodify(value, encoding=DEFAULT_ENCODING, error='replace'):
         msg = "Value '%s' could not be coerced to Unicode" % value
         log.exception(msg)
         raise Exception(msg)
+    if strip_null:
+        return value.replace('\0', '')
     return value
 
 
@@ -1183,7 +1203,7 @@ def read_dbnames(filename):
         man_builds = [(build, name) for name, build in man_builds]
         db_names = DBNames(db_names + man_builds)
     except Exception as e:
-        log.error("ERROR: Unable to read builds file: %s", e)
+        log.error("ERROR: Unable to read builds file: %s", unicodify(e))
     if len(db_names) < 1:
         db_names = DBNames([(db_names.default_value, db_names.default_name)])
     return db_names
@@ -1280,7 +1300,7 @@ def umask_fix_perms(path, umask, unmasked_perms, gid=None):
                                                                                                                     path,
                                                                                                                     oct(perms),
                                                                                                                     oct(stat.S_IMODE(st.st_mode)),
-                                                                                                                    e))
+                                                                                                                    unicodify(e)))
     # fix group
     if gid is not None and st.st_gid != gid:
         try:
@@ -1295,7 +1315,7 @@ def umask_fix_perms(path, umask, unmasked_perms, gid=None):
             log.warning('Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % (desired_group,
                                                                                                         path,
                                                                                                         current_group,
-                                                                                                        e))
+                                                                                                        unicodify(e)))
 
 
 def docstring_trim(docstring):
@@ -1429,9 +1449,9 @@ def send_mail(frm, to, subject, body, config, html=None):
 
     to = listify(to)
     if html:
-        msg = email_mime_multipart.MIMEMultipart('alternative')
+        msg = MIMEMultipart('alternative')
     else:
-        msg = email_mime_text.MIMEText(body.encode('ascii', 'replace'))
+        msg = MIMEText(body, 'plain', 'utf-8')
 
     msg['To'] = ', '.join(to)
     msg['From'] = frm
@@ -1443,8 +1463,8 @@ def send_mail(frm, to, subject, body, config, html=None):
         return
 
     if html:
-        mp_text = email_mime_text.MIMEText(body.encode('ascii', 'replace'), 'plain')
-        mp_html = email_mime_text.MIMEText(html.encode('ascii', 'replace'), 'html')
+        mp_text = MIMEText(body, 'plain', 'utf-8')
+        mp_html = MIMEText(html, 'html', 'utf-8')
         msg.attach(mp_text)
         msg.attach(mp_html)
 
@@ -1457,28 +1477,28 @@ def send_mail(frm, to, subject, body, config, html=None):
     if not smtp_ssl:
         try:
             s.starttls()
-            log.debug('Initiated SSL/TLS connection to SMTP server: %s' % config.smtp_server)
+            log.debug('Initiated SSL/TLS connection to SMTP server: %s', config.smtp_server)
         except RuntimeError as e:
-            log.warning('SSL/TLS support is not available to your Python interpreter: %s' % e)
+            log.warning('SSL/TLS support is not available to your Python interpreter: %s', unicodify(e))
         except smtplib.SMTPHeloError as e:
-            log.error("The server didn't reply properly to the HELO greeting: %s" % e)
+            log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e))
             s.close()
             raise
         except smtplib.SMTPException as e:
-            log.warning('The server does not support the STARTTLS extension: %s' % e)
+            log.warning('The server does not support the STARTTLS extension: %s', unicodify(e))
     if config.smtp_username and config.smtp_password:
         try:
             s.login(config.smtp_username, config.smtp_password)
         except smtplib.SMTPHeloError as e:
-            log.error("The server didn't reply properly to the HELO greeting: %s" % e)
+            log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e))
             s.close()
             raise
         except smtplib.SMTPAuthenticationError as e:
-            log.error("The server didn't accept the username/password combination: %s" % e)
+            log.error("The server didn't accept the username/password combination: %s", unicodify(e))
             s.close()
             raise
         except smtplib.SMTPException as e:
-            log.error("No suitable authentication method was found: %s" % e)
+            log.error("No suitable authentication method was found: %s", unicodify(e))
             s.close()
             raise
     s.sendmail(frm, to, msg.as_string())
@@ -1641,7 +1661,7 @@ def url_get(base_url, password_mgr=None, pathspec=None, params=None):
     response = urlopener.open(full_url)
     content = response.read()
     response.close()
-    return content
+    return unicodify(content)
 
 
 def download_to_file(url, dest_file_path, timeout=30, chunk_size=2 ** 20):
diff --git a/lib/galaxy/util/getargspec.py b/lib/galaxy/util/getargspec.py
new file mode 100644
index 00000000000..47871901683
--- /dev/null
+++ b/lib/galaxy/util/getargspec.py
@@ -0,0 +1,9 @@
+import inspect
+
+
+def getfullargspec(func):
+    try:
+        return inspect.getfullargspec(func)
+    except AttributeError:
+        # on python 2
+        return inspect.getargspec(func)
diff --git a/lib/galaxy/util/json.py b/lib/galaxy/util/json.py
index c0fc6d54115..80f7779c946 100644
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -10,6 +10,8 @@ import string
 
 from six import iteritems, string_types
 
+from ..util import unicodify
+
 __all__ = ("safe_dumps", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response")
 
 log = logging.getLogger(__name__)
@@ -95,7 +97,7 @@ def validate_jsonrpc_request(request, regular_methods, notification_methods):
         return False, request, jsonrpc_response(id=None,
                                                 error=dict(code=-32700,
                                                            message='Parse error',
-                                                           data=str(e)))
+                                                           data=unicodify(e)))
     try:
         assert 'jsonrpc' in request, \
             'This server requires JSON-RPC 2.0 and no "jsonrpc" member was sent with the Request object as per the JSON-RPC 2.0 Specification.'
@@ -106,7 +108,7 @@ def validate_jsonrpc_request(request, regular_methods, notification_methods):
         return False, request, jsonrpc_response(request=request,
                                                 error=dict(code=-32600,
                                                            message='Invalid Request',
-                                                           data=str(e)))
+                                                           data=unicodify(e)))
     try:
         assert request['method'] in (regular_methods + notification_methods)
     except AssertionError:
@@ -121,7 +123,7 @@ def validate_jsonrpc_request(request, regular_methods, notification_methods):
         return False, request, jsonrpc_response(request=request,
                                                 error=dict(code=-32600,
                                                            message='Invalid Request',
-                                                           data=str(e)))
+                                                           data=unicodify(e)))
     return True, request, None
 
 
@@ -129,8 +131,8 @@ def validate_jsonrpc_response(response, id=None):
     try:
         response = json.loads(response)
     except Exception as e:
-        log.error('Response was not valid JSON: %s' % str(e))
-        log.debug('Response was: %s' % response)
+        log.error('Response was not valid JSON: %s', unicodify(e))
+        log.debug('Response was: %s', response)
         return False, response
     try:
         assert 'jsonrpc' in response, \
diff --git a/lib/galaxy/util/jstree.py b/lib/galaxy/util/jstree.py
index 49906c52db9..f5b3001c939 100644
--- a/lib/galaxy/util/jstree.py
+++ b/lib/galaxy/util/jstree.py
@@ -47,26 +47,17 @@ class Node(dictobj.DictionaryObject):
     For example, users may want to pass "attr" or some other valid jsTree options.
 
     Example:
-      >>> import jstree
-      >>> node = jstree.Node('a', None)
-      >>> print(node)
-      Node({'text': 'a', 'children': MutableDictionaryObject({})})
-      >>> print(node.jsonData())
-      {'text': 'a'}
+      >>> node = Node('a', None)
+      >>> assert node._items == {'text': 'a', 'children': dictobj.MutableDictionaryObject({})}
+      >>> assert node.jsonData() == {'text': 'a'}
 
-      >>> import jstree
-      >>> node = jstree.Node('a', 1)
-      >>> print(node)
-      Node({'text': 'a', 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 1}), 'id': 1})
-      >>> print(node.jsonData())
-      {'text': 'a', 'id': 1, 'li_attr': {'id': 1}}
+      >>> node = Node('a', 1)
+      >>> assert node._items == {'text': 'a', 'children': dictobj.MutableDictionaryObject({}), 'li_attr': dictobj.DictionaryObject({'id': 1}), 'id': 1}
+      >>> assert node.jsonData() == {'text': 'a', 'id': 1, 'li_attr': {'id': 1}}
 
-      >>> import jstree
-      >>> node = jstree.Node('a', 5, icon="folder", state = {'opened': True})
-      >>> print(node)
-      Node({'text': 'a', 'id': 5, 'state': DictionaryObject({'opened': True}), 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 5}), 'icon': 'folder'})
-      >>> print(node.jsonData())
-      {'text': 'a', 'state': {'opened': True}, 'id': 5, 'li_attr': {'id': 5}, 'icon': 'folder'}
+      >>> node = Node('a', 5, icon="folder", state = {'opened': True})
+      >>> assert node._items == {'text': 'a', 'id': 5, 'state': dictobj.DictionaryObject({'opened': True}), 'children': dictobj.MutableDictionaryObject({}), 'li_attr': dictobj.DictionaryObject({'id': 5}), 'icon': 'folder'}
+      >>> assert node.jsonData() == {'text': 'a', 'state': {'opened': True}, 'id': 5, 'li_attr': {'id': 5}, 'icon': 'folder'}
     """
     super(Node, self).__init__()
 
diff --git a/lib/galaxy/util/monitors.py b/lib/galaxy/util/monitors.py
index 04a1f76359a..ee43d940ff3 100644
--- a/lib/galaxy/util/monitors.py
+++ b/lib/galaxy/util/monitors.py
@@ -3,8 +3,8 @@ from __future__ import absolute_import
 import logging
 import threading
 
-from galaxy.web.stack import register_postfork_function
 from .sleeper import Sleeper
+from .web_compat import register_postfork_function
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/util/pastescript/loadwsgi.py b/lib/galaxy/util/pastescript/loadwsgi.py
index 8d773283fcf..cae59562798 100644
--- a/lib/galaxy/util/pastescript/loadwsgi.py
+++ b/lib/galaxy/util/pastescript/loadwsgi.py
@@ -12,6 +12,7 @@ import pkg_resources
 from six import iteritems
 from six.moves.urllib.parse import unquote
 
+from galaxy.util.getargspec import getfullargspec
 from galaxy.util.properties import NicerConfigParser
 
 
@@ -58,11 +59,11 @@ def fix_type_error(exc_info, callable, varargs, kwargs):
     if exc_info is None:
         exc_info = sys.exc_info()
     if (exc_info[0] != TypeError or
-            str(exc_info[1]).find('arguments') == -1 or
+            str(exc_info[1]).find('argument') == -1 or
             getattr(exc_info[1], '_type_error_fixed', False)):
         return exc_info
     exc_info[1]._type_error_fixed = True
-    argspec = inspect.formatargspec(*inspect.getargspec(callable))
+    argspec = inspect.formatargspec(*getfullargspec(callable))
     args = ', '.join(map(_short_repr, varargs))
     if kwargs and args:
         args += ', '
diff --git a/lib/galaxy/util/plugin_config.py b/lib/galaxy/util/plugin_config.py
index 1a4ce87f212..894601e7f75 100644
--- a/lib/galaxy/util/plugin_config.py
+++ b/lib/galaxy/util/plugin_config.py
@@ -30,12 +30,14 @@ def plugins_dict(module, plugin_type_identifier):
     return plugin_dict
 
 
-def load_plugins(plugins_dict, plugin_source, extra_kwds={}):
+def load_plugins(plugins_dict, plugin_source, extra_kwds=None, plugin_type_keys=('type',)):
+    if extra_kwds is None:
+        extra_kwds = {}
     source_type, source = plugin_source
     if source_type == "xml":
         return __load_plugins_from_element(plugins_dict, source, extra_kwds)
     else:
-        return __load_plugins_from_dicts(plugins_dict, source, extra_kwds)
+        return __load_plugins_from_dicts(plugins_dict, source, extra_kwds, plugin_type_keys=plugin_type_keys)
 
 
 def __load_plugins_from_element(plugins_dict, plugins_element, extra_kwds):
@@ -58,11 +60,16 @@ def __load_plugins_from_element(plugins_dict, plugins_element, extra_kwds):
     return plugins
 
 
-def __load_plugins_from_dicts(plugins_dict, configs, extra_kwds):
+def __load_plugins_from_dicts(plugins_dict, configs, extra_kwds, plugin_type_keys):
     plugins = []
 
     for config in configs:
-        plugin_type = config["type"]
+        plugin_type = None
+        for plugin_type_key in plugin_type_keys:
+            if plugin_type_key in config:
+                plugin_type = config[plugin_type_key]
+                break
+        assert plugin_type is not None, "Could not determine plugin type for [%s]" % config
         plugin_kwds = config
         plugin_kwds.update(extra_kwds)
         plugin = plugins_dict[plugin_type](**plugin_kwds)
diff --git a/lib/galaxy/util/template.py b/lib/galaxy/util/template.py
index 1fb97f6ed59..c5d22066664 100644
--- a/lib/galaxy/util/template.py
+++ b/lib/galaxy/util/template.py
@@ -1,10 +1,51 @@
 """Entry point for the usage of Cheetah templating within Galaxy."""
+from __future__ import absolute_import
+
+import sys
+import traceback
+from lib2to3.refactor import RefactoringTool
+
+import packaging.version
+from Cheetah.Compiler import Compiler
+from Cheetah.NameMapper import NotFound
 from Cheetah.Template import Template
+from past.translation import myfixes
 
 from . import unicodify
 
+# Skip libpasteurize fixers, which make sure code is py2 and py3 compatible.
+# This is not needed, we only translate code on py3.
+myfixes = [f for f in myfixes if not f.startswith('libpasteurize')]
+refactoring_tool = RefactoringTool(myfixes, {'print_function': True})
 
-def fill_template(template_text, context=None, **kwargs):
+
+class FixedModuleCodeCompiler(Compiler):
+
+    module_code = None
+
+    def getModuleCode(self):
+        self._moduleDef = self.module_code
+        return self._moduleDef
+
+
+def create_compiler_class(module_code):
+
+    class CustomCompilerClass(FixedModuleCodeCompiler):
+        pass
+
+    setattr(CustomCompilerClass, 'module_code', module_code)
+
+    return CustomCompilerClass
+
+
+def fill_template(template_text,
+                  context=None,
+                  retry=10,
+                  compiler_class=Compiler,
+                  first_exception=None,
+                  futurized=False,
+                  python_template_version='3',
+                  **kwargs):
     """Fill a cheetah template out for specified context.
 
     If template_text is None, an exception will be thrown, if context
@@ -15,4 +56,62 @@ def fill_template(template_text, context=None, **kwargs):
         raise TypeError("Template text specified as None to fill_template.")
     if not context:
         context = kwargs
-    return unicodify(Template(source=template_text, searchList=[context]))
+    if isinstance(python_template_version, str):
+        python_template_version = packaging.version.parse(python_template_version)
+    klass = Template.compile(source=template_text, compilerClass=compiler_class)
+    t = klass(searchList=[context])
+    try:
+        return unicodify(t)
+    except NotFound as e:
+        if first_exception is None:
+            first_exception = e
+        if sys.version_info.major > 2 and python_template_version.release[0] < 3 and retry > 0:
+            tb = e.__traceback__
+            last_stack = traceback.extract_tb(tb)[-1]
+            if last_stack.name == '<listcomp>':
+                # On python 3 list, dict and set comprehensions as well as generator expressions
+                # have their own local scope, which prevents accessing frame variables in cheetah.
+                # We can work around this by replacing `$var` with `var`, but we only do this for
+                # list comprehensions, as this has never worked for dict or set comprehensions or
+                # generator expressions in Cheetah.
+                var_not_found = e.args[0].split("'")[1]
+                replace_str = 'VFFSL(SL,"%s",True)' % var_not_found
+                lineno = last_stack.lineno - 1
+                module_code = t._CHEETAH_generatedModuleCode.splitlines()
+                module_code[lineno] = module_code[lineno].replace(replace_str, var_not_found)
+                module_code = "\n".join(module_code)
+                compiler_class = create_compiler_class(module_code)
+                return fill_template(template_text=template_text,
+                                     context=context,
+                                     retry=retry - 1,
+                                     compiler_class=compiler_class,
+                                     first_exception=first_exception,
+                                     python_template_version=python_template_version,
+                                     )
+        raise first_exception or e
+    except Exception as e:
+        if first_exception is None:
+            first_exception = e
+        if sys.version_info.major > 2 and python_template_version.release[0] < 3 and not futurized:
+            # Possibly an error caused by attempting to run python 2
+            # template code on python 3. Run the generated module code
+            # through futurize and hope for the best.
+            module_code = t._CHEETAH_generatedModuleCode
+            module_code = futurize_preprocessor(module_code)
+            compiler_class = create_compiler_class(module_code)
+            return fill_template(template_text=template_text,
+                                 context=context,
+                                 retry=retry,
+                                 compiler_class=compiler_class,
+                                 first_exception=first_exception,
+                                 futurized=True,
+                                 python_template_version=python_template_version,
+                                 )
+        raise first_exception or e
+
+
+def futurize_preprocessor(source):
+    source = str(refactoring_tool.refactor_string(source, name='auto_translate_cheetah'))
+    # libfuturize.fixes.fix_unicode_keep_u' breaks from Cheetah.compat import unicode
+    source = source.replace('from Cheetah.compat import str', 'from Cheetah.compat import unicode')
+    return source
diff --git a/lib/galaxy/util/watcher.py b/lib/galaxy/util/watcher.py
index e90141756cc..b8417b34fa1 100644
--- a/lib/galaxy/util/watcher.py
+++ b/lib/galaxy/util/watcher.py
@@ -21,7 +21,7 @@ except ImportError:
     can_watch = False
 
 from galaxy.util.hash_util import md5_hash_file
-from galaxy.web.stack import register_postfork_function
+from .web_compat import register_postfork_function
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/util/web_compat.py b/lib/galaxy/util/web_compat.py
new file mode 100644
index 00000000000..e3a98359f3d
--- /dev/null
+++ b/lib/galaxy/util/web_compat.py
@@ -0,0 +1,10 @@
+"""Work around for gross circular dependency between galaxy.util and galaxy.web_stack.
+
+Provide a function that will delay to forking in a uwsgi environment but run immediately
+otherwise.
+"""
+try:
+    from galaxy.web_stack import register_postfork_function
+except ImportError:
+    def register_postfork_function(f, *args, **kwargs):
+        f(*args, **kwargs)
diff --git a/lib/galaxy/util/xml_macros.py b/lib/galaxy/util/xml_macros.py
index f03b8dac8b5..b02796080e1 100644
--- a/lib/galaxy/util/xml_macros.py
+++ b/lib/galaxy/util/xml_macros.py
@@ -19,6 +19,7 @@ def load_with_references(path):
 
     # Collect tokens
     tokens = _macros_of_type(root, 'token', lambda el: el.text or '')
+    tokens = expand_nested_tokens(tokens)
 
     # Expand xml macros
     macro_dict = _macros_of_type(root, 'xml', lambda el: XmlMacroDef(el))
@@ -82,8 +83,18 @@ def _macros_of_type(root, type, el_func):
     return macro_dict
 
 
+def expand_nested_tokens(tokens):
+    for token_name in tokens.keys():
+        for current_token_name, current_token_value in tokens.items():
+            if token_name in current_token_value:
+                if token_name == current_token_name:
+                    raise Exception("Token '%s' cannot contain itself" % token_name)
+                tokens[current_token_name] = current_token_value.replace(token_name, tokens[token_name])
+    return tokens
+
+
 def _expand_tokens(elements, tokens):
-    if not tokens or not elements:
+    if not tokens or elements is None:
         return
 
     for element in elements:
@@ -103,11 +114,11 @@ def _expand_tokens_for_el(element, tokens):
     _expand_tokens(list(element), tokens)
 
 
-def _expand_tokens_str(str, tokens):
+def _expand_tokens_str(s, tokens):
     for key, value in tokens.items():
-        if str.find(key) > -1:
-            str = str.replace(key, value)
-    return str
+        if key in s:
+            s = s.replace(key, value)
+    return s
 
 
 def _expand_macros(elements, macros, tokens):
@@ -139,7 +150,7 @@ def _expand_macro(element, expand_el, macros, tokens):
 
     # HACK for elementtree, newer implementations (etree/lxml) won't
     # require this parent_map data structure but elementtree does not
-    # track parents or recongnize .find('..').
+    # track parents or recognize .find('..').
     # TODO fix this now that we're not using elementtree
     parent_map = dict((c, p) for p in element.iter() for c in p)
     _xml_replace(expand_el, expanded_elements, parent_map)
diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
index 701b600c93d..0f46519cd48 100644
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
-VERSION_MAJOR = "19.05"
+VERSION_MAJOR = "19.09"
 VERSION_MINOR = "dev"
 VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '')
diff --git a/lib/galaxy/visualization/plugins/interactive_environments.py b/lib/galaxy/visualization/plugins/interactive_environments.py
index b7c1016f41c..180345c7c1b 100644
--- a/lib/galaxy/visualization/plugins/interactive_environments.py
+++ b/lib/galaxy/visualization/plugins/interactive_environments.py
@@ -19,7 +19,10 @@ from galaxy import model, web
 from galaxy.containers import ContainerPort
 from galaxy.containers.docker_model import DockerVolume
 from galaxy.managers import api_keys
-from galaxy.util import string_as_bool_or_none
+from galaxy.util import (
+    string_as_bool_or_none,
+    unicodify
+)
 from galaxy.util.bunch import Bunch
 
 
@@ -432,6 +435,8 @@ class InteractiveEnvironmentRequest(object):
         ))
         p = Popen(raw_cmd, stdout=PIPE, stderr=PIPE, close_fds=True)
         stdout, stderr = p.communicate()
+        stdout = unicodify(stdout)
+        stderr = unicodify(stderr)
         if p.returncode != 0:
             log.error("Container Launch error\n\n%s\n%s" % (stdout, stderr))
             return None
diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py
index 88b10178aa5..8442484bad2 100644
--- a/lib/galaxy/visualization/plugins/registry.py
+++ b/lib/galaxy/visualization/plugins/registry.py
@@ -223,7 +223,7 @@ class VisualizationsRegistry(object):
 
     def get_plugins(self):
         result = []
-        for plugin in self.plugins.itervalues():
+        for plugin in self.plugins.values():
             result.append(plugin.to_dict())
         return sorted(result, key=lambda k: k.get('html'))
 
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 85ed202db1f..41c1d66722e 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -2,7 +2,6 @@
 Contains functionality needed in every web interface
 """
 import logging
-import re
 
 from six import string_types
 from sqlalchemy import true
@@ -54,13 +53,6 @@ log = logging.getLogger(__name__)
 SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
 
 
-def _is_valid_slug(slug):
-    """ Returns true if slug is valid. """
-
-    VALID_SLUG_RE = re.compile(r"^[a-z0-9\-]+$")
-    return VALID_SLUG_RE.match(slug)
-
-
 class BaseController(object):
     """
     Base class for Galaxy web application controllers.
@@ -190,12 +182,12 @@ class BaseAPIController(BaseController):
                                              check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
 
         except exceptions.ItemDeletionException as e:
-            raise HTTPBadRequest(detail="Invalid %s id ( %s ) specified: %s" % (class_name, str(id), str(e)))
+            raise HTTPBadRequest(detail="Invalid %s id ( %s ) specified: %s" % (class_name, str(id), util.unicodify(e)))
         except exceptions.MessageException as e:
             raise HTTPBadRequest(detail=e.err_msg)
         except Exception as e:
             log.exception("Exception in get_object check for %s %s.", class_name, str(id))
-            raise HTTPInternalServerError(comment=str(e))
+            raise HTTPInternalServerError(comment=util.unicodify(e))
 
     def validate_in_users_and_groups(self, trans, payload):
         """
@@ -238,6 +230,12 @@ class BaseAPIController(BaseController):
             keys = keys.split(',')
         return dict(view=view, keys=keys, default_view=default_view)
 
+    def _parse_order_by(self, manager, order_by_string):
+        ORDER_BY_SEP_CHAR = ','
+        if ORDER_BY_SEP_CHAR in order_by_string:
+            return [manager.parse_order_by(o) for o in order_by_string.split(ORDER_BY_SEP_CHAR)]
+        return manager.parse_order_by(order_by_string)
+
 
 class JSAppLauncher(BaseUIController):
     """
@@ -308,7 +306,9 @@ class JSAppLauncher(BaseUIController):
             'toolbox'                       : trans.app.toolbox.to_dict(trans, in_panel=False),
             'toolbox_in_panel'              : trans.app.toolbox.to_dict(trans),
             'message_box_visible'           : trans.app.config.message_box_visible,
-            'show_inactivity_warning'       : trans.app.config.user_activation_on and trans.user and not trans.user.active
+            'show_inactivity_warning'       : trans.app.config.user_activation_on and trans.user and not trans.user.active,
+            'tool_shed_urls'                : list(trans.app.tool_shed_registry.tool_sheds.values()) if trans.app.tool_shed_registry else [],
+            'tool_dynamic_configs'          : list(trans.app.toolbox.dynamic_conf_filenames())
         }
 
         # TODO: move to user
@@ -1112,7 +1112,7 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         title_err = slug_err = ""
         if not title:
             title_err = "visualization name is required"
-        elif slug and not _is_valid_slug(slug):
+        elif slug and not managers_base.is_valid_slug(slug):
             slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
         elif slug and trans.sa_session.query(trans.model.Visualization).filter_by(user=user, slug=slug, deleted=False).first():
             slug_err = "visualization identifier must be unique"
@@ -1355,7 +1355,7 @@ class SharableMixin(object):
 
     def _is_valid_slug(self, slug):
         """ Returns true if slug is valid. """
-        return _is_valid_slug(slug)
+        return managers_base.is_valid_slug(slug)
 
     @web.expose
     @web.require_login("modify Galaxy items")
diff --git a/lib/galaxy/web/framework/decorators.py b/lib/galaxy/web/framework/decorators.py
index d7e726c55fd..14779e5d501 100644
--- a/lib/galaxy/web/framework/decorators.py
+++ b/lib/galaxy/web/framework/decorators.py
@@ -1,4 +1,3 @@
-import inspect
 import logging
 from functools import wraps
 from json import loads
@@ -12,6 +11,7 @@ from galaxy.util import (
     parse_non_hex_float,
     unicodify
 )
+from galaxy.util.getargspec import getfullargspec
 from galaxy.util.json import safe_dumps
 from galaxy.web.framework import url_for
 
@@ -176,7 +176,7 @@ def __extract_payload_from_request(trans, func, kwargs):
         # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from
         # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods.
         payload = kwargs.copy()
-        named_args, _, _, _ = inspect.getargspec(func)
+        named_args = getfullargspec(func).args
         for arg in named_args:
             payload.pop(arg, None)
         for k, v in payload.items():
diff --git a/lib/galaxy/web/framework/middleware/error.py b/lib/galaxy/web/framework/middleware/error.py
index 0c337164b2a..792bdfb7199 100644
--- a/lib/galaxy/web/framework/middleware/error.py
+++ b/lib/galaxy/web/framework/middleware/error.py
@@ -9,10 +9,10 @@ Error handler middleware
 When an exception is thrown from the wrapper application, this logs
 the exception and displays an error page.
 """
-import cgi
 import sys
 import traceback
 
+import markupsafe
 import six
 from paste import (
     request,
@@ -449,7 +449,7 @@ def send_report(rep, exc_data, html=True):
 
             <pre>%s</pre>
             </p>""" % (
-                cgi.escape(str(rep)), output.getvalue())
+                markupsafe.escape(str(rep)), output.getvalue())
         else:
             return (
                 "Additionally an error occurred while sending the "
diff --git a/lib/galaxy/web/framework/middleware/profile.py b/lib/galaxy/web/framework/middleware/profile.py
index d09da18d9aa..c3434d7cb40 100644
--- a/lib/galaxy/web/framework/middleware/profile.py
+++ b/lib/galaxy/web/framework/middleware/profile.py
@@ -2,11 +2,11 @@
 Middleware that profiles the request with cProfile and displays profiling
 information at the bottom of each page.
 """
-import cgi
 import cProfile
 import pstats
 import threading
 
+import markupsafe
 from paste import response
 
 
@@ -93,9 +93,9 @@ def pstats_as_html(stats, *sel_list):
     funcs, order_message, select_message = get_func_list(stats, sel_list)
     # Deal with any ordering or selection messages
     if order_message:
-        rval.append("<div>%s</div>" % cgi.escape(order_message))
+        rval.append("<div>%s</div>" % markupsafe.escape(order_message))
     if select_message:
-        rval.append("<div>%s</div>" % cgi.escape(select_message))
+        rval.append("<div>%s</div>" % markupsafe.escape(select_message))
     # Build a table for the functions
     if list:
         rval.append("<table>")
@@ -114,7 +114,7 @@ def pstats_as_html(stats, *sel_list):
             ncalls = str(nc)
             if nc != cc:
                 ncalls = ncalls + '/' + str(cc)
-            rval.append("<td>%s</td>" % cgi.escape(ncalls))
+            rval.append("<td>%s</td>" % markupsafe.escape(ncalls))
             # tottime
             rval.append("<td>%0.8f</td>" % tt)
             # percall
@@ -122,7 +122,7 @@ def pstats_as_html(stats, *sel_list):
                 percall = ""
             else:
                 percall = "%0.8f" % (tt / nc)
-            rval.append("<td>%s</td>" % cgi.escape(percall))
+            rval.append("<td>%s</td>" % markupsafe.escape(percall))
             # cumtime
             rval.append("<td>%0.8f</td>" % ct)
             # ctpercall
@@ -130,9 +130,9 @@ def pstats_as_html(stats, *sel_list):
                 ctpercall = ""
             else:
                 ctpercall = "%0.8f" % (ct / cc)
-            rval.append("<td>%s</td>" % cgi.escape(ctpercall))
+            rval.append("<td>%s</td>" % markupsafe.escape(ctpercall))
             # location
-            rval.append("<td>%s</td>" % cgi.escape(func_std_string(func)))
+            rval.append("<td>%s</td>" % markupsafe.escape(func_std_string(func)))
             # row complete
             rval.append("</tr>")
         rval.append("</table>")
diff --git a/lib/galaxy/web/framework/middleware/sentry.py b/lib/galaxy/web/framework/middleware/sentry.py
index e8db6491c35..767dbfb7dff 100644
--- a/lib/galaxy/web/framework/middleware/sentry.py
+++ b/lib/galaxy/web/framework/middleware/sentry.py
@@ -13,7 +13,7 @@ try:
 except ImportError:
     Client = None
 
-from galaxy.web.stack import register_postfork_function
+from galaxy.web_stack import register_postfork_function
 
 
 RAVEN_IMPORT_MESSAGE = ('The Python raven package is required to use this '
diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index f64e0a1d05b..284598d0260 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -39,7 +39,7 @@ from galaxy.web.framework import (
     helpers,
     url_for
 )
-from galaxy.web.stack import get_app_kwds
+from galaxy.web_stack import get_app_kwds
 
 log = logging.getLogger(__name__)
 
@@ -125,7 +125,7 @@ class WebApplication(base.WebApplication):
                 try:
                     module = import_module(module_name)
                 except ControllerUnavailable as exc:
-                    log.debug("%s could not be loaded: %s" % (module_name, str(exc)))
+                    log.debug("%s could not be loaded: %s", module_name, unicodify(exc))
                     continue
                 # Look for a controller inside the modules
                 for key in dir(module):
@@ -150,7 +150,7 @@ class WebApplication(base.WebApplication):
                 try:
                     module = import_module(module_name)
                 except ControllerUnavailable as exc:
-                    log.debug("%s could not be loaded: %s" % (module_name, str(exc)))
+                    log.debug("%s could not be loaded: %s", module_name, unicodify(exc))
                     continue
                 for key in dir(module):
                     T = getattr(module, key)
@@ -637,7 +637,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
             try:
                 safe_makedirs(os.path.join(self.app.config.user_library_import_dir, user.email))
             except ConfigurationError as e:
-                self.log_event(str(e))
+                self.log_event(unicodify(e))
 
     def user_checks(self, user):
         """
@@ -650,24 +650,27 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
         Associate the user's last accessed history (if exists) with their new session
         """
         history = None
+        set_permissions = False
         try:
             users_last_session = user.galaxy_sessions[0]
-            last_accessed = True
         except Exception:
             users_last_session = None
-            last_accessed = False
         if (prev_galaxy_session and
                 prev_galaxy_session.current_history and not
                 prev_galaxy_session.current_history.deleted and
-                prev_galaxy_session.current_history.datasets):
-            if prev_galaxy_session.current_history.user is None or prev_galaxy_session.current_history.user == user:
-                # If the previous galaxy session had a history, associate it with the new
-                # session, but only if it didn't belong to a different user.
-                history = prev_galaxy_session.current_history
-                if prev_galaxy_session.user is None:
-                    # Increase the user's disk usage by the amount of the previous history's datasets if they didn't already own it.
-                    for hda in history.datasets:
-                        user.adjust_total_disk_usage(hda.quota_amount(user))
+                prev_galaxy_session.current_history.datasets and
+                (prev_galaxy_session.current_history.user is None or
+                 prev_galaxy_session.current_history.user == user)):
+            # If the previous galaxy session had a history, associate it with the new session, but only if it didn't
+            # belong to a different user.
+            history = prev_galaxy_session.current_history
+            if prev_galaxy_session.user is None:
+                # Increase the user's disk usage by the amount of the previous history's datasets if they didn't already
+                # own it.
+                for hda in history.datasets:
+                    user.adjust_total_disk_usage(hda.quota_amount(user))
+                # Only set default history permissions if the history is from the previous session and anonymous
+                set_permissions = True
         elif self.galaxy_session.current_history:
             history = self.galaxy_session.current_history
         if (not history and users_last_session and
@@ -681,8 +684,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
         if history.user is None:
             history.user = user
         self.galaxy_session.current_history = history
-        if not last_accessed:
-            # Only set default history permissions if current history is not from a previous session
+        if set_permissions:
             self.app.security_agent.history_set_default_permissions(history, dataset=True, bypass_manage_permission=True)
         self.sa_session.add_all((prev_galaxy_session, self.galaxy_session, history))
 
diff --git a/lib/galaxy/web/proxy/js/lib/mapper.js b/lib/galaxy/web/proxy/js/lib/mapper.js
index 54fb097078e..78af6256dac 100644
--- a/lib/galaxy/web/proxy/js/lib/mapper.js
+++ b/lib/galaxy/web/proxy/js/lib/mapper.js
@@ -1,5 +1,6 @@
 var fs = require('fs');
 var sqlite3 = require('sqlite3')
+var watch = require('node-watch');
 
 
 var endsWith = function(subjectString, searchString) {
@@ -67,7 +68,7 @@ var mapFor = function(path) {
     }
     console.log("Watching path " + path);
     loadMap();
-    fs.watch(path, loadMap);
+    watch(path, loadMap);
     return map;
 };
 
diff --git a/lib/galaxy/web/proxy/js/package.json b/lib/galaxy/web/proxy/js/package.json
index e74db4d284f..7a4aa13d4f6 100644
--- a/lib/galaxy/web/proxy/js/package.json
+++ b/lib/galaxy/web/proxy/js/package.json
@@ -14,6 +14,7 @@
     "commander": "~2.19.0",
     "eventemitter3": "3.1.0",
     "http-proxy": "1.17.0",
+    "node-watch": "0.6.2",
     "sqlite3": "4.0.4"
   }
 }
diff --git a/lib/galaxy/web/stack/__init__.py b/lib/galaxy/web_stack/__init__.py
similarity index 100%
rename from lib/galaxy/web/stack/__init__.py
rename to lib/galaxy/web_stack/__init__.py
diff --git a/lib/galaxy/web/stack/handlers.py b/lib/galaxy/web_stack/handlers.py
similarity index 84%
rename from lib/galaxy/web/stack/handlers.py
rename to lib/galaxy/web_stack/handlers.py
index 9c6bbce60d5..89b1108b91c 100644
--- a/lib/galaxy/web/stack/handlers.py
+++ b/lib/galaxy/web_stack/handlers.py
@@ -48,22 +48,58 @@ class ConfiguresHandlers(object):
             else:
                 self.handlers[tag] = [handler_id]
 
-    def _init_handlers(self, config_element):
+    @staticmethod
+    def xml_to_dict(config, config_element):
+        handling_config_dict = {}
+
+        processes = {}
+        handling_config_dict["processes"] = processes
+
         # Parse handlers
         if config_element is not None:
-            for handler in self._findall_with_required(config_element, 'handler'):
+            for handler in ConfiguresHandlers._findall_with_required(config_element, 'handler'):
                 handler_id = handler.get('id')
-                if handler_id in self.handlers:
+                if handler_id in processes:
                     log.error("Handler '%s' overlaps handler with the same name, ignoring", handler_id)
                 else:
                     log.debug("Read definition for handler '%s'", handler_id)
-                    self.add_handler(
-                        handler_id,
-                        [x.strip() for x in handler.get('tags', self.DEFAULT_HANDLER_TAG).split(',')]
-                    )
-            self.default_handler_id = self._get_default(self.app.config, config_element, list(self.handlers.keys()))
+                    plugins = []
+                    for plugin in ConfiguresHandlers._findall_with_required(handler, 'plugin', ['id']):
+                        plugins.append(plugin.get("id"))
+                    tags = [x.strip() for x in handler.get('tags', ConfiguresHandlers.DEFAULT_HANDLER_TAG).split(',')]
+                    handler_def = {"tags": tags}
+                    if plugins:
+                        handler_def["plugins"] = plugins
+                    processes[handler_id] = handler_def
+            default_handler = ConfiguresHandlers.get_xml_default(config, config_element)
+            if default_handler:
+                handling_config_dict["default"] = default_handler
+
+            assign = listify(config_element.attrib.get('assign_with', []), do_strip=True)
+            if len(assign) > 0:
+                handling_config_dict["assign"] = assign
+            max_grab_str = config_element.attrib.get('max_grab', None)
+            if max_grab_str:
+                handling_config_dict["max_grab"] = int(max_grab_str)
+
+        return handling_config_dict
+
+    def _init_handlers(self, handling_config_dict=None):
+        handling_config_dict = handling_config_dict or {}
+        for handler_id, process in handling_config_dict.get("processes", {}).items():
+            process = process or {}
+            if handler_id in self.handlers:
+                log.error("Handler '%s' overlaps handler with the same name, ignoring", handler_id)
+            else:
+                log.debug("Read definition for handler '%s'", handler_id)
+                self._parse_handler(handler_id, process)
+                self.add_handler(handler_id, process.get("tags") or [self.DEFAULT_HANDLER_TAG])
+
+        self.default_handler_id = self._ensure_default_set(handling_config_dict.get("default"), list(self.handlers.keys()), required=False)
+
+    def _init_handler_assignment_methods(self, handling_config_dict=None):
+        handling_config_dict = handling_config_dict or {}
 
-    def _init_handler_assignment_methods(self, config_element=None):
         self.__is_handler = None
         # This is set by the stack job handler init code
         self.pool_for_tag = {}
@@ -75,8 +111,8 @@ class ConfiguresHandlers(object):
             HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED: self._assign_db_tag,
             HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE: self._assign_uwsgi_mule_message_handler,
         }
-        if config_element is not None:
-            for method in listify(config_element.attrib.get('assign_with', []), do_strip=True):
+        if handling_config_dict:
+            for method in handling_config_dict.get("assign", []):
                 method = method.lower()
                 assert method in HANDLER_ASSIGNMENT_METHODS, \
                     "Invalid job handler assignment method '%s', must be one of: %s" % (
@@ -88,7 +124,9 @@ class ConfiguresHandlers(object):
                     self.handler_assignment_methods = [method]
             if self.handler_assignment_methods == [HANDLER_ASSIGNMENT_METHODS.MEM_SELF]:
                 self.app.config.track_jobs_in_database = False
-            self.handler_max_grab = int(config_element.attrib.get('max_grab', self.handler_max_grab))
+            self.handler_max_grab = handling_config_dict.get('max_grab', self.handler_max_grab)
+            if self.handler_max_grab is not None:
+                self.handler_max_grab = int(self.handler_max_grab)
 
     def _set_default_handler_assignment_methods(self):
         if not self.handler_assignment_methods_configured:
@@ -115,7 +153,18 @@ class ConfiguresHandlers(object):
     def _parse_handler(self, handler_id, handler_def):
         pass
 
-    def _get_default(self, config, parent, names, auto=False):
+    @staticmethod
+    def get_xml_default(config, parent):
+        rval = parent.get('default')
+        if 'default_from_environ' in parent.attrib:
+            environ_var = parent.attrib['default_from_environ']
+            rval = os.environ.get(environ_var, rval)
+        elif 'default_from_config' in parent.attrib:
+            config_val = parent.attrib['default_from_config']
+            rval = config.config_dict.get(config_val, rval)
+        return rval
+
+    def _get_default(self, config, parent, names, auto=False, required=True):
         """
         Returns the default attribute set in a parent tag like <handlers> or
         <destinations>, or return the ID of the child, if there is no explicit
@@ -127,29 +176,29 @@ class ConfiguresHandlers(object):
         :type names: list of str
         :param auto: Automatically set a default if there is no default in the parent tag and there is only one child.
         :type auto: bool
+        :param required: Require a default to be set or determined automatically, else raise Exception
+        :type required: bool
 
         :returns: str -- id or tag representing the default.
         """
+        rval = ConfiguresHandlers.get_xml_default(config, parent)
+        return self._ensure_default_set(rval, names, auto=auto, required=required)
 
-        rval = parent.get('default')
-        if 'default_from_environ' in parent.attrib:
-            environ_var = parent.attrib['default_from_environ']
-            rval = os.environ.get(environ_var, rval)
-        elif 'default_from_config' in parent.attrib:
-            config_val = parent.attrib['default_from_config']
-            rval = config.config_dict.get(config_val, rval)
-
+    def _ensure_default_set(self, rval, names, auto=False, required=True):
         if rval is not None:
             # If the parent element has a 'default' attribute, use the id or tag in that attribute
-            if self.deterministic_handler_assignment and rval not in names:
-                raise Exception("<%s> default attribute '%s' does not match a defined id or tag in a child element" % (parent.tag, rval))
-            log.debug("<%s> default set to child with id or tag '%s'" % (parent.tag, rval))
+            if required and rval not in names:
+                raise Exception("default attribute '%s' does not match a defined id or tag in a child element" % (rval))
+            log.debug("default set to child with id or tag '%s'" % (rval))
         elif auto and len(names) == 1:
-            log.info("Setting <%s> default to child with id '%s'" % (parent.tag, names[0]))
+            log.info("Setting default to child with id '%s'" % (names[0]))
             rval = names[0]
+        elif required:
+            raise Exception("No default specified, please specify a valid id or tag with the 'default' attribute")
         return rval
 
-    def _findall_with_required(self, parent, match, attribs=None):
+    @staticmethod
+    def _findall_with_required(parent, match, attribs=None):
         """Like ``xml.etree.ElementTree.Element.findall()``, except only returns children that have the specified attribs.
 
         :param parent: Parent element in which to find.
@@ -180,7 +229,7 @@ class ConfiguresHandlers(object):
 
     @property
     def deterministic_handler_assignment(self):
-        return self.handler_assignment_methods and all(
+        return self.handler_assignment_methods and any(
             filter(lambda x: x in (
                 HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE,
                 HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN,
diff --git a/lib/galaxy/web/stack/message.py b/lib/galaxy/web_stack/message.py
similarity index 100%
rename from lib/galaxy/web/stack/message.py
rename to lib/galaxy/web_stack/message.py
diff --git a/lib/galaxy/web/stack/transport.py b/lib/galaxy/web_stack/transport.py
similarity index 100%
rename from lib/galaxy/web/stack/transport.py
rename to lib/galaxy/web_stack/transport.py
diff --git a/lib/galaxy/webapps/galaxy/api/authenticate.py b/lib/galaxy/webapps/galaxy/api/authenticate.py
index 8e860638201..78074926dcf 100644
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -87,7 +87,7 @@ class AuthenticationController(BaseAPIController):
             try:
                 email, password = unicodify(b64decode(smart_str(split[0]))).split(':')
             except Exception as e:
-                raise exceptions.ActionInputError(str(e))
+                raise exceptions.ActionInputError(e)
 
         # If there are only two elements, check the first and ensure it says
         # 'basic' so that we know we're about to decode the right thing. If not,
diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py
index 49237b9d316..03cc7f17310 100644
--- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py
+++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py
@@ -18,6 +18,7 @@ from galaxy.exceptions import (
     RequestParameterMissingException
 )
 from galaxy.managers import cloudauthzs
+from galaxy.util import unicodify
 from galaxy.web import (
     expose_api
 )
@@ -151,7 +152,7 @@ class CloudAuthzController(BaseAPIController):
         except Exception as e:
             log.exception(msg_template.format("exception while creating the new cloudauthz record"))
             raise InternalServerError('An unexpected error has occurred while responding to the create request of the '
-                                      'cloudauthz API.' + str(e))
+                                      'cloudauthz API.' + unicodify(e))
 
     @expose_api
     def delete(self, trans, encoded_authz_id, **kwargs):
@@ -188,7 +189,7 @@ class CloudAuthzController(BaseAPIController):
             log.exception(msg_template.format("exception while deleting the cloudauthz record with "
                                               "ID: `{}`.".format(encoded_authz_id)))
             raise InternalServerError('An unexpected error has occurred while responding to the DELETE request of the '
-                                      'cloudauthz API.' + str(e))
+                                      'cloudauthz API.' + unicodify(e))
 
     @expose_api
     def update(self, trans, encoded_authz_id, payload, **kwargs):
@@ -249,4 +250,4 @@ class CloudAuthzController(BaseAPIController):
             log.exception(msg_template.format("exception while updating the cloudauthz record with "
                                               "ID: `{}`.".format(encoded_authz_id)))
             raise InternalServerError('An unexpected error has occurred while responding to the PUT request of the '
-                                      'cloudauthz API.' + str(e))
+                                      'cloudauthz API.' + unicodify(e))
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index 66bbd59bcb6..b729933f8cf 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -35,9 +35,14 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
 
     def __init__(self, app):
         super(DatasetsController, self).__init__(app)
+        self.history_manager = managers.histories.HistoryManager(app)
         self.hda_manager = managers.hdas.HDAManager(app)
-        self.hda_serializer = managers.hdas.HDASerializer(self.app)
+        self.hda_serializer = managers.hdas.HDASerializer(app)
+        self.hdca_serializer = managers.hdcas.HDCASerializer(app)
+        self.serializer_by_type = {'dataset': self.hda_serializer, 'dataset_collection': self.hdca_serializer}
         self.ldda_manager = managers.lddas.LDDAManager(app)
+        self.history_contents_manager = managers.history_contents.HistoryContentsManager(app)
+        self.history_contents_filters = managers.history_contents.HistoryContentsFilters(app)
 
     def _parse_serialization_params(self, kwd, default_view):
         view = kwd.get('view', None)
@@ -47,13 +52,72 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
         return dict(view=view, keys=keys, default_view=default_view)
 
     @web.expose_api
-    def index(self, trans, **kwd):
+    def index(self,
+              trans,
+              limit=500,
+              offset=0,
+              history_id=None,
+              **kwd):
         """
-        GET /api/datasets
-        Lists datasets.
+        GET /api/datasets/
+
+        Search datasets or collections using a query system
+
+        :rtype:     list
+        :returns:   dictionaries containing summary of dataset or dataset_collection information
+
+        The list returned can be filtered by using two optional parameters:
+            q:      string, generally a property name to filter by followed
+                    by an (often optional) hyphen and operator string.
+            qv:     string, the value to filter by
+
+        ..example:
+            To filter the list to only those created after 2015-01-29,
+            the query string would look like:
+                '?q=create_time-gt&qv=2015-01-29'
+
+            Multiple filters can be sent in using multiple q/qv pairs:
+                '?q=create_time-gt&qv=2015-01-29&q=name-contains&qv=experiment-1'
+
+        The list returned can be paginated using two optional parameters:
+            limit:  integer, defaults to no value and no limit (return all)
+                    how many items to return
+            offset: integer, defaults to 0 and starts at the beginning
+                    skip the first ( offset - 1 ) items and begin returning
+                    at the Nth item
+
+        ..example:
+            limit and offset can be combined. Skip the first two and return five:
+                '?limit=5&offset=3'
+
+        The list returned can be ordered using the optional parameter:
+            order:  string containing one of the valid ordering attributes followed
+                    (optionally) by '-asc' or '-dsc' for ascending and descending
+                    order respectively. Orders can be stacked as a comma-
+                    separated list of values.
+
+        ..example:
+            To sort by name descending then create time descending:
+                '?order=name-dsc,create_time'
+
+        The ordering attributes and their default orders are:
+            hid defaults to 'hid-asc'
+            create_time defaults to 'create_time-dsc'
+            update_time defaults to 'update_time-dsc'
+            name    defaults to 'name-asc'
+
+        'order' defaults to 'create_time'
         """
-        trans.response.status = 501
-        return 'not implemented'
+        filter_params = self.parse_filter_params(kwd)
+        filters = self.history_contents_filters.parse_filters(filter_params)
+        order_by = self._parse_order_by(manager=self.history_contents_manager, order_by_string=kwd.get('order', 'create_time-dsc'))
+        container = None
+        if history_id:
+            container = self.history_manager.get_accessible(self.decode_id(history_id), trans.user)
+        contents = self.history_contents_manager.contents(
+            container=container, filters=filters, limit=limit, offset=offset, order_by=order_by, user_id=trans.user.id,
+        )
+        return [self.serializer_by_type[content.history_content_type].serialize_to_view(content, user=trans.user, trans=trans, view='summary') for content in contents]
 
     @web.legacy_expose_api_anonymous
     def show(self, trans, id, hda_ldda='hda', data_type=None, provider=None, **kwd):
@@ -62,10 +126,7 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
         Displays information about and/or content of a dataset.
         """
         # Get dataset.
-        try:
-            dataset = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=id)
-        except Exception as e:
-            return str(e)
+        dataset = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=id)
 
         # Use data type to return particular type of data.
         try:
@@ -92,9 +153,8 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
                 else:
                     rval = dataset.to_dict()
 
-        except Exception as e:
-            rval = "Error in dataset API at listing contents: " + str(e)
-            log.error(rval + ": %s" % str(e), exc_info=True)
+        except Exception:
+            log.exception('Error in dataset API at listing contents')
             trans.response.status = 500
         return rval
 
@@ -363,7 +423,7 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
             log.exception("Error getting display data for dataset (%s) from history (%s)",
                           history_content_id, history_id)
             trans.response.status = 500
-            rval = "Could not get display data for dataset: %s" % e
+            rval = "Could not get display data for dataset: %s" % util.unicodify(e)
         return rval
 
     @web.legacy_expose_api_raw_anonymous
@@ -384,7 +444,7 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
             log.exception("Error getting metadata_file (%s) for dataset (%s) from history (%s)",
                           metadata_file, history_content_id, history_id)
             trans.response.status = 500
-            rval = "Could not get metadata for dataset: %s" % e
+            rval = "Could not get metadata for dataset: %s" % util.unicodify(e)
         return rval
 
     @web.expose_api_anonymous
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index 3040341594f..782d6b31ba9 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -5,7 +5,10 @@ import logging
 
 from galaxy import exceptions
 from galaxy.datatypes.data import Data
-from galaxy.util import asbool
+from galaxy.util import (
+    asbool,
+    unicodify
+)
 from galaxy.web import expose_api_anonymous_and_sessionless
 from galaxy.web.base.controller import BaseAPIController
 
@@ -36,10 +39,10 @@ class DatatypesController(BaseAPIController):
                         continue
                     rval.append(datatype_info_dict)
                 return rval
-        except Exception as exception:
-            log.error('could not get datatypes: %s', str(exception), exc_info=True)
-            if not isinstance(exception, exceptions.MessageException):
-                raise exceptions.InternalServerError(str(exception))
+        except Exception as e:
+            log.exception('Could not get datatypes')
+            if not isinstance(e, exceptions.MessageException):
+                raise exceptions.InternalServerError(unicodify(e))
             else:
                 raise
 
@@ -70,10 +73,10 @@ class DatatypesController(BaseAPIController):
                 class_to_classes[n] = dict((t, True) for t in types)
             return dict(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)
 
-        except Exception as exception:
-            log.error('could not get datatype mapping: %s', str(exception), exc_info=True)
-            if not isinstance(exception, exceptions.MessageException):
-                raise exceptions.InternalServerError(str(exception))
+        except Exception as e:
+            log.exception('Could not get datatype mapping')
+            if not isinstance(e, exceptions.MessageException):
+                raise exceptions.InternalServerError(unicodify(e))
             else:
                 raise
 
@@ -90,10 +93,10 @@ class DatatypesController(BaseAPIController):
                 if datatype is not None:
                     rval.append(datatype)
             return rval
-        except Exception as exception:
-            log.error('could not get datatypes: %s', str(exception), exc_info=True)
-            if not isinstance(exception, exceptions.MessageException):
-                raise exceptions.InternalServerError(str(exception))
+        except Exception as e:
+            log.exception('Could not get datatypes')
+            if not isinstance(e, exceptions.MessageException):
+                raise exceptions.InternalServerError(unicodify(e))
             else:
                 raise
 
diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py
index d6fb30694ac..8ee9745f23c 100644
--- a/lib/galaxy/webapps/galaxy/api/folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py
@@ -287,7 +287,8 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM
                 return self._copy_hdca_to_library_folder(trans, self.hda_manager, decoded_hdca_id, encoded_folder_id_16, ldda_message)
         except Exception as exc:
             # TODO handle exceptions better within the mixins
-            if 'not accessible to the current user' in str(exc) or 'You are not allowed to access this dataset' in str(exc):
+            exc_message = util.unicodify(exc)
+            if 'not accessible to the current user' in exc_message or 'You are not allowed to access this dataset' in exc_message:
                 raise exceptions.ItemAccessibilityException('You do not have access to the requested item')
             else:
                 log.exception(exc)
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index 2a300d580b1..f7b68e00dad 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -4,6 +4,7 @@ API operations on Group objects.
 import logging
 
 from galaxy import web
+from galaxy.util import unicodify
 from galaxy.web.base.controller import BaseAPIController, url_for
 
 log = logging.getLogger(__name__)
@@ -36,7 +37,7 @@ class GroupRolesAPIController(BaseAPIController):
                                  url=url_for('group_role', group_id=group_id, id=encoded_id, )))
         except Exception as e:
             rval = "Error in group API at listing roles"
-            log.error(rval + ": %s" % str(e))
+            log.error(rval + ": %s", unicodify(e))
             trans.response.status = 500
         return rval
 
@@ -63,7 +64,7 @@ class GroupRolesAPIController(BaseAPIController):
                 item = "role %s not in group %s" % (role.name, group.name)
         except Exception as e:
             item = "Error in group_role API group %s role %s" % (group.name, role.name)
-            log.error(item + ": %s" % str(e))
+            log.error(item + ": %s", unicodify(e))
         return item
 
     @web.legacy_expose_api
@@ -95,7 +96,7 @@ class GroupRolesAPIController(BaseAPIController):
                             url=url_for('group_role', group_id=group_id, id=role_id))
         except Exception as e:
             item = "Error in group_role API Adding role %s to group %s" % (role.name, group.name)
-            log.error(item + ": %s" % str(e))
+            log.error(item + ": %s", unicodify(e))
         return item
 
     @web.legacy_expose_api
@@ -122,5 +123,5 @@ class GroupRolesAPIController(BaseAPIController):
                 item = "role %s not in group %s" % (role.name, group.name)
         except Exception as e:
             item = "Error in group_role API Removing role %s from group %s" % (role.name, group.name)
-            log.error(item + ": %s" % str(e))
+            log.error(item + ": %s", unicodify(e))
         return item
diff --git a/lib/galaxy/webapps/galaxy/api/group_users.py b/lib/galaxy/webapps/galaxy/api/group_users.py
index db4f4dd7105..5d5190f83c8 100644
--- a/lib/galaxy/webapps/galaxy/api/group_users.py
+++ b/lib/galaxy/webapps/galaxy/api/group_users.py
@@ -4,6 +4,7 @@ API operations on Group objects.
 import logging
 
 from galaxy import web
+from galaxy.util import unicodify
 from galaxy.web.base.controller import BaseAPIController, url_for
 
 log = logging.getLogger(__name__)
@@ -36,7 +37,7 @@ class GroupUsersAPIController(BaseAPIController):
                                  url=url_for('group_user', group_id=group_id, id=encoded_id, )))
         except Exception as e:
             rval = "Error in group API at listing users"
-            log.error(rval + ": %s" % str(e))
+            log.error(rval + ": %s", unicodify(e))
             trans.response.status = 500
         return rval
 
@@ -63,7 +64,7 @@ class GroupUsersAPIController(BaseAPIController):
                 item = "user %s not in group %s" % (user.email, group.name)
         except Exception as e:
             item = "Error in group_user API group %s user %s" % (group.name, user.email)
-            log.error(item + ": %s" % str(e))
+            log.error(item + ": %s", unicodify(e))
         return item
 
     @web.legacy_expose_api
@@ -95,7 +96,7 @@ class GroupUsersAPIController(BaseAPIController):
                             url=url_for('group_user', group_id=group_id, id=user_id))
         except Exception as e:
             item = "Error in group_user API Adding user %s to group %s" % (user.email, group.name)
-            log.error(item + ": %s" % str(e))
+            log.error(item + ": %s", unicodify(e))
         return item
 
     @web.legacy_expose_api
@@ -122,5 +123,5 @@ class GroupUsersAPIController(BaseAPIController):
                 item = "user %s not in group %s" % (user.email, group.name)
         except Exception as e:
             item = "Error in group_user API Removing user %s from group %s" % (user.email, group.name)
-            log.error(item + ": %s" % str(e))
+            log.error(item + ": %s", unicodify(e))
         return item
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index 55b2639fa50..4ebb6e71b0f 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -149,7 +149,7 @@ class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistory
         # and any sent in from the query string
         filters += self.filters.parse_filters(filter_params)
 
-        order_by = self._parse_order_by(kwd.get('order', 'create_time-dsc'))
+        order_by = self._parse_order_by(manager=self.manager, order_by_string=kwd.get('order', 'create_time-dsc'))
         histories = self.manager.list(filters=filters, order_by=order_by, limit=limit, offset=offset)
 
         rval = []
@@ -182,13 +182,6 @@ class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistory
         # otherwise, do the default filter of removing the deleted histories
         return [self.app.model.History.deleted == false()]
 
-    def _parse_order_by(self, order_by_string):
-        ORDER_BY_SEP_CHAR = ','
-        manager = self.manager
-        if ORDER_BY_SEP_CHAR in order_by_string:
-            return [manager.parse_order_by(o) for o in order_by_string.split(ORDER_BY_SEP_CHAR)]
-        return manager.parse_order_by(order_by_string)
-
     @expose_api_anonymous
     def show(self, trans, id, deleted='False', **kwd):
         """
@@ -254,7 +247,7 @@ class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistory
         limit, offset = self.parse_limit_offset(kwd)
         filter_params = self.parse_filter_params(kwd)
         filters = self.filters.parse_filters(filter_params)
-        order_by = self._parse_order_by(kwd.get('order', 'create_time-dsc'))
+        order_by = self._parse_order_by(manager=self.manager, order_by_string=kwd.get('order', 'create_time-dsc'))
         histories = self.manager.list_published(filters=filters, order_by=order_by, limit=limit, offset=offset)
         rval = []
         for history in histories:
@@ -280,7 +273,7 @@ class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistory
         limit, offset = self.parse_limit_offset(kwd)
         filter_params = self.parse_filter_params(kwd)
         filters = self.filters.parse_filters(filter_params)
-        order_by = self._parse_order_by(kwd.get('order', 'create_time-dsc'))
+        order_by = self._parse_order_by(manager=self.manager, order_by_string=kwd.get('order', 'create_time-dsc'))
         histories = self.manager.list_shared_with(current_user,
             filters=filters, order_by=order_by, limit=limit, offset=offset)
         rval = []
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index d164eaee2f3..0d716cf0161 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -295,7 +295,7 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         except Exception as e:
             log.exception("Error in API while creating dataset collection archive")
             trans.response.status = 500
-            return {'error': str(e)}
+            return {'error': util.unicodify(e)}
 
     def __stream_dataset_collection(self, trans, dataset_collection_instance):
         archive_type_string = 'w|gz'
@@ -866,7 +866,7 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         filter_params = self.parse_filter_params(kwd)
         filters = self.history_contents_filters.parse_filters(filter_params)
         limit, offset = self.parse_limit_offset(kwd)
-        order_by = self._parse_order_by(kwd.get('order', 'hid-asc'))
+        order_by = self._parse_order_by(manager=self.history_contents_manager, order_by_string=kwd.get('order', 'hid-asc'))
         serialization_params = self._parse_serialization_params(kwd, 'summary')
         # TODO: > 16.04: remove these
         # TODO: remove 'dataset_details' and the following section when the UI doesn't need it
@@ -905,13 +905,6 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         split = type_id.split(TYPE_ID_SEP, 1)
         return TYPE_ID_SEP.join([split[0], self.app.security.encode_id(split[1])])
 
-    def _parse_order_by(self, order_by_string):
-        ORDER_BY_SEP_CHAR = ','
-        manager = self.history_contents_manager
-        if ORDER_BY_SEP_CHAR in order_by_string:
-            return [manager.parse_order_by(o) for o in order_by_string.split(ORDER_BY_SEP_CHAR)]
-        return manager.parse_order_by(order_by_string)
-
     @expose_api_raw
     def archive(self, trans, history_id, filename='', format='tgz', dry_run=True, **kwd):
         """
diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
index 813db8bca9c..5f571b94049 100644
--- a/lib/galaxy/webapps/galaxy/api/job_files.py
+++ b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -99,6 +99,8 @@ class JobFilesAPIController(BaseAPIController):
         else:
             input_file = payload.get("file",
                                      payload.get("__file", None)).file
+        target_dir = os.path.dirname(path)
+        util.safe_makedirs(target_dir)
         try:
             shutil.move(input_file.name, path)
         finally:
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index f42c83a998b..0c4c9985d27 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -12,24 +12,25 @@ from sqlalchemy import or_
 from galaxy import exceptions
 from galaxy import model
 from galaxy import util
-from galaxy.managers.datasets import DatasetManager
-from galaxy.managers.jobs import JobSearch
+from galaxy.managers.jobs import JobManager, JobSearch
 from galaxy.web import (
     expose_api,
     expose_api_anonymous,
 )
-from galaxy.web.base.controller import BaseAPIController
-from galaxy.web.base.controller import UsesLibraryMixinItems
+from galaxy.web.base.controller import (
+    BaseAPIController,
+    UsesVisualizationMixin
+)
 from galaxy.work.context import WorkRequestContext
 
 log = logging.getLogger(__name__)
 
 
-class JobController(BaseAPIController, UsesLibraryMixinItems):
+class JobController(BaseAPIController, UsesVisualizationMixin):
 
     def __init__(self, app):
         super(JobController, self).__init__(app)
-        self.dataset_manager = DatasetManager(app)
+        self.job_manager = JobManager(app)
         self.job_search = JobSearch(app)
 
     @expose_api
@@ -166,7 +167,7 @@ class JobController(BaseAPIController, UsesLibraryMixinItems):
                         raw_value=str(metric_value),
                     )
 
-                job_dict['job_metrics'] = [metric_to_dict(metric) for metric in job.metrics]
+                job_dict['job_metrics'] = self._metrics_as_dict(trans, job)
         return job_dict
 
     @expose_api
@@ -181,6 +182,8 @@ class JobController(BaseAPIController, UsesLibraryMixinItems):
         has_duplicate_inputs = False
         for job_input_assoc in job.input_datasets:
             input_dataset_instance = job_input_assoc.dataset
+            if input_dataset_instance is None:
+                continue
             if input_dataset_instance.get_total_size() == 0:
                 has_empty_inputs = True
             input_instance_id = input_dataset_instance.id
@@ -265,6 +268,163 @@ class JobController(BaseAPIController, UsesLibraryMixinItems):
             exceptions.RequestParameterInvalidException("Job with id '%s' is not paused" % (job.tool_id))
         return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)
 
+    @expose_api_anonymous
+    def metrics(self, trans, **kwd):
+        """
+        * GET /api/jobs/{job_id}/metrics
+        * GET /api/datasets/{dataset_id}/metrics
+            Return job metrics for specified job. Job accessibility checks are slightly
+            different than dataset checks, so both methods are available.
+
+        :type   job_id: string
+        :param  job_id: Encoded job id
+
+        :type   dataset_id: string
+        :param  dataset_id: Encoded HDA or LDDA id
+
+        :type   hda_ldda: string
+        :param  hda_ldda: hda if dataset_id is an HDA id (default), ldda if
+                          it is an ldda id.
+
+        :rtype:     list
+        :returns:   list containing job metrics
+        """
+        job = self.__get_job(trans, **kwd)
+        if not trans.user_is_admin and not trans.app.config.expose_potentially_sensitive_job_metrics:
+            return []
+
+        return self._metrics_as_dict(trans, job)
+
+    def _metrics_as_dict(self, trans, job):
+
+        def metric_to_dict(metric):
+            metric_name = metric.metric_name
+            metric_value = metric.metric_value
+            metric_plugin = metric.plugin
+            title, value = trans.app.job_metrics.format(metric_plugin, metric_name, metric_value)
+            return dict(
+                title=title,
+                value=value,
+                plugin=metric_plugin,
+                name=metric_name,
+                raw_value=str(metric_value),
+            )
+
+        metrics = [m for m in job.metrics if m.plugin != 'env' or trans.user_is_admin]
+        return list(map(metric_to_dict, metrics))
+
+    @expose_api_anonymous
+    def parameters_display(self, trans, **kwd):
+        """
+        * GET /api/jobs/{job_id}/parameters_display
+        * GET /api/datasets/{dataset_id}/parameters_display
+
+            Resolve parameters as a list for nested display. More client logic
+            here than is ideal but it is hard to reason about tool parameter
+            types on the client relative to the server. Job accessibility checks
+            are slightly different than dataset checks, so both methods are
+            available.
+
+            This API endpoint is unstable and tied heavily to Galaxy's JS client code,
+            this endpoint will change frequently.
+
+        :type   job_id: string
+        :param  job_id: Encoded job id
+
+        :type   dataset_id: string
+        :param  dataset_id: Encoded HDA or LDDA id
+
+        :type   hda_ldda: string
+        :param  hda_ldda: hda if dataset_id is an HDA id (default), ldda if
+                          it is an ldda id.
+
+        :rtype:     list
+        :returns:   job parameters for for display
+        """
+        job = self.__get_job(trans, **kwd)
+
+        def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None):
+            if upgrade_messages is None:
+                upgrade_messages = {}
+
+            rval = []
+
+            for input_index, input in enumerate(input_params.values()):
+                if input.name in param_values:
+                    if input.type == "repeat":
+                        for i in range(len(param_values[input.name])):
+                            rval.extend(inputs_recursive(input.inputs, param_values[input.name][i], depth=depth + 1))
+                    elif input.type == "section":
+                        # Get the value of the current Section parameter
+                        rval.append(dict(text=input.name, depth=depth))
+                        rval.extend(inputs_recursive(input.inputs, param_values[input.name], depth=depth + 1, upgrade_messages=upgrade_messages.get(input.name)))
+                    elif input.type == "conditional":
+                        try:
+                            current_case = param_values[input.name]['__current_case__']
+                            is_valid = True
+                        except Exception:
+                            current_case = None
+                            is_valid = False
+                        if is_valid:
+                            rval.append(dict(text=input.test_param.label, depth=depth, value=input.cases[current_case].value))
+                            rval.extend(inputs_recursive(input.cases[current_case].inputs, param_values[input.name], depth=depth + 1, upgrade_messages=upgrade_messages.get(input.name)))
+                        else:
+                            rval.append(dict(text=input.name, depth=depth, notes="The previously used value is no longer valid.", error=True))
+                    elif input.type == "upload_dataset":
+                        rval.append(dict(text=input.group_title(param_values), depth=depth, value="%s uploaded datasets" % len(param_values[input.name])))
+                    elif input.type == "data":
+                        value = []
+                        for i, element in enumerate(util.listify(param_values[input.name])):
+                            if element.history_content_type == "dataset":
+                                hda = element
+                                encoded_id = trans.security.encode_id(hda.id)
+                                value.append({"src": "hda", "id": encoded_id, "hid": hda.hid, "name": hda.name})
+                            else:
+                                value.append({"hid": element.hid, "name": element.name})
+                        rval.append(dict(text=input.label, depth=depth, value=value))
+                    elif input.visible:
+                        if hasattr(input, "label") and input.label:
+                            label = input.label
+                        else:
+                            # value for label not required, fallback to input name (same as tool panel)
+                            label = input.name
+                        rval.append(dict(text=label, depth=depth, value=input.value_to_display_text(param_values[input.name]), notes=upgrade_messages.get(input.name, '')))
+                else:
+                    # Parameter does not have a stored value.
+                    # Get parameter label.
+                    if input.type == "conditional":
+                        label = input.test_param.label
+                    elif input.type == "repeat":
+                        label = input.label()
+                    else:
+                        label = input.label or input.name
+                    rval.append(dict(text=label, depth=depth, notes="not used (parameter was added after this job was run)"))
+
+            return rval
+
+        # Load the tool
+        toolbox = self.app.toolbox
+        tool = toolbox.get_tool(job.tool_id, job.tool_version)
+        assert tool is not None, 'Requested tool has not been loaded.'
+
+        params_objects = None
+        upgrade_messages = {}
+        has_parameter_errors = False
+
+        # Load parameter objects, if a parameter type has changed, it's possible for the value to no longer be valid
+        try:
+            params_objects = job.get_param_values(self.app, ignore_errors=False)
+        except Exception:
+            params_objects = job.get_param_values(self.app, ignore_errors=True)
+            # use different param_objects in the following line, since we want to display original values as much as possible
+            upgrade_messages = tool.check_and_update_param_values(job.get_param_values(self.app, ignore_errors=True),
+                                                                  trans,
+                                                                  update_values=False)
+            has_parameter_errors = True
+
+        parameters = inputs_recursive(tool.inputs, params_objects, depth=1, upgrade_messages=upgrade_messages)
+        return {"parameters": parameters, "has_parameter_errors": has_parameter_errors}
+
     @expose_api_anonymous
     def build_for_rerun(self, trans, id, **kwd):
         """
@@ -306,23 +466,18 @@ class JobController(BaseAPIController, UsesLibraryMixinItems):
                 dataset_dict = dict(src="ldda", id=trans.security.encode_id(dataset.id))
         return dict(name=job_dataset_association.name, dataset=dataset_dict)
 
-    def __get_job(self, trans, id):
-        try:
-            decoded_job_id = self.decode_id(id)
-        except Exception:
-            raise exceptions.MalformedId()
-        job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
-        if job is None:
-            raise exceptions.ObjectNotFound()
-        belongs_to_user = (job.user == trans.user) if job.user else (job.session_id == trans.get_galaxy_session().id)
-        if not trans.user_is_admin and not belongs_to_user:
-            # Check access granted via output datasets.
-            if not job.output_datasets:
-                raise exceptions.ItemAccessibilityException("Job has no output datasets.")
-            for data_assoc in job.output_datasets:
-                if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user):
-                    raise exceptions.ItemAccessibilityException("You are not allowed to rerun this job.")
-        return job
+    def __get_job(self, trans, job_id=None, dataset_id=None, **kwd):
+        if job_id is not None:
+            try:
+                decoded_job_id = self.decode_id(job_id)
+            except Exception:
+                raise exceptions.MalformedId()
+            return self.job_manager.get_accessible_job(trans, decoded_job_id)
+        else:
+            hda_ldda = kwd.get("hda_ldda", "hda")
+            # Following checks dataset accessible
+            dataset_instance = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=dataset_id)
+            return dataset_instance.creating_job
 
     @expose_api
     def create(self, trans, payload, **kwd):
diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py
index 4922761245a..85d662b55a0 100644
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -99,7 +99,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         except NoResultFound:
             raise exceptions.RequestParameterInvalidException('No library found with the id provided.')
         except Exception as e:
-            raise exceptions.InternalServerError('Error loading from the database.' + str(e))
+            raise exceptions.InternalServerError('Error loading from the database.' + util.unicodify(e))
         if not (trans.user_is_admin or trans.app.security_agent.can_access_library(current_user_roles, library)):
             raise exceptions.RequestParameterInvalidException('No library found with the id provided.')
         encoded_id = 'F' + trans.security.encode_id(library.root_folder.id)
@@ -226,7 +226,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
             # security is checked in the downstream controller
             parent = self.get_library_folder(trans, folder_id, check_ownership=False, check_accessible=False)
         except Exception as e:
-            return str(e)
+            return util.unicodify(e)
         # The rest of the security happens in the library_common controller.
         real_folder_id = trans.security.encode_id(parent.id)
 
@@ -480,5 +480,5 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
             log.exception('library_contents API, delete: uncaught exception: %s, %s',
                           id, str(kwd))
             trans.response.status = 500
-            rval.update({'error': str(exc)})
+            rval.update({'error': util.unicodify(exc)})
         return rval
diff --git a/lib/galaxy/webapps/galaxy/api/library_datasets.py b/lib/galaxy/webapps/galaxy/api/library_datasets.py
index 9df56b74509..56d2a8fe61e 100644
--- a/lib/galaxy/webapps/galaxy/api/library_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/library_datasets.py
@@ -86,7 +86,7 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
         try:
             ldda = self.get_library_dataset_dataset_association(trans, id=encoded_ldda_id, check_ownership=False, check_accessible=False)
         except Exception as e:
-            raise exceptions.ObjectNotFound('Requested version of library dataset was not found.' + str(e))
+            raise exceptions.ObjectNotFound('Requested version of library dataset was not found.' + util.unicodify(e))
 
         if ldda not in library_dataset.expired_datasets:
             raise exceptions.ObjectNotFound('Given library dataset does not have the requested version.')
@@ -533,7 +533,7 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
                 except HTTPInternalServerError:
                     raise exceptions.InternalServerError('Internal error.')
                 except Exception as e:
-                    raise exceptions.InternalServerError('Unknown error.' + str(e))
+                    raise exceptions.InternalServerError('Unknown error.' + util.unicodify(e))
 
         folders_to_download = kwd.get('folder_ids%5B%5D', None)
         if folders_to_download is None:
@@ -640,7 +640,7 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
                         raise exceptions.ObjectNotFound("Requested dataset not found. ")
                     except Exception as e:
                         log.exception("Unable to add composite parent %s to temporary library download archive", ldda.dataset.file_name)
-                        raise exceptions.InternalServerError("Unable to add composite parent to temporary library download archive. " + str(e))
+                        raise exceptions.InternalServerError("Unable to add composite parent to temporary library download archive. " + util.unicodify(e))
 
                     flist = glob.glob(os.path.join(ldda.dataset.extra_files_path, '*.*'))  # glob returns full paths
                     for fpath in flist:
@@ -659,8 +659,8 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
                             log.exception("Requested dataset %s does not exist on the host.", fpath)
                             raise exceptions.ObjectNotFound("Requested dataset not found.")
                         except Exception as e:
-                            log.exception("Unable to add %s to temporary library download archive %s" % (fname, outfname))
-                            raise exceptions.InternalServerError("Unable to add dataset to temporary library download archive . " + str(e))
+                            log.exception("Unable to add %s to temporary library download archive %s", fname, outfname)
+                            raise exceptions.InternalServerError("Unable to add dataset to temporary library download archive . " + util.unicodify(e))
                 else:
                     try:
                         if format == 'zip':
@@ -675,7 +675,7 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
                         raise exceptions.ObjectNotFound("Requested dataset not found.")
                     except Exception as e:
                         log.exception("Unable to add %s to temporary library download archive %s", ldda.dataset.file_name, outfname)
-                        raise exceptions.InternalServerError("Unknown error. " + str(e))
+                        raise exceptions.InternalServerError("Unknown error. " + util.unicodify(e))
             lname = 'selected_dataset'
             fname = lname.replace(' ', '_') + '_files'
             if format == 'zip':
diff --git a/lib/galaxy/webapps/galaxy/api/page_revisions.py b/lib/galaxy/webapps/galaxy/api/page_revisions.py
index faf2be37035..f240f6e9155 100644
--- a/lib/galaxy/webapps/galaxy/api/page_revisions.py
+++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py
@@ -3,9 +3,9 @@ API for updating Galaxy Pages
 """
 import logging
 
-from galaxy import exceptions
+from galaxy.managers.base import get_object
+from galaxy.managers.pages import PageManager
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import expose_api
 from galaxy.web.base.controller import (
     BaseAPIController,
@@ -18,6 +18,10 @@ log = logging.getLogger(__name__)
 
 class PageRevisionsController(BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin):
 
+    def __init__(self, app):
+        super(PageRevisionsController, self).__init__(app)
+        self.manager = PageManager(app)
+
     @expose_api
     def index(self, trans, page_id, **kwd):
         """
@@ -30,13 +34,13 @@ class PageRevisionsController(BaseAPIController, SharableItemSecurityMixin, Uses
         :rtype:     list
         :returns:   dictionaries containing different revisions of the page
         """
-        page = self._get_page(trans, page_id)
-        self._verify_page_ownership(trans, page)
-
-        r = trans.sa_session.query(trans.app.model.PageRevision).filter_by(page_id=trans.security.decode_id(page_id))
+        page = get_object(trans, page_id, 'Page', check_ownership=False, check_accessible=True)
+        r = trans.sa_session.query(trans.app.model.PageRevision).filter_by(page_id=page.id)
         out = []
         for page in r:
-            out.append(self.encode_all_ids(trans, page.to_dict(), True))
+            as_dict = self.encode_all_ids(trans, page.to_dict(), True)
+            self.manager.rewrite_content_for_export(trans, as_dict)
+            out.append(as_dict)
         return out
 
     @expose_api
@@ -54,42 +58,8 @@ class PageRevisionsController(BaseAPIController, SharableItemSecurityMixin, Uses
         :rtype:     dictionary
         :returns:   Dictionary with 'success' or 'error' element to indicate the result of the request
         """
-        content = payload.get("content", None)
-        if not content:
-            raise exceptions.ObjectAttributeMissingException("content undefined or empty")
-
-        page = self._get_page(trans, page_id)
-        self._verify_page_ownership(trans, page)
-
-        if 'title' in payload:
-            title = payload['title']
-        else:
-            title = page.title
-
-        content = sanitize_html(content)
-
-        page_revision = trans.app.model.PageRevision()
-        page_revision.title = title
-        page_revision.page = page
-        page.latest_revision = page_revision
-        page_revision.content = content
-
-        # Persist
-        session = trans.sa_session
-        session.flush()
-
-        return page_revision.to_dict(view="element")
-
-    def _get_page(self, trans, page_id):
-        page = None
-        try:
-            page = trans.sa_session.query(trans.app.model.Page).get(trans.security.decode_id(page_id))
-        except Exception:
-            pass
-        if not page:
-            raise exceptions.ObjectNotFound()
-        return page
-
-    def _verify_page_ownership(self, trans, page):
-        if not self.security_check(trans, page, True, True):
-            raise exceptions.ItemOwnershipException()
+        page = get_object(trans, page_id, 'Page', check_ownership=True)
+        page_revision = self.manager.save_new_revision(trans, page, payload)
+        rval = self.encode_all_ids(trans, page_revision.to_dict(view="element"), True)
+        self.manager.rewrite_content_for_export(trans, rval)
+        return rval
diff --git a/lib/galaxy/webapps/galaxy/api/pages.py b/lib/galaxy/webapps/galaxy/api/pages.py
index a5a8ac3d75e..c86090a29f0 100644
--- a/lib/galaxy/webapps/galaxy/api/pages.py
+++ b/lib/galaxy/webapps/galaxy/api/pages.py
@@ -3,13 +3,12 @@ API for updating Galaxy Pages
 """
 import logging
 
-from galaxy import exceptions
+from galaxy.managers.base import get_object
 from galaxy.managers.pages import (
     PageManager,
     PageSerializer
 )
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import expose_api
 from galaxy.web.base.controller import (
     BaseAPIController,
@@ -81,39 +80,10 @@ class PagesController(BaseAPIController, SharableItemSecurityMixin, UsesAnnotati
         :rtype:     dict
         :returns:   Dictionary return of the Page.to_dict call
         """
-        user = trans.get_user()
-
-        if not payload.get("title", None):
-            raise exceptions.ObjectAttributeMissingException("Page name is required")
-        elif not payload.get("slug", None):
-            raise exceptions.ObjectAttributeMissingException("Page id is required")
-        elif not self._is_valid_slug(payload["slug"]):
-            raise exceptions.ObjectAttributeInvalidException("Page identifier must consist of only lowercase letters, numbers, and the '-' character")
-        elif trans.sa_session.query(trans.app.model.Page).filter_by(user=user, slug=payload["slug"], deleted=False).first():
-            raise exceptions.DuplicatedSlugException("Page slug must be unique")
-
-        content = payload.get("content", "")
-        content = sanitize_html(content)
-
-        # Create the new stored page
-        page = trans.app.model.Page()
-        page.title = payload['title']
-        page.slug = payload['slug']
-        page_annotation = sanitize_html(payload.get("annotation", ""))
-        self.add_item_annotation(trans.sa_session, trans.get_user(), page, page_annotation)
-        page.user = user
-        # And the first (empty) page revision
-        page_revision = trans.app.model.PageRevision()
-        page_revision.title = payload['title']
-        page_revision.page = page
-        page.latest_revision = page_revision
-        page_revision.content = content
-        # Persist
-        session = trans.sa_session
-        session.add(page)
-        session.flush()
-
+        page = self.manager.create(trans, payload)
         rval = self.encode_all_ids(trans, page.to_dict(), True)
+        rval['content'] = page.latest_revision.content
+        self.manager.rewrite_content_for_export(trans, rval)
         return rval
 
     @expose_api
@@ -128,7 +98,7 @@ class PagesController(BaseAPIController, SharableItemSecurityMixin, UsesAnnotati
         :rtype:     dict
         :returns:   Dictionary with 'success' or 'error' element to indicate the result of the request
         """
-        page = self._get_page(trans, id)
+        page = get_object(trans, id, 'Page', check_ownership=True)
 
         # Mark a page as deleted
         page.deleted = True
@@ -147,22 +117,8 @@ class PagesController(BaseAPIController, SharableItemSecurityMixin, UsesAnnotati
         :rtype:     dict
         :returns:   Dictionary return of the Page.to_dict call with the 'content' field populated by the most recent revision
         """
-        page = self._get_page(trans, id)
-        self.security_check(trans, page, check_ownership=False, check_accessible=True)
+        page = get_object(trans, id, 'Page', check_ownership=False, check_accessible=True)
         rval = self.encode_all_ids(trans, page.to_dict(), True)
         rval['content'] = page.latest_revision.content
+        self.manager.rewrite_content_for_export(trans, rval)
         return rval
-
-    def _get_page(self, trans, id):  # Fetches page object and verifies security.
-        try:
-            page = trans.sa_session.query(trans.app.model.Page).get(trans.security.decode_id(id))
-        except Exception:
-            page = None
-
-        if not page:
-            raise exceptions.ObjectNotFound()
-
-        if page.user != trans.user and not trans.user_is_admin:
-            raise exceptions.ItemOwnershipException()
-
-        return page
diff --git a/lib/galaxy/webapps/galaxy/api/quotas.py b/lib/galaxy/webapps/galaxy/api/quotas.py
index a6d5a244674..075bc444b42 100644
--- a/lib/galaxy/webapps/galaxy/api/quotas.py
+++ b/lib/galaxy/webapps/galaxy/api/quotas.py
@@ -71,12 +71,12 @@ class QuotaAPIController(BaseAPIController, AdminActions, UsesQuotaMixin, QuotaP
         try:
             self.validate_in_users_and_groups(trans, payload)
         except Exception as e:
-            raise HTTPBadRequest(detail=str(e))
+            raise HTTPBadRequest(detail=util.unicodify(e))
         params = self.get_quota_params(payload)
         try:
             quota, message = self._create_quota(params)
         except ActionInputError as e:
-            raise HTTPBadRequest(detail=str(e))
+            raise HTTPBadRequest(detail=util.unicodify(e))
         item = quota.to_dict(value_mapper={'id': trans.security.encode_id})
         item['url'] = url_for('quota', id=trans.security.encode_id(quota.id))
         item['message'] = message
@@ -92,7 +92,7 @@ class QuotaAPIController(BaseAPIController, AdminActions, UsesQuotaMixin, QuotaP
         try:
             self.validate_in_users_and_groups(trans, payload)
         except Exception as e:
-            raise HTTPBadRequest(detail=str(e))
+            raise HTTPBadRequest(detail=util.unicodify(e))
 
         quota = self.get_quota(trans, id, deleted=False)
 
@@ -116,7 +116,7 @@ class QuotaAPIController(BaseAPIController, AdminActions, UsesQuotaMixin, QuotaP
             try:
                 message = method(quota, params)
             except ActionInputError as e:
-                raise HTTPBadRequest(detail=str(e))
+                raise HTTPBadRequest(detail=util.unicodify(e))
             messages.append(message)
         return '; '.join(messages)
 
@@ -139,7 +139,7 @@ class QuotaAPIController(BaseAPIController, AdminActions, UsesQuotaMixin, QuotaP
             if util.string_as_bool(payload.get('purge', False)):
                 message += self._purge_quota(quota, params)
         except ActionInputError as e:
-            raise HTTPBadRequest(detail=str(e))
+            raise HTTPBadRequest(detail=util.unicodify(e))
         return message
 
     @web.legacy_expose_api
@@ -153,4 +153,4 @@ class QuotaAPIController(BaseAPIController, AdminActions, UsesQuotaMixin, QuotaP
         try:
             return self._undelete_quota(quota)
         except ActionInputError as e:
-            raise HTTPBadRequest(detail=str(e))
+            raise HTTPBadRequest(detail=util.unicodify(e))
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index e56fa74367b..918b830d803 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -10,7 +10,8 @@ from operator import itemgetter
 from galaxy import exceptions
 from galaxy.util import (
     jstree,
-    smart_str
+    smart_str,
+    unicodify
 )
 from galaxy.util.path import (
     safe_path,
@@ -58,9 +59,9 @@ class RemoteFilesAPIController(BaseAPIController):
                     try:
                         userdir_jstree = self.__create_jstree(full_import_dir, disable, whitelist=trans.app.config.user_library_import_symlink_whitelist)
                         response = userdir_jstree.jsonData()
-                    except Exception as exception:
-                        log.debug(str(exception))
-                        raise exceptions.InternalServerError('Could not create tree representation of the given folder: ' + str(full_import_dir))
+                    except Exception as e:
+                        log.debug(unicodify(e))
+                        raise exceptions.InternalServerError('Could not create tree representation of the given folder: %s' % full_import_dir)
                     if not response:
                         raise exceptions.ObjectNotFound('You do not have any files in your user directory. Use FTP to upload there.')
                 elif format == 'ajax':
@@ -68,8 +69,8 @@ class RemoteFilesAPIController(BaseAPIController):
                 else:
                     try:
                         response = self.__load_all_filenames(full_import_dir, whitelist=trans.app.config.user_library_import_symlink_whitelist)
-                    except Exception as exception:
-                        log.error('Could not get user import files: %s', str(exception), exc_info=True)
+                    except Exception:
+                        log.exception('Could not get user import files')
                         raise exceptions.InternalServerError('Could not get the files from your user directory folder.')
             else:
                 raise exceptions.InternalServerError('Could not get the files from your user directory folder.')
@@ -82,16 +83,16 @@ class RemoteFilesAPIController(BaseAPIController):
                 try:
                     importdir_jstree = self.__create_jstree(base_dir, disable, whitelist=trans.app.config.user_library_import_symlink_whitelist)
                     response = importdir_jstree.jsonData()
-                except Exception as exception:
-                    log.debug(str(exception))
-                    raise exceptions.InternalServerError('Could not create tree representation of the given folder: ' + str(base_dir))
+                except Exception as e:
+                    log.debug(unicodify(e))
+                    raise exceptions.InternalServerError('Could not create tree representation of the given folder: %s' % base_dir)
             elif format == 'ajax':
                 raise exceptions.NotImplemented('Not implemented yet. Sorry.')
             else:
                 try:
                     response = self.__load_all_filenames(base_dir, trans.app.config.user_library_import_symlink_whitelist)
-                except Exception as exception:
-                    log.error('Could not get user import files: %s', str(exception), exc_info=True)
+                except Exception:
+                    log.exception('Could not get user import files')
                     raise exceptions.InternalServerError('Could not get the files from your import directory folder.')
         else:
             user_ftp_base_dir = trans.app.config.ftp_upload_dir
@@ -104,8 +105,8 @@ class RemoteFilesAPIController(BaseAPIController):
                 else:
                     log.warning('You do not have an FTP directory named as your login at this Galaxy instance.')
                     return None
-            except Exception as exception:
-                log.warning('Could not get ftp files: %s', str(exception), exc_info=True)
+            except Exception:
+                log.warning('Could not get ftp files', exc_info=True)
                 return None
         return response
 
diff --git a/lib/galaxy/webapps/galaxy/api/search.py b/lib/galaxy/webapps/galaxy/api/search.py
index 19fc35bb566..8f11f776b9a 100644
--- a/lib/galaxy/webapps/galaxy/api/search.py
+++ b/lib/galaxy/webapps/galaxy/api/search.py
@@ -6,6 +6,7 @@ import logging
 from galaxy import web
 from galaxy.exceptions import ItemAccessibilityException
 from galaxy.model.search import GalaxySearchEngine
+from galaxy.util import unicodify
 from galaxy.web.base.controller import (
     BaseAPIController,
     SharableItemSecurityMixin
@@ -29,14 +30,14 @@ class SearchController(BaseAPIController, SharableItemSecurityMixin):
             try:
                 query = se.query(query_txt)
             except Exception as e:
-                return {'error': str(e)}
+                return {'error': unicodify(e)}
             if query is not None:
                 query.decode_query_ids(trans)
                 current_user_roles = trans.get_current_user_roles()
                 try:
                     results = query.process(trans)
                 except Exception as e:
-                    return {'error': str(e)}
+                    return {'error': unicodify(e)}
                 for item in results:
                     append = False
                     if trans.user_is_admin:
diff --git a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
index c28eadb7207..5fea48074d4 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
@@ -3,7 +3,7 @@ API operations allowing clients to manage tool dependencies.
 """
 import logging
 
-from galaxy.tools.deps import views
+from galaxy.tool_util.deps import views
 from galaxy.web import (
     expose_api,
     require_admin
diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
index 44ddba75e44..cf6bfb1da34 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -186,7 +186,7 @@ class ToolShedRepositoriesController(BaseAPIController):
             raw_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
         except Exception as e:
             message = "Error attempting to retrieve the latest installable revision from tool shed %s for repository %s owned by %s: %s" % \
-                (str(tool_shed_url), str(name), str(owner), str(e))
+                (str(tool_shed_url), str(name), str(owner), util.unicodify(e))
             log.debug(message)
             return dict(status='error', error=message)
         if raw_text:
@@ -762,7 +762,7 @@ class ToolShedRepositoriesController(BaseAPIController):
                     results['successful_count'] += 1
             except Exception as e:
                 message = "Error resetting metadata on repository %s owned by %s: %s" % \
-                    (str(repository.name), str(repository.owner), str(e))
+                    (str(repository.name), str(repository.owner), util.unicodify(e))
                 results['unsuccessful_count'] += 1
             results['repository_status'].append(message)
         stop_time = strftime("%Y-%m-%d %H:%M:%S")
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 1504abb1248..d86a11d5b9b 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -455,6 +455,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
     def create(self, trans, payload, **kwd):
         """
         POST /api/tools
+        Execute tool with a given parameter payload
         """
         tool_id = payload.get("tool_id")
         tool_uuid = payload.get("tool_uuid")
@@ -469,8 +470,6 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         if action == 'rerun':
             raise Exception("'rerun' action has been deprecated")
 
-        # -- Execute tool. --
-
         # Get tool.
         tool_version = payload.get('tool_version', None)
         tool_id = payload.get('tool_id', None)
@@ -504,21 +503,14 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
         # Set up inputs.
         inputs = payload.get('inputs', {})
+
         # Find files coming in as multipart file data and add to inputs.
         for k, v in payload.items():
             if k.startswith('files_') or k.startswith('__files_'):
                 inputs[k] = v
 
         # for inputs that are coming from the Library, copy them into the history
-        input_patch = {}
-        for k, v in inputs.items():
-            if isinstance(v, dict) and v.get('src', '') == 'ldda' and 'id' in v:
-                ldda = trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(self.decode_id(v['id']))
-                if trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset):
-                    input_patch[k] = ldda.to_history_dataset_association(target_history, add_to_history=True)
-
-        for k, v in input_patch.items():
-            inputs[k] = v
+        self._patch_library_inputs(trans, inputs, target_history)
 
         # TODO: encode data ids and decode ids.
         # TODO: handle dbkeys
@@ -567,6 +559,27 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
         return rval
 
+    def _patch_library_inputs(self, trans, inputs, target_history):
+        """
+        Transform inputs from the data libaray to history items.
+        """
+        for k, v in inputs.items():
+            new_value = self._patch_library_dataset(trans, v, target_history)
+            if new_value:
+                v = new_value
+            elif isinstance(v, dict) and 'values' in v:
+                for index, value in enumerate(v['values']):
+                    patched = self._patch_library_dataset(trans, value, target_history)
+                    if patched:
+                        v['values'][index] = patched
+            inputs[k] = v
+
+    def _patch_library_dataset(self, trans, v, target_history):
+        if isinstance(v, dict) and 'id' in v and v.get('src') == 'ldda':
+            ldda = trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(self.decode_id(v['id']))
+            if trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset):
+                return ldda.to_history_dataset_association(target_history, add_to_history=True)
+
     #
     # -- Helper methods --
     #
diff --git a/lib/galaxy/webapps/galaxy/api/toolshed.py b/lib/galaxy/webapps/galaxy/api/toolshed.py
index bc2433ae22e..1ab675c9175 100644
--- a/lib/galaxy/webapps/galaxy/api/toolshed.py
+++ b/lib/galaxy/webapps/galaxy/api/toolshed.py
@@ -8,9 +8,11 @@ from six.moves.urllib.parse import (
 )
 
 from galaxy import (
+    exceptions,
     util,
     web
 )
+from galaxy.exceptions import MessageException
 from galaxy.web import expose_api
 from galaxy.web.base.controller import BaseAPIController
 from tool_shed.util import (
@@ -167,14 +169,17 @@ class ToolShedController(BaseAPIController):
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed_url)
         url = util.build_url(tool_shed_url, pathspec=['api', 'categories'])
         categories = []
-        for category in json.loads(util.url_get(url)):
-            api_url = web.url_for(controller='api/tool_shed',
-                                  action='category',
-                                  tool_shed_url=urlquote(tool_shed_url),
-                                  category_id=category['id'],
-                                  qualified=True)
-            category['url'] = api_url
-            categories.append(category)
+        try:
+            for category in json.loads(util.url_get(url)):
+                api_url = web.url_for(controller='api/tool_shed',
+                                      action='category',
+                                      tool_shed_url=urlquote(tool_shed_url),
+                                      category_id=category['id'],
+                                      qualified=True)
+                category['url'] = api_url
+                categories.append(category)
+        except Exception:
+            raise exceptions.ObjectNotFound("Tool Shed %s is not responding." % tool_shed_url)
         return categories
 
     @expose_api
@@ -310,3 +315,26 @@ class ToolShedController(BaseAPIController):
             return {}
         response = json.loads(util.url_get(tool_shed_url, params=dict(q=q), pathspec=['api', 'repositories']))
         return response
+
+    @expose_api
+    @web.require_admin
+    def request(self, trans, **params):
+        """
+        GET /api/tool_shed/request
+        """
+        tool_shed_url = params.pop("tool_shed_url")
+        controller = params.pop("controller")
+        if controller is None:
+            raise MessageException("Please provide a toolshed controller name.")
+        tool_shed_registry = trans.app.tool_shed_registry
+        if tool_shed_registry is None:
+            raise MessageException("Toolshed registry not available.")
+        if tool_shed_url in tool_shed_registry.tool_sheds.values():
+            pathspec = ["api", controller]
+            if "id" in params:
+                pathspec.append(params.pop("id"))
+            if "action" in params:
+                pathspec.append(params.pop("action"))
+            return json.loads(util.url_get(tool_shed_url, params=dict(params), pathspec=pathspec))
+        else:
+            raise MessageException("Invalid toolshed url.")
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 38527127a7b..51d21275bcc 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -466,7 +466,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(self.decode_id(workflow_id))
         except Exception as e:
             trans.response.status = 400
-            return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str(e))
+            return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, util.unicodify(e))
 
         # check to see if user has permissions to selected workflow
         if stored_workflow.user != trans.user and not trans.user_is_admin:
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 6eb8fa7a76c..d754e7c09bb 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -101,6 +101,7 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs):
 
     webapp.add_client_route('/admin/data_tables', 'admin')
     webapp.add_client_route('/admin/data_types', 'admin')
+    webapp.add_client_route('/admin/jobs', 'admin')
     webapp.add_client_route('/admin/data_manager{path_info:.*}', 'admin')
     webapp.add_client_route('/admin/error_stack', 'admin')
     webapp.add_client_route('/admin/users', 'admin')
@@ -111,6 +112,7 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs):
     webapp.add_client_route('/admin/groups', 'admin')
     webapp.add_client_route('/admin/repositories', 'admin')
     webapp.add_client_route('/admin/tool_versions', 'admin')
+    webapp.add_client_route('/admin/toolshed', 'admin')
     webapp.add_client_route('/admin/quotas', 'admin')
     webapp.add_client_route('/admin/form/{form_id}', 'admin')
     webapp.add_client_route('/admin/api_keys', 'admin')
@@ -889,6 +891,11 @@ def populate_api_routes(webapp, app):
     webapp.mapper.connect('resume', '/api/jobs/{id}/resume', controller='jobs', action='resume', conditions=dict(method=['PUT']))
     webapp.mapper.connect('job_error', '/api/jobs/{id}/error', controller='jobs', action='error', conditions=dict(method=['POST']))
     webapp.mapper.connect('common_problems', '/api/jobs/{id}/common_problems', controller='jobs', action='common_problems', conditions=dict(method=['GET']))
+    # Job metrics and parameters by job id or dataset id (for slightly different accessibility checking)
+    webapp.mapper.connect('metrics', '/api/jobs/{job_id}/metrics', controller='jobs', action='metrics', conditions=dict(method=['GET']))
+    webapp.mapper.connect('dataset_metrics', '/api/datasets/{dataset_id}/metrics', controller='jobs', action='metrics', conditions=dict(method=['GET']))
+    webapp.mapper.connect('parameters_display', '/api/jobs/{job_id}/parameters_display', controller='jobs', action='parameters_display', conditions=dict(method=['GET']))
+    webapp.mapper.connect('dataset_parameters_display', '/api/datasets/{dataset_id}/parameters_display', controller='jobs', action='parameters_display', conditions=dict(method=['GET']))
 
     # Job files controllers. Only for consumption by remote job runners.
     webapp.mapper.resource('file',
@@ -954,6 +961,12 @@ def populate_api_routes(webapp, app):
                           action='search',
                           conditions=dict(method=["GET", "POST"]))
 
+    webapp.mapper.connect('tool_shed_request',
+                          '/api/tool_shed/request',
+                          controller='toolshed',
+                          action='request',
+                          conditions=dict(method=["GET"]))
+
     webapp.mapper.connect('tool_shed_status',
                           '/api/tool_shed/status',
                           controller='toolshed',
@@ -1153,7 +1166,7 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
                                           args=(conf,),
                                           kwargs=dict(templating_formatters=build_template_error_formatters()))
         except MiddlewareWrapUnsupported as exc:
-            log.warning(str(exc))
+            log.warning(util.unicodify(exc))
             import galaxy.web.framework.middleware.error
             app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
     else:
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 546d85dc360..aebc3dbbb8e 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -1,4 +1,5 @@
-
+# When committing this file, make sure to run make config-rebuild to rebuild
+# all sample YAML and RST files, and add those to your commit.
 type: map
 desc: |
   Galaxy is configured by default to be usable in a single-user development
@@ -102,10 +103,10 @@ mapping:
         default: false
         required: false
         desc: |
-          Enable's a per request sql debugging option. If this is set to true, append
-          ?sql_debug=1 to web request URLs to enable detailed logging on the backend of SQL
-          queries generated during that request. This is useful for debugging slow endpoints
-          during development.
+          Enables a per request sql debugging option. If this is set to true,
+          append ?sql_debug=1 to web request URLs to enable detailed logging on
+          the backend of SQL queries generated during that request. This is
+          useful for debugging slow endpoints during development.
 
       install_database_connection:
         type: str
@@ -128,6 +129,27 @@ mapping:
           migrate the database forward after updates. This is not recommended for production
           use.
 
+      database_wait:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          Wait for database to become available instead of failing immediately.
+
+      database_wait_attempts:
+        type: int
+        default: 60
+        required: false
+        desc: |
+          Number of attempts before failing if database_wait is enabled.
+
+      database_wait_sleep:
+        type: float
+        default: 1.
+        required: false
+        desc: |
+          Time to sleep between attempts if database_wait is enabled (in seconds).
+
       file_path:
         type: str
         default: database/files
@@ -376,9 +398,9 @@ mapping:
         default: ''
         required: false
         desc: |
-          Container resolvers configuration (beta). Setup a file describing container
-          resolvers to use when discovering containers for Galaxy. If this is set to
-          None, the default containers loaded is determined by
+          Container resolvers configuration (beta). Set up a file describing
+          container resolvers to use when discovering containers for Galaxy. If
+          this is set to None, the default containers loaded is determined by
           enable_beta_mulled_containers.
 
       involucro_path:
@@ -853,7 +875,7 @@ mapping:
         desc: |
           Galaxy can display data at various external browsers.  These options specify
           which browsers should be available.  URLs and builds available at these
-          browsers are defined in the specifield files.
+          browsers are defined in the specified files.
 
           If use_remote_user = True, display application servers will be denied access
           to Galaxy and so displaying datasets in these sites will fail.
@@ -949,14 +971,15 @@ mapping:
         default: http://localhost:8080
         required: false
         desc: |
-          URL (with schema http/https) of the Galaxy instance as accessible within your
-          local network - if specified used as a default by pulsar file staging and
-          Jupyter Docker container for communicating back with Galaxy via the API.
+          URL (with schema http/https) of the Galaxy instance as accessible
+          within your local network - if specified used as a default by pulsar
+          file staging and Jupyter Docker container for communicating back with
+          Galaxy via the API.
 
-          If you are attempting to setup GIEs on Mac OS X with Docker for Mac - this
-          should likely be the IP address of your machine on the virtualbox network (vboxnet0)
-          setup for the Docker host VM. This can found by running ifconfig and using the
-          IP address of the network vboxnet0.
+          If you are attempting to set up GIEs on Mac OS X with Docker Desktop
+          for Mac and your Galaxy instance runs on port 8080 this should be
+          'http://host.docker.internal:8080'.  For more details see
+          https://docs.docker.com/docker-for-mac/networking/
 
       galaxy_infrastructure_web_port:
         type: int
@@ -1271,7 +1294,7 @@ mapping:
         default: 8800
         required: false
         desc: |
-          Set the port and IP for the the dynamic proxy to bind to, this must match
+          Set the port and IP for the dynamic proxy to bind to, this must match
           the external configuration if dynamic_proxy_manage is False.
 
       dynamic_proxy_bind_ip:
@@ -1279,7 +1302,7 @@ mapping:
         default: 0.0.0.0
         required: false
         desc: |
-          Set the port and IP for the the dynamic proxy to bind to, this must match
+          Set the port and IP for the dynamic proxy to bind to, this must match
           the external configuration if dynamic_proxy_manage is False.
 
       dynamic_proxy_debug:
@@ -2332,6 +2355,16 @@ mapping:
           the system on which Galaxy is started.  Advanced job running capabilities can
           be configured through the job configuration file.
 
+      job_config:
+        !include job_config_schema.yml
+
+      dependency_resolvers:
+        type: seq
+        desc: |
+          Rather than specifying a dependency_resolvers_config_file, the definition of the
+          resolvers to enable can be embedded into Galaxy's config with this option.
+          This has no effect if a dependency_resolvers_config_file is used.
+
       default_job_resubmission_condition:
         type: str
         required: false
diff --git a/lib/galaxy/webapps/galaxy/controllers/_create_history_template.py b/lib/galaxy/webapps/galaxy/controllers/_create_history_template.py
index 24a2b8c0deb..290c8f4495f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/_create_history_template.py
+++ b/lib/galaxy/webapps/galaxy/controllers/_create_history_template.py
@@ -142,7 +142,7 @@ def inputs_recursive(trans, input_params, param_values, depth=1, upgrade_message
     if upgrade_messages is None:
         upgrade_messages = {}
 
-    for input_index, input in enumerate(input_params.itervalues()):
+    for input_index, input in enumerate(input_params.values()):
         if input.name in param_values:
             if input.type == "repeat":
                 for i in range(len(param_values[input.name])):
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index f001821285a..c4c24ebed04 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -566,7 +566,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         )
 
         for data_table_elem_name, data_table in sorted_data_tables:
-            for filename, file_dict in data_table.filenames.iteritems():
+            for filename, file_dict in data_table.filenames.items():
                 file_missing = ['file missing'] \
                     if not file_dict.get('found') else []
                 data.append({
@@ -645,7 +645,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                 try:
                     quotas.append(get_quota(trans, quota_id))
                 except MessageException as e:
-                    return self.message_exception(trans, str(e))
+                    return self.message_exception(trans, util.unicodify(e))
             operation = kwargs.pop('operation').lower()
             try:
                 if operation == 'delete':
@@ -1600,15 +1600,26 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
             return {'message' : 'User \'%s\' has been updated with %d associated roles and %d associated groups (private roles are not displayed).' % (user.email, len(in_roles) - 1, len(in_groups))}
 
     @web.expose
+    @web.json
     @web.require_admin
-    def jobs(self, trans, stop=[], stop_msg=None, cutoff=180, job_lock=None, ajl_submit=None, **kwd):
+    def jobs_control(self, trans, job_lock=None, **kwd):
+        if job_lock is not None:
+            job_lock = True if job_lock == 'true' else False
+            galaxy.queue_worker.send_control_task(trans.app, 'admin_job_lock', kwargs={'job_lock': job_lock}, get_response=True)
+        job_lock = trans.app.job_manager.job_lock
+        return {'job_lock': job_lock}
+
+    @web.expose
+    @web.json
+    @web.require_admin
+    def jobs_list(self, trans, stop=[], stop_msg=None, cutoff=180, **kwd):
         deleted = []
-        msg = None
-        status = None
+        message = kwd.get('message', '')
+        status = kwd.get('status', 'info')
         job_ids = util.listify(stop)
         if job_ids and stop_msg in [None, '']:
-            msg = 'Please enter an error message to display to the user describing why the job was terminated'
-            status = 'error'
+            message = 'Please enter an error message to display to the user describing why the job was terminated'
+            return self.message_exception(trans, message)
         elif job_ids:
             if stop_msg[-1] not in PUNCTUATION:
                 stop_msg += '.'
@@ -1624,24 +1635,14 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                     trans.app.job_manager.stop(job, message=error_msg)
                 deleted.append(str(job_id))
         if deleted:
-            msg = 'Queued job'
+            message = 'Queued job'
             if len(deleted) > 1:
-                msg += 's'
-            msg += ' for deletion: '
-            msg += ', '.join(deleted)
+                message += 's'
+            message += ' for deletion: '
+            message += ', '.join(deleted)
             status = 'done'
             trans.sa_session.flush()
-        if ajl_submit:
-            if job_lock == 'on':
-                galaxy.queue_worker.send_control_task(trans.app, 'admin_job_lock',
-                                                      kwargs={'job_lock': True})
-                job_lock = True
-            else:
-                galaxy.queue_worker.send_control_task(trans.app, 'admin_job_lock',
-                                                      kwargs={'job_lock': False})
-                job_lock = False
-        else:
-            job_lock = trans.app.job_manager.job_lock
+        job_lock = trans.app.job_manager.job_lock
         cutoff_time = datetime.utcnow() - timedelta(seconds=int(cutoff))
         jobs = trans.sa_session.query(trans.app.model.Job) \
                                .filter(and_(trans.app.model.Job.table.c.update_time < cutoff_time,
@@ -1655,33 +1656,44 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                          or_(trans.app.model.Job.state == trans.app.model.Job.states.ERROR,
                              trans.app.model.Job.state == trans.app.model.Job.states.OK))) \
             .order_by(trans.app.model.Job.table.c.update_time.desc()).all()
-        last_updated = {}
-        for job in jobs:
-            delta = datetime.utcnow() - job.update_time
-            if delta.days > 0:
-                last_updated[job.id] = '%s hours' % (delta.days * 24 + int(delta.seconds / 60 / 60))
-            elif delta > timedelta(minutes=59):
-                last_updated[job.id] = '%s hours' % int(delta.seconds / 60 / 60)
-            else:
-                last_updated[job.id] = '%s minutes' % int(delta.seconds / 60)
-        finished = {}
-        for job in recent_jobs:
-            delta = datetime.utcnow() - job.update_time
-            if delta.days > 0:
-                finished[job.id] = '%s hours' % (delta.days * 24 + int(delta.seconds / 60 / 60))
-            elif delta > timedelta(minutes=59):
-                finished[job.id] = '%s hours' % int(delta.seconds / 60 / 60)
-            else:
-                finished[job.id] = '%s minutes' % int(delta.seconds / 60)
-        return trans.fill_template('/admin/jobs.mako',
-                                   jobs=jobs,
-                                   recent_jobs=recent_jobs,
-                                   last_updated=last_updated,
-                                   finished=finished,
-                                   cutoff=cutoff,
-                                   msg=msg,
-                                   status=status,
-                                   job_lock=job_lock)
+
+        def prepare_jobs_list(jobs):
+            res = []
+            for job in jobs:
+                delta = datetime.utcnow() - job.update_time
+                update_time = ""
+                if delta.days > 0:
+                    update_time = '%s hours ago' % (delta.days * 24 + int(delta.seconds / 60 / 60))
+                elif delta > timedelta(minutes=59):
+                    update_time = '%s hours ago' % int(delta.seconds / 60 / 60)
+                else:
+                    update_time = '%s minutes ago' % int(delta.seconds / 60)
+                inputs = ""
+                try:
+                    inputs = ", ".join(['{} {}'.format(da.dataset.id, da.dataset.state) for da in job.input_datasets])
+                except Exception:
+                    inputs = 'Unable to determine inputs'
+                res.append({
+                    'job_info': {
+                        'id': job.id,
+                        'info_url': "{}?jobid={}".format(web.url_for(controller="admin", action="job_info"), job.id)
+                    },
+                    'user': job.history.user.email if job.history and job.history.user else 'anonymous',
+                    'update_time': update_time,
+                    'tool_id': job.tool_id,
+                    'state': job.state,
+                    'input_dataset': inputs,
+                    'command_line': job.command_line,
+                    'job_runner_name': job.job_runner_name,
+                    'job_runner_external_id': job.job_runner_external_id
+                })
+            return res
+        return {'jobs': prepare_jobs_list(jobs),
+                'recent_jobs': prepare_jobs_list(recent_jobs),
+                'cutoff': cutoff,
+                'message': message,
+                'status': status,
+                'job_lock': job_lock}
 
     @web.expose
     @web.require_admin
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 022f495a9a9..713ca2246fb 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -7,7 +7,7 @@ from sqlalchemy import or_
 
 import tool_shed.repository_types.util as rt_util
 from galaxy import util, web
-from galaxy.tools.deps import views
+from galaxy.tool_util.deps import views
 from galaxy.util import unicodify
 from galaxy.web.form_builder import CheckboxField
 from tool_shed.galaxy_install import (
@@ -54,7 +54,7 @@ class AdminToolshed(AdminGalaxy):
             message = 'The <b>%s</b> repository has been activated.' % escape(repository.name)
             status = 'done'
         except Exception as e:
-            error_message = "Error activating repository %s: %s" % (escape(repository.name), str(e))
+            error_message = "Error activating repository %s: %s" % (escape(repository.name), unicodify(e))
             log.exception(error_message)
             message = '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository.  Click <a href="%s">here</a> to uninstall the repository.' \
                 % (error_message, web.url_for(controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id(repository.id)))
@@ -542,7 +542,7 @@ class AdminToolshed(AdminGalaxy):
             tsr_ids_for_monitoring = [trans.security.encode_id(tsr.id) for tsr in tool_shed_repositories]
             return json.dumps(tsr_ids_for_monitoring)
         except install_manager.RepositoriesInstalledException as e:
-            return self.message_exception(trans, str(e))
+            return self.message_exception(trans, unicodify(e))
 
     @web.expose
     @web.require_admin
@@ -845,7 +845,7 @@ class AdminToolshed(AdminGalaxy):
                     message = 'The updates available for the repository <b>%s</b> ' % escape(str(repository.name))
                     message += 'include newly defined repository or tool dependency definitions, and attempting '
                     message += 'to update the repository resulted in the following error.  Contact the Tool Shed '
-                    message += 'administrator if necessary.<br/>%s' % str(e)
+                    message += 'administrator if necessary.<br/>%s' % unicodify(e)
                     return trans.show_error_message(message)
                 changeset_revisions = updating_to_changeset_revision
             else:
diff --git a/lib/galaxy/webapps/galaxy/controllers/async.py b/lib/galaxy/webapps/galaxy/controllers/async.py
index bc9ff54a222..68feeb0788b 100644
--- a/lib/galaxy/webapps/galaxy/controllers/async.py
+++ b/lib/galaxy/webapps/galaxy/controllers/async.py
@@ -10,7 +10,10 @@ import requests
 from six.moves.urllib.parse import urlencode
 
 from galaxy import jobs, web
-from galaxy.util import Params
+from galaxy.util import (
+    Params,
+    unicodify,
+)
 from galaxy.util.hash_util import hmac_new
 from galaxy.web.base.controller import BaseUIController
 
@@ -171,7 +174,7 @@ class ASync(BaseUIController):
                     raise Exception(text)
                 data.state = data.blurb = data.states.RUNNING
             except Exception as e:
-                data.info = str(e)
+                data.info = unicodify(e)
                 data.state = data.blurb = data.states.ERROR
 
             trans.sa_session.flush()
diff --git a/lib/galaxy/webapps/galaxy/controllers/data_manager.py b/lib/galaxy/webapps/galaxy/controllers/data_manager.py
index 493731321fc..fb5c47ce231 100644
--- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py
+++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py
@@ -23,7 +23,7 @@ class DataManager(BaseUIController):
         message = kwd.get('message', '')
         status = kwd.get('status', 'info')
         data_managers = []
-        for data_manager_id, data_manager in sorted(trans.app.data_managers.data_managers.iteritems(),
+        for data_manager_id, data_manager in sorted(trans.app.data_managers.data_managers.items(),
                                                     key=lambda data_manager: data_manager[1].name):
             data_managers.append({'toolUrl': web.url_for(controller='root',
                                                          tool_id=data_manager.tool.id),
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index f93f0b7df4e..40df1ea0913 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -483,7 +483,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 try:
                     message = data.datatype.convert_dataset(trans, data, target_type)
                 except Exception as e:
-                    return self.message_exception(trans, str(e))
+                    return self.message_exception(trans, util.unicodify(e))
         elif operation == 'permission':
             if not trans.user:
                 return self.message_exception(trans, 'You must be logged in if you want to change permissions.')
@@ -830,7 +830,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                             action_param = display_link.get_param_name_by_url(action_param)
                         except ValueError as e:
                             log.debug(e)
-                            return paste.httpexceptions.HTTPNotFound(str(e))
+                            return paste.httpexceptions.HTTPNotFound(util.unicodify(e))
                         value = display_link.get_param_value(action_param)
                         assert value, "An invalid parameter name was provided: %s" % action_param
                         assert value.parameter.viewable, "This parameter is not viewable."
diff --git a/lib/galaxy/webapps/galaxy/controllers/openid.py b/lib/galaxy/webapps/galaxy/controllers/openid.py
index 6cf4e3eb0d2..f892d0d05f7 100644
--- a/lib/galaxy/webapps/galaxy/controllers/openid.py
+++ b/lib/galaxy/webapps/galaxy/controllers/openid.py
@@ -7,6 +7,7 @@ import logging
 from galaxy import web
 from galaxy.openid.openid_manager import OpenIDManager
 from galaxy.openid.providers import OpenIDProviders
+from galaxy.util import unicodify
 from galaxy.web import url_for
 from galaxy.web.base.controller import BaseUIController
 
@@ -41,7 +42,7 @@ class OpenID(BaseUIController):
             if request is None:
                 return trans.show_error_message("No OpenID services are available at %s." % openid_provider_obj.op_endpoint_url)
         except Exception as e:
-            return trans.show_error_message("Failed to begin OpenID authentication: %s." % str(e))
+            return trans.show_error_message("Failed to begin OpenID authentication: %s." % unicodify(e))
         if request is not None:
             self.openid_manager.add_sreg(trans, request, required=openid_provider_obj.sreg_required, optional=openid_provider_obj.sreg_optional)
             if request.shouldSendRedirect():
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 78b00076b42..3981b90f860 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -1,9 +1,5 @@
-import re
-from json import loads
 
 from markupsafe import escape
-from six.moves.html_entities import name2codepoint
-from six.moves.html_parser import HTMLParser
 from sqlalchemy import (
     and_,
     desc,
@@ -16,11 +12,18 @@ from sqlalchemy.orm import (
 )
 
 from galaxy import (
-    managers,
+    exceptions,
     model,
     util,
     web
 )
+from galaxy.managers.hdas import HDAManager
+from galaxy.managers.histories import HistoryManager, HistorySerializer
+from galaxy.managers.pages import (
+    get_page_identifiers,
+    PageContentProcessor,
+    PageManager,
+)
 from galaxy.model.item_attrs import UsesItemRatings
 from galaxy.util import unicodify
 from galaxy.util.sanitize_html import sanitize_html
@@ -40,55 +43,6 @@ from galaxy.web.framework.helpers import (
 )
 
 
-# Copied from https://github.com/kurtmckee/feedparser
-_cp1252 = {
-    128: u'\u20ac',  # euro sign
-    130: u'\u201a',  # single low-9 quotation mark
-    131: u'\u0192',  # latin small letter f with hook
-    132: u'\u201e',  # double low-9 quotation mark
-    133: u'\u2026',  # horizontal ellipsis
-    134: u'\u2020',  # dagger
-    135: u'\u2021',  # double dagger
-    136: u'\u02c6',  # modifier letter circumflex accent
-    137: u'\u2030',  # per mille sign
-    138: u'\u0160',  # latin capital letter s with caron
-    139: u'\u2039',  # single left-pointing angle quotation mark
-    140: u'\u0152',  # latin capital ligature oe
-    142: u'\u017d',  # latin capital letter z with caron
-    145: u'\u2018',  # left single quotation mark
-    146: u'\u2019',  # right single quotation mark
-    147: u'\u201c',  # left double quotation mark
-    148: u'\u201d',  # right double quotation mark
-    149: u'\u2022',  # bullet
-    150: u'\u2013',  # en dash
-    151: u'\u2014',  # em dash
-    152: u'\u02dc',  # small tilde
-    153: u'\u2122',  # trade mark sign
-    154: u'\u0161',  # latin small letter s with caron
-    155: u'\u203a',  # single right-pointing angle quotation mark
-    156: u'\u0153',  # latin small ligature oe
-    158: u'\u017e',  # latin small letter z with caron
-    159: u'\u0178',  # latin capital letter y with diaeresis
-}
-
-
-PAGE_MAXRAW = 10**15
-
-
-def _get_page_identifiers(item_id, app):
-    # Assume if item id is integer and less than 10**15, it's unencoded.
-    try:
-        decoded_id = int(item_id)
-        if decoded_id >= PAGE_MAXRAW:
-            raise ValueError("Identifier larger than maximum expected raw int, must be already encoded.")
-        encoded_id = app.security.encode_id(item_id)
-    except ValueError:
-        # It's an encoded id.
-        encoded_id = item_id
-        decoded_id = app.security.decode_id(item_id)
-    return (encoded_id, decoded_id)
-
-
 def format_bool(b):
     if b:
         return "yes"
@@ -300,166 +254,6 @@ class VisualizationSelectionGrid(ItemSelectionGrid):
 
 
 # Adapted from the _BaseHTMLProcessor class of https://github.com/kurtmckee/feedparser
-class _PageContentProcessor(HTMLParser, object):
-    """
-    Processes page content to produce HTML that is suitable for display.
-    For now, processor renders embedded objects.
-    """
-    bare_ampersand = re.compile(r"&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)")
-    elements_no_end_tag = set([
-        'area', 'base', 'basefont', 'br', 'col', 'command', 'embed', 'frame',
-        'hr', 'img', 'input', 'isindex', 'keygen', 'link', 'meta', 'param',
-        'source', 'track', 'wbr'
-    ])
-
-    def __init__(self, trans, render_embed_html_fn):
-        HTMLParser.__init__(self)
-        self.trans = trans
-        self.ignore_content = False
-        self.num_open_tags_for_ignore = 0
-        self.render_embed_html_fn = render_embed_html_fn
-
-    def reset(self):
-        self.pieces = []
-        HTMLParser.reset(self)
-
-    def _shorttag_replace(self, match):
-        tag = match.group(1)
-        if tag in self.elements_no_end_tag:
-            return '<' + tag + ' />'
-        else:
-            return '<' + tag + '></' + tag + '>'
-
-    def feed(self, data):
-        data = re.compile(r'<!((?!DOCTYPE|--|\[))', re.IGNORECASE).sub(r'&lt;!\1', data)
-        data = re.sub(r'<([^<>\s]+?)\s*/>', self._shorttag_replace, data)
-        data = data.replace('&#39;', "'")
-        data = data.replace('&#34;', '"')
-        HTMLParser.feed(self, data)
-        HTMLParser.close(self)
-
-    def handle_starttag(self, tag, attrs):
-        """
-        Called for each start tag
-
-        attrs is a list of (attr, value) tuples, e.g. for <pre class='screen'>,
-        tag='pre', attrs=[('class', 'screen')]
-        """
-
-        # If ignoring content, just increment tag count and ignore.
-        if self.ignore_content:
-            self.num_open_tags_for_ignore += 1
-            return
-
-        # Not ignoring tag; look for embedded content.
-        embedded_item = False
-        for attribute in attrs:
-            if (attribute[0] == "class") and ("embedded-item" in attribute[1].split(" ")):
-                embedded_item = True
-                break
-        # For embedded content, set ignore flag to ignore current content and add new content for embedded item.
-        if embedded_item:
-            # Set processing attributes to ignore content.
-            self.ignore_content = True
-            self.num_open_tags_for_ignore = 1
-
-            # Insert content for embedded element.
-            for attribute in attrs:
-                name = attribute[0]
-                if name == "id":
-                    # ID has form '<class_name>-<encoded_item_id>'
-                    item_class, item_id = attribute[1].split("-")
-                    embed_html = self.render_embed_html_fn(self.trans, item_class, item_id)
-                    self.pieces.append(embed_html)
-            return
-
-        # Default behavior: not ignoring and no embedded content.
-        uattrs = []
-        strattrs = ''
-        if attrs:
-            for key, value in attrs:
-                value = value.replace('>', '&gt;').replace('<', '&lt;').replace('"', '&quot;')
-                value = self.bare_ampersand.sub("&amp;", value)
-                uattrs.append((key, value))
-            strattrs = ''.join(' %s="%s"' % (k, v) for k, v in uattrs)
-        if tag in self.elements_no_end_tag:
-            self.pieces.append('<%s%s />' % (tag, strattrs))
-        else:
-            self.pieces.append('<%s%s>' % (tag, strattrs))
-
-    def handle_endtag(self, tag):
-        """
-        Called for each end tag
-
-        E.g. for </pre>, tag will be 'pre'
-        """
-        # If ignoring content, see if current tag is the end of content to ignore.
-        if self.ignore_content:
-            self.num_open_tags_for_ignore -= 1
-            if self.num_open_tags_for_ignore == 0:
-                # Done ignoring content.
-                self.ignore_content = False
-            return
-
-        # Default behavior: reconstruct the original end tag.
-        if tag not in self.elements_no_end_tag:
-            self.pieces.append("</%s>" % tag)
-
-    def handle_charref(self, ref):
-        # called for each character reference, e.g. for '&#160;', ref will be '160'
-        # Reconstruct the original character reference.
-        ref = ref.lower()
-        if ref.startswith('x'):
-            value = int(ref[1:], 16)
-        else:
-            value = int(ref)
-
-        if value in _cp1252:
-            self.pieces.append('&#%s;' % hex(ord(_cp1252[value]))[1:])
-        else:
-            self.pieces.append('&#%s;' % ref)
-
-    def handle_entityref(self, ref):
-        # called for each entity reference, e.g. for '&copy;', ref will be 'copy'
-        # Reconstruct the original entity reference.
-        if ref in name2codepoint or ref == 'apos':
-            self.pieces.append('&%s;' % ref)
-        else:
-            self.pieces.append('&amp;%s' % ref)
-
-    def handle_data(self, text):
-        """
-        Called for each block of plain text
-
-        Called outside of any tag and not containing any character or entity
-        references. Store the original text verbatim.
-        """
-        if self.ignore_content:
-            return
-        self.pieces.append(text)
-
-    def handle_comment(self, text):
-        # called for each HTML comment, e.g. <!-- insert Javascript code here -->
-        # Reconstruct the original comment.
-        self.pieces.append('<!--%s-->' % text)
-
-    def handle_decl(self, text):
-        # called for the DOCTYPE, if present, e.g.
-        # <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
-        #     "http://www.w3.org/TR/html4/loose.dtd">
-        # Reconstruct original DOCTYPE
-        self.pieces.append('<!%s>' % text)
-
-    def handle_pi(self, text):
-        # called for each processing instruction, e.g. <?instruction>
-        # Reconstruct original processing instruction.
-        self.pieces.append('<?%s>' % text)
-
-    def output(self):
-        '''Return processed HTML as a single string'''
-        return ''.join(self.pieces)
-
-
 class PageController(BaseUIController, SharableMixin,
                      UsesStoredWorkflowMixin, UsesVisualizationMixin, UsesItemRatings):
 
@@ -473,9 +267,10 @@ class PageController(BaseUIController, SharableMixin,
 
     def __init__(self, app):
         super(PageController, self).__init__(app)
-        self.history_manager = managers.histories.HistoryManager(app)
-        self.history_serializer = managers.histories.HistorySerializer(self.app)
-        self.hda_manager = managers.hdas.HDAManager(app)
+        self.page_manager = PageManager(app)
+        self.history_manager = HistoryManager(app)
+        self.history_serializer = HistorySerializer(self.app)
+        self.hda_manager = HDAManager(app)
 
     @web.expose
     @web.json
@@ -541,37 +336,11 @@ class PageController(BaseUIController, SharableMixin,
                 }]
             }
         else:
-            user = trans.get_user()
-            p_title = payload.get('title')
-            p_slug = payload.get('slug')
-            p_annotation = payload.get('annotation')
-            if not p_title:
-                return self.message_exception(trans, 'Please provide a page name is required.')
-            elif not p_slug:
-                return self.message_exception(trans, 'Please provide a unique identifier.')
-            elif not self._is_valid_slug(p_slug):
-                return self.message_exception(trans, 'Page identifier can only contain lowercase letters, numbers, and dashes (-).')
-            elif trans.sa_session.query(model.Page).filter_by(user=user, slug=p_slug, deleted=False).first():
-                return self.message_exception(trans, 'Page id must be unique.')
-            else:
-                # Create the new stored page
-                p = model.Page()
-                p.title = p_title
-                p.slug = p_slug
-                p.user = user
-                if p_annotation:
-                    p_annotation = sanitize_html(p_annotation)
-                    self.add_item_annotation(trans.sa_session, user, p, p_annotation)
-                # And the first (empty) page revision
-                p_revision = model.PageRevision()
-                p_revision.title = p_title
-                p_revision.page = p
-                p.latest_revision = p_revision
-                p_revision.content = ""
-                # Persist
-                trans.sa_session.add(p)
-                trans.sa_session.flush()
-            return {'message': 'Page \'%s\' successfully created.' % p.title, 'status': 'success'}
+            try:
+                page = self.page_manager.create(trans, payload)
+            except exceptions.MessageException as e:
+                return self.message_exception(trans, unicodify(e))
+            return {'message': 'Page \'%s\' successfully created.' % page.title, 'status': 'success'}
 
     @web.legacy_expose_api
     @web.require_login("edit pages")
@@ -637,11 +406,7 @@ class PageController(BaseUIController, SharableMixin,
         id = self.decode_id(id)
         page = trans.sa_session.query(model.Page).get(id)
         assert page.user == trans.user
-        content = page.latest_revision.content
-        processor = _PageContentProcessor(trans, _placeholderRenderForEdit)
-        processor.feed(content)
-        content = unicodify(processor.output(), 'utf-8')
-        return trans.fill_template("page/editor.mako", page=page, content=content)
+        return trans.fill_template("page/editor.mako", page=page)
 
     @web.expose
     @web.require_login("use Galaxy pages")
@@ -685,57 +450,11 @@ class PageController(BaseUIController, SharableMixin,
 
     @web.expose
     @web.require_login()
-    def save(self, trans, id, content, annotations):
+    def save(self, trans, id, content):
         id = self.decode_id(id)
         page = trans.sa_session.query(model.Page).get(id)
         assert page.user == trans.user
-
-        # Sanitize content
-        content = sanitize_html(content)
-        processor = _PageContentProcessor(trans, _placeholderRenderForSave)
-        processor.feed(content)
-        # Output is string, so convert to unicode for saving.
-        content = unicodify(processor.output(), 'utf-8')
-
-        # Add a new revision to the page with the provided content.
-        page_revision = model.PageRevision()
-        page_revision.title = page.title
-        page_revision.page = page
-        page.latest_revision = page_revision
-        page_revision.content = content
-
-        # Save annotations.
-        annotations = loads(annotations)
-        for annotation_dict in annotations:
-            item_id = self.decode_id(annotation_dict['item_id'])
-            item_class = self.get_class(annotation_dict['item_class'])
-            item = trans.sa_session.query(item_class).filter_by(id=item_id).first()
-            if not item:
-                raise RuntimeError("cannot find annotated item")
-            text = sanitize_html(annotation_dict['text'])
-
-            # Add/update annotation.
-            if item_id and item_class and text:
-                # Get annotation association.
-                annotation_assoc_class = eval("model.%sAnnotationAssociation" % item_class.__name__)
-                annotation_assoc = trans.sa_session.query(annotation_assoc_class).filter_by(user=trans.get_user())
-                if item_class == model.History.__class__:
-                    annotation_assoc = annotation_assoc.filter_by(history=item)
-                elif item_class == model.HistoryDatasetAssociation.__class__:
-                    annotation_assoc = annotation_assoc.filter_by(hda=item)
-                elif item_class == model.StoredWorkflow.__class__:
-                    annotation_assoc = annotation_assoc.filter_by(stored_workflow=item)
-                elif item_class == model.WorkflowStep.__class__:
-                    annotation_assoc = annotation_assoc.filter_by(workflow_step=item)
-                annotation_assoc = annotation_assoc.first()
-                if not annotation_assoc:
-                    # Create association.
-                    annotation_assoc = annotation_assoc_class()
-                    item.annotations.append(annotation_assoc)
-                    annotation_assoc.user = trans.get_user()
-                # Set annotation user text.
-                annotation_assoc.annotation = text
-        trans.sa_session.flush()
+        self.page_manager.save_new_revision(trans, page, {"content": content})
 
     @web.expose
     @web.require_login()
@@ -760,7 +479,7 @@ class PageController(BaseUIController, SharableMixin,
         self.security_check(trans, page, False, True)
 
         # Process page content.
-        processor = _PageContentProcessor(trans, self._get_embed_html)
+        processor = PageContentProcessor(trans, self._get_embed_html)
         processor.feed(page.latest_revision.content)
         # Output is string, so convert to unicode for display.
         page_content = unicodify(processor.output(), 'utf-8')
@@ -942,7 +661,7 @@ class PageController(BaseUIController, SharableMixin,
     def _get_embed_html(self, trans, item_class, item_id):
         """ Returns HTML for embedding an item in a page. """
         item_class = self.get_class(item_class)
-        encoded_id, decoded_id = _get_page_identifiers(item_id, trans.app)
+        encoded_id, decoded_id = get_page_identifiers(item_id, trans.app)
         if item_class == model.History:
             return self._get_embedded_history_html(trans, decoded_id)
 
@@ -967,52 +686,3 @@ class PageController(BaseUIController, SharableMixin,
 
         elif item_class == model.Page:
             pass
-
-
-PLACEHOLDER_TEMPLATE = '''<div class="embedded-item {class_shorthand_lower} placeholder" id="{item_class}-{item_id}"><p class="title">Embedded Galaxy {class_shorthand} - '{item_name}'</p><p class="content">[Do not edit this block; Galaxy will fill it in with the annotated {class_shorthand} when it is displayed]</p></div>'''
-
-# This is a mapping of the id portion of page contents to the cssclass/shortname.
-PAGE_CLASS_MAPPING = {
-    'History': 'History',
-    'HistoryDatasetAssociation': 'Dataset',
-    'StoredWorkflow': 'Workflow',
-    'Visualization': 'Visualization'
-}
-
-
-def _placeholderRenderForEdit(trans, item_class, item_id):
-    return _placeholderRenderForSave(trans, item_class, item_id, encode=True)
-
-
-def _placeholderRenderForSave(trans, item_class, item_id, encode=False):
-    encoded_item_id, decoded_item_id = _get_page_identifiers(item_id, trans.app)
-    item_name = ''
-    if item_class == 'History':
-        history = trans.sa_session.query(trans.model.History).get(decoded_item_id)
-        history = managers.base.security_check(trans, history, False, True)
-        item_name = history.name
-    elif item_class == 'HistoryDatasetAssociation':
-        hda = trans.sa_session.query(trans.model.HistoryDatasetAssociation).get(decoded_item_id)
-        hda_manager = managers.hdas.HDAManager(trans.app)
-        hda = hda_manager.get_accessible(decoded_item_id, trans.user)
-        item_name = hda.name
-    elif item_class == 'StoredWorkflow':
-        wf = trans.sa_session.query(trans.model.StoredWorkflow).get(decoded_item_id)
-        wf = managers.base.security_check(trans, wf, False, True)
-        item_name = wf.name
-    elif item_class == 'Visualization':
-        visualization = trans.sa_session.query(trans.model.Visualization).get(decoded_item_id)
-        visualization = managers.base.security_check(trans, visualization, False, True)
-        item_name = visualization.title
-    class_shorthand = PAGE_CLASS_MAPPING[item_class]
-    if encode:
-        item_id = encoded_item_id
-    else:
-        item_id = decoded_item_id
-    return PLACEHOLDER_TEMPLATE.format(
-        item_class=item_class,
-        class_shorthand=class_shorthand,
-        class_shorthand_lower=class_shorthand.lower(),
-        item_id=item_id,
-        item_name=item_name
-    )
diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py
index d486d5e439a..00e8e012b57 100644
--- a/lib/galaxy/webapps/galaxy/controllers/root.py
+++ b/lib/galaxy/webapps/galaxy/controllers/root.py
@@ -21,7 +21,8 @@ from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.util import (
     FILENAME_VALID_CHARS,
     listify,
-    string_as_bool
+    string_as_bool,
+    unicodify,
 )
 from galaxy.web.base import controller
 
@@ -341,7 +342,7 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
             trans.log_event("Added dataset %d to history %d" % (data.id, trans.history.id))
             return trans.show_ok_message("Dataset " + str(data.hid) + " added to history " + str(history_id) + ".")
         except Exception as e:
-            msg = "Failed to add dataset to history: %s" % (e)
+            msg = "Failed to add dataset to history: %s" % unicodify(e)
             log.error(msg)
             trans.log_event(msg)
             return trans.show_error_message("Adding File to History has Failed")
diff --git a/lib/galaxy/webapps/galaxy/controllers/tag.py b/lib/galaxy/webapps/galaxy/controllers/tag.py
index 25e74fdf576..0320f2be72e 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tag.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tag.py
@@ -90,7 +90,6 @@ class TagsController(BaseUIController, UsesTagsMixin):
         user = trans.user
         item_class = self.get_class(item_class)
         q = '' if q is None else q
-        q = q.encode('utf-8')
         if q.find(":") == -1:
             return self._get_tag_autocomplete_names(trans, q, limit, timestamp, user, item, item_class)
         else:
diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
index 5a456179d4c..e3a6b805565 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -77,7 +77,7 @@ class ToolRunner(BaseUIController):
         try:
             vars = tool.handle_input(trans, params.__dict__, history=history)
         except Exception as e:
-            error(str(e))
+            error(galaxy.util.unicodify(e))
         if len(params) > 0:
             trans.log_event('Tool params: %s' % (str(params)), tool_id=tool_id)
         return trans.fill_template('root/tool_runner.mako', **vars)
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 471ec720ece..513475172f1 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -32,6 +32,10 @@ from galaxy.web.base.controller import (
 log = logging.getLogger(__name__)
 
 
+def _filtered_registration_params_dict(payload):
+    return {k: v for (k, v) in payload.items() if k in ['email', 'username', 'password', 'confirm', 'subscribe']}
+
+
 class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
     installed_len_files = None
 
@@ -74,40 +78,38 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
                 trans.log_event("Assigning role to newly created user")
                 trans.app.security_agent.associate_user_role(user, role)
 
-    def __autoregistration(self, trans, login, password, status, kwd, no_password_check=False, cntrller=None):
+    def __autoregistration(self, trans, login, password):
         """
         Does the autoregistration if enabled. Returns a message
         """
-        autoreg = trans.app.auth_manager.check_auto_registration(trans, login, password, no_password_check=no_password_check)
+        autoreg = trans.app.auth_manager.check_auto_registration(trans, login, password)
         user = None
-        success = False
         if autoreg["auto_reg"]:
-            kwd["email"] = autoreg["email"]
-            kwd["username"] = autoreg["username"]
-            message = " ".join([validate_email(trans, kwd["email"], allow_empty=True),
-                                validate_publicname(trans, kwd["username"])]).rstrip()
+            email = autoreg["email"]
+            username = autoreg["username"]
+            message = " ".join([validate_email(trans, email, allow_empty=True),
+                                validate_publicname(trans, username)]).rstrip()
             if not message:
-                message, status, user, success = self.__register(trans, **kwd)
-                if success:
-                    # The handle_user_login() method has a call to the history_set_default_permissions() method
-                    # (needed when logging in with a history), user needs to have default permissions set before logging in
-                    if not trans.user_is_admin:
-                        trans.handle_user_login(user)
-                        trans.log_event("User (auto) created a new account")
-                        trans.log_event("User logged in")
-                    if "attributes" in autoreg and "roles" in autoreg["attributes"]:
-                        self.__handle_role_and_group_auto_creation(
-                            trans, user, autoreg["attributes"]["roles"],
-                            auto_create_groups=autoreg["auto_create_groups"],
-                            auto_create_roles=autoreg["auto_create_roles"],
-                            auto_assign_roles_to_groups_only=autoreg["auto_assign_roles_to_groups_only"])
-                else:
-                    message = "Auto-registration failed, contact your local Galaxy administrator. %s" % message
+                user = self.user_manager.create(email=email, username=username, password="")
+                if trans.app.config.user_activation_on:
+                    self.user_manager.send_activation_email(trans, email, username)
+                # The handle_user_login() method has a call to the history_set_default_permissions() method
+                # (needed when logging in with a history), user needs to have default permissions set before logging in
+                if not trans.user_is_admin:
+                    trans.handle_user_login(user)
+                    trans.log_event("User (auto) created a new account")
+                    trans.log_event("User logged in")
+                if "attributes" in autoreg and "roles" in autoreg["attributes"]:
+                    self.__handle_role_and_group_auto_creation(
+                        trans, user, autoreg["attributes"]["roles"],
+                        auto_create_groups=autoreg["auto_create_groups"],
+                        auto_create_roles=autoreg["auto_create_roles"],
+                        auto_assign_roles_to_groups_only=autoreg["auto_assign_roles_to_groups_only"])
             else:
                 message = "Auto-registration failed, contact your local Galaxy administrator. %s" % message
         else:
             message = "No such user or invalid password."
-        return message, status, user, success
+        return message, user
 
     @expose_api_anonymous_and_sessionless
     def login(self, trans, payload={}, **kwd):
@@ -132,8 +134,8 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         )).first()
         log.debug("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file)
         if user is None:
-            message, status, user, success = self.__autoregistration(trans, login, password, status, kwd)
-            if not success:
+            message, user = self.__autoregistration(trans, login, password)
+            if message:
                 return self.message_exception(trans, message)
         elif user.deleted:
             message = "This account has been marked deleted, contact your local Galaxy administrator to restore the account."
@@ -177,7 +179,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         Exposed function for use outside of the class. E.g. when user click on the resend link in the masthead.
         """
         message, status = self.resend_activation_email(trans, None, None)
-        if status == 'done':
+        if status:
             return trans.show_ok_message(message)
         else:
             return trans.show_error_message(message)
@@ -192,14 +194,12 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
             username = trans.user.username
         is_activation_sent = self.user_manager.send_activation_email(trans, email, username)
         if is_activation_sent:
-            message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address <b>%s</b> including the spam/trash folder.<br><a target="_top" href="%s">Return to the home page</a>.' % (escape(email), url_for('/'))
-            status = 'error'
+            message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address <b>%s</b> including the spam/trash folder. <a target="_top" href="%s">Return to the home page</a>.' % (escape(email), url_for('/'))
         else:
-            message = 'This account has not been activated yet but we are unable to send the activation link. Please contact your local Galaxy administrator.<br><a target="_top" href="%s">Return to the home page</a>.' % url_for('/')
-            status = 'error'
+            message = 'This account has not been activated yet but we are unable to send the activation link. Please contact your local Galaxy administrator. <a target="_top" href="%s">Return to the home page</a>.' % url_for('/')
             if trans.app.config.error_email_to is not None:
-                message += '<br>Error contact: %s' % trans.app.config.error_email_to
-        return message, status
+                message += ' Error contact: %s.' % trans.app.config.error_email_to
+        return message, is_activation_sent
 
     def is_outside_grace_period(self, trans, create_time):
         """
@@ -233,7 +233,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin):
         message = trans.check_csrf_token(payload)
         if message:
             return self.message_exception(trans, message)
-        user, message = self.user_manager.register(trans, **payload)
+        user, message = self.user_manager.register(trans, **_filtered_registration_params_dict(payload))
         if message:
             return self.message_exception(trans, message, sanitize=False)
         elif user and not trans.user_is_admin:
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index a8c06c6dea9..b56104af9c9 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -623,7 +623,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         """
         log.exception('error rendering visualization (%s)', visualization_name)
         if trans.debug:
-            raise
+            raise exception
         return trans.show_error_message(
             "There was an error rendering the visualization. " +
             "Contact your Galaxy administrator if the problem persists." +
diff --git a/lib/galaxy/webapps/galaxy/job_config_schema.yml b/lib/galaxy/webapps/galaxy/job_config_schema.yml
new file mode 100644
index 00000000000..f025bc85be1
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/job_config_schema.yml
@@ -0,0 +1,116 @@
+desc: Description of job running configuration, can be embedded into Galaxy configuration
+  or loaded from an additional file with the job_config_file option.
+type: map
+mapping:
+  runners:
+    type: map
+    mapping:
+      dynamic:
+        type: map
+        mapping:
+          rules_module:
+            type: str
+      regex;(.+):
+        type: map
+        allowempty: true
+        mapping:
+          workers:
+            type: int
+          load:
+            type: str
+          enabled:
+            type: bool
+  handling:
+    type: map
+    allowempty: true
+  execution: 
+    type: map
+    allowempty: true
+    mapping:
+      default:
+        type: str
+      environments:
+        type: map
+        mapping:
+          regex;(.+):
+            type: map
+            allowempty: true
+            mapping:
+              runner:
+                type: str
+              tags:
+                type: seq
+                sequence:
+                  - type: str
+              shell:
+                type: str
+              env:
+                type: seq
+                sequence:
+                  - type: map
+                    mapping:
+                      name:
+                        type: str
+                      raw:
+                        type: bool
+                      value:
+                        type: str
+                      file:
+                        type: str
+                      execute:
+                        type: str
+              resubmit:
+                type: seq
+                sequence:
+                  - type: map
+                    mapping:
+                      delay:
+                        type:  any  # str or number
+                      condition:
+                        type: str
+                      environment:
+                        type: str
+                      handler:
+                        type: str
+
+  tools: 
+    type: seq
+    sequence:
+      - type: map
+        allowempty: true
+        mapping:
+          id:
+            type: str
+          handler:
+            type: str
+          environment:
+            type: str
+          resources:
+            type: str
+  resources:
+    type: map
+    mapping:
+      default:
+        type: str
+      groups:
+        type: map
+        mapping:
+          regex;(.+):
+            type: seq
+            sequence:
+              - type: str
+  limits:
+    type: seq
+    sequence:
+      - type: map
+        mapping:
+          type:
+            type: str
+          value:
+            type: any
+          window:
+            type: int
+          id:
+            type: str
+          tag:
+            type: str
diff --git a/lib/galaxy/webapps/reports/app.py b/lib/galaxy/webapps/reports/app.py
index 25d12eb9688..69392b4fd92 100644
--- a/lib/galaxy/webapps/reports/app.py
+++ b/lib/galaxy/webapps/reports/app.py
@@ -4,7 +4,7 @@ import time
 
 import galaxy.model
 from galaxy.security import idencoding
-from galaxy.web.stack import application_stack_instance
+from galaxy.web_stack import application_stack_instance
 from . import config
 
 log = logging.getLogger(__name__)
diff --git a/lib/galaxy/webapps/reports/buildapp.py b/lib/galaxy/webapps/reports/buildapp.py
index 40e92c2a00d..af42f0d657a 100644
--- a/lib/galaxy/webapps/reports/buildapp.py
+++ b/lib/galaxy/webapps/reports/buildapp.py
@@ -11,7 +11,10 @@ from paste import httpexceptions
 import galaxy.model
 import galaxy.model.mapping
 import galaxy.web.framework.webapp
-from galaxy.util import asbool
+from galaxy.util import (
+    asbool,
+    unicodify,
+)
 from galaxy.util.properties import load_app_properties
 from galaxy.webapps.util import (
     build_template_error_formatters,
@@ -128,7 +131,7 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
                                           args=(conf,),
                                           kwargs=dict(templating_formatters=build_template_error_formatters()))
         except MiddlewareWrapUnsupported as exc:
-            log.warning(str(exc))
+            log.warning(unicodify(exc))
             import galaxy.web.framework.middleware.error
             app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
     else:
diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py
index f6dc928c308..0d044512a9f 100644
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -312,7 +312,7 @@ class RepositoriesController(BaseAPIController):
             # Open for reading with transparent compression.
             tar_archive = tarfile.open(capsule_file_path, 'r:*')
         except tarfile.ReadError as e:
-            log.debug('Error opening capsule file %s: %s' % (str(capsule_file_name), str(e)))
+            log.debug('Error opening capsule file %s: %s', capsule_file_name, util.unicodify(e))
             return {}
         irm = capsule_manager.ImportRepositoryManager(self.app,
                                                       trans.request.host,
@@ -492,8 +492,8 @@ class RepositoriesController(BaseAPIController):
         if not conf.whoosh_index_dir:
             raise ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.')
         search_term = q.strip()
-        if len(search_term) < 3:
-            raise RequestParameterInvalidException('The search term has to be at least 3 characters long.')
+        if len(search_term) < 1:
+            raise RequestParameterInvalidException('The search term has to be at least one character long.')
 
         repo_search = RepoSearch()
 
@@ -502,12 +502,14 @@ class RepositoriesController(BaseAPIController):
                                        'repo_long_description_boost',
                                        'repo_homepage_url_boost',
                                        'repo_remote_repository_url_boost',
+                                       'categories_boost',
                                        'repo_owner_username_boost'])
         boosts = Boosts(float(conf.get('repo_name_boost', 0.9)),
                         float(conf.get('repo_description_boost', 0.6)),
                         float(conf.get('repo_long_description_boost', 0.5)),
                         float(conf.get('repo_homepage_url_boost', 0.3)),
                         float(conf.get('repo_remote_repository_url_boost', 0.2)),
+                        float(conf.get('categories_boost', 0.5)),
                         float(conf.get('repo_owner_username_boost', 0.3)))
 
         results = repo_search.search(trans,
@@ -633,7 +635,7 @@ class RepositoriesController(BaseAPIController):
                     results['successful_count'] += 1
             except Exception as e:
                 message = "Error resetting metadata on repository %s owned by %s: %s" % \
-                    (str(repository.name), str(repository.user.username), str(e))
+                    (str(repository.name), str(repository.user.username), util.unicodify(e))
                 results['unsuccessful_count'] += 1
             status = '%s : %s' % (str(repository.name), message)
             results['repository_status'].append(status)
@@ -723,7 +725,7 @@ class RepositoriesController(BaseAPIController):
                     results['status'] = 'ok'
             except Exception as e:
                 message = "Error resetting metadata on repository %s owned by %s: %s" % \
-                    (str(repository.name), str(repository.user.username), str(e))
+                    (str(repository.name), str(repository.user.username), util.unicodify(e))
                 results['status'] = 'error'
             status = '%s : %s' % (str(repository.name), message)
             results['repository_status'].append(status)
diff --git a/lib/galaxy/webapps/tool_shed/api/tools.py b/lib/galaxy/webapps/tool_shed/api/tools.py
index d96225f1f44..fd3f08c0373 100644
--- a/lib/galaxy/webapps/tool_shed/api/tools.py
+++ b/lib/galaxy/webapps/tool_shed/api/tools.py
@@ -90,8 +90,8 @@ class ToolsController(BaseAPIController):
         if not conf.whoosh_index_dir:
             raise exceptions.ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.')
         search_term = q.strip()
-        if len(search_term) < 3:
-            raise exceptions.RequestParameterInvalidException('The search term has to be at least 3 characters long.')
+        if len(search_term) < 1:
+            raise exceptions.RequestParameterInvalidException('The search term has to be at least one character long.')
 
         tool_search = ToolSearch()
 
diff --git a/lib/galaxy/webapps/tool_shed/app.py b/lib/galaxy/webapps/tool_shed/app.py
index 0fdd8ecec6d..785e480b05a 100644
--- a/lib/galaxy/webapps/tool_shed/app.py
+++ b/lib/galaxy/webapps/tool_shed/app.py
@@ -13,7 +13,7 @@ from galaxy.config import configure_logging
 from galaxy.model.tags import CommunityTagHandler
 from galaxy.security import idencoding
 from galaxy.util.dbkeys import GenomeBuilds
-from galaxy.web.stack import application_stack_instance
+from galaxy.web_stack import application_stack_instance
 from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
 from . import config
 
diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py
index e129d724aac..176a0ac750d 100644
--- a/lib/galaxy/webapps/tool_shed/buildapp.py
+++ b/lib/galaxy/webapps/tool_shed/buildapp.py
@@ -281,7 +281,7 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
                                               args=(conf,),
                                               kwargs=dict(templating_formatters=build_template_error_formatters()))
             except MiddlewareWrapUnsupported as exc:
-                log.warning(str(exc))
+                log.warning(util.unicodify(exc))
                 import galaxy.web.framework.middleware.error
                 app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
         else:
diff --git a/lib/galaxy/webapps/tool_shed/config_schema.yml b/lib/galaxy/webapps/tool_shed/config_schema.yml
index 92e2e6466ca..f4a2eec0508 100644
--- a/lib/galaxy/webapps/tool_shed/config_schema.yml
+++ b/lib/galaxy/webapps/tool_shed/config_schema.yml
@@ -14,7 +14,7 @@ mapping:
         desc: |
           Verbosity of console log messages.  Acceptable values can be found here:
           https://docs.python.org/library/logging.html#logging-levels
-      
+
       database_connection:
         type: str
         default: sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE
@@ -24,35 +24,35 @@ mapping:
           may use a SQLAlchemy connection string to specify an external database
           instead.  This string takes many options which are explained in detail in the
           config file documentation.
-      
+
       hgweb_config_dir:
         type: str
         required: false
         desc: |
           Where the hgweb.config file is stored.
           The default is the Galaxy installation directory.
-      
+
       file_path:
         type: str
         default: database/community_files
         required: false
         desc: |
           Where Tool Shed repositories are stored.
-      
+
       new_file_path:
         type: str
         default: database/tmp
         required: false
         desc: |
           Where temporary files are stored.
-      
+
       builds_file_path:
         type: str
         default: tool-data/shared/ucsc/builds.txt
         required: false
         desc: |
           File containing old-style genome builds
-      
+
       pretty_datetime_format:
         type: str
         default: $locale (UTC)
@@ -65,7 +65,7 @@ mapping:
           - $locale (complete format string for the server locale),
           - $iso8601 (complete format string as specified by ISO 8601 international
             standard).
-      
+
       toolshed_search_on:
         type: bool
         default: true
@@ -76,7 +76,7 @@ mapping:
           you can generate search index and allow full text API searching over
           the repositories and tools within the Tool Shed given that you specify
           the following two config options.
-      
+
       whoosh_index_dir:
         type: str
         default: database/toolshed_whoosh_indexes
@@ -87,84 +87,91 @@ mapping:
           you can generate search index and allow full text API searching over
           the repositories and tools within the Tool Shed given that you specify
           the following two config options.
-      
+
       repo_name_boost:
         type: float
         default: 0.9
         required: false
         desc: |
           For searching repositories at /api/repositories:
-      
+
       repo_description_boost:
         type: float
         default: 0.6
         required: false
         desc: |
           For searching repositories at /api/repositories:
-      
+
       repo_long_description_boost:
         type: float
         default: 0.5
         required: false
         desc: |
           For searching repositories at /api/repositories:
-      
+
       repo_homepage_url_boost:
         type: float
         default: 0.3
         required: false
         desc: |
           For searching repositories at /api/repositories:
-      
+
       repo_remote_repository_url_boost:
         type: float
         default: 0.2
         required: false
         desc: |
           For searching repositories at /api/repositories:
-      
+
       repo_owner_username_boost:
         type: float
         default: 0.3
         required: false
         desc: |
           For searching repositories at /api/repositories:
-      
+
+      categories_boost:
+        type: float
+        default: 0.5
+        required: false
+        desc: |
+          For searching repositories at /api/repositories:
+
       tool_name_boost:
         type: float
         default: 1.2
         required: false
         desc: |
           For searching tools at /api/tools
-      
+
       tool_description_boost:
         type: float
         default: 0.6
         required: false
         desc: |
           For searching tools at /api/tools
-      
+
       tool_help_boost:
         type: float
         default: 0.4
         required: false
         desc: |
           For searching tools at /api/tools
-      
+
       tool_repo_owner_username:
         type: float
         default: 0.3
         required: false
         desc: |
           For searching tools at /api/tools
-      
+
       ga_code:
         type: str
         required: false
         desc: |
           You can enter tracking code here to track visitor's behavior
           through your Google Analytics account. Example: UA-XXXXXXXX-Y
-      
+
       id_secret:
         type: str
         default: changethisinproductiontoo
@@ -177,7 +184,7 @@ mapping:
           them access to others' sessions.
           One simple way to generate a value for this is with the shell command:
             python -c 'from __future__ import print_function; import time; print(time.time())' | md5sum | cut -f 1 -d ' '
-      
+
       use_remote_user:
         type: bool
         default: false
@@ -187,7 +194,7 @@ mapping:
           Apache).  The upstream proxy should set a REMOTE_USER header in the request.
           Enabling remote user disables regular logins.  For more information, see:
           https://galaxyproject.org/admin/config/apache-external-user-auth/
-      
+
       remote_user_secret:
         type: str
         default: changethisinproductiontoo
@@ -226,35 +233,35 @@ mapping:
         desc: |
           If use_remote_user is enabled, you can set this to a URL that will log your
           users out.
-      
+
       debug:
         type: bool
         default: false
         required: false
         desc: |
           Configuration for debugging middleware
-      
+
       use_lint:
         type: bool
         default: false
         required: false
         desc: |
           Check for WSGI compliance.
-      
+
       use_printdebug:
         type: bool
         default: true
         required: false
         desc: |
           Intercept print statements and show them on the returned page.
-      
+
       use_interactive:
         type: bool
         default: false
         required: false
         desc: |
           NEVER enable this on a public site (even test or QA)
-      
+
       admin_users:
         type: str
         required: false
@@ -263,7 +270,7 @@ mapping:
           users (email addresses).  These users will have access to the Admin section
           of the server, and will have access to create users, groups, roles,
           libraries, and more.
-      
+
       require_login:
         type: bool
         default: false
@@ -286,21 +293,21 @@ mapping:
         desc: |
           Allow administrators to delete accounts.
 
-      
+
       smtp_server:
         type: str
         default: smtp.your_tool_shed_server
         required: false
         desc: |
           For use by email messages sent from the Tool Shed.
-      
+
       email_from:
         type: str
         default: your_tool_shed_email@server
         required: false
         desc: |
           For use by email messages sent from the Tool Shed.
-      
+
       smtp_username:
         type: str
         required: false
@@ -308,7 +315,7 @@ mapping:
           If your SMTP server requires a username and password, you can provide them
           here (password in cleartext here, but if your server supports STARTTLS it
           will be sent over the network encrypted).
-      
+
       smtp_password:
         type: str
         required: false
@@ -316,28 +323,28 @@ mapping:
           If your SMTP server requires a username and password, you can provide them
           here (password in cleartext here, but if your server supports STARTTLS it
           will be sent over the network encrypted).
-      
+
       smtp_ssl:
         type: bool
         default: false
         required: false
         desc: |
           If your SMTP server requires SSL from the beginning of the connection
-      
+
       support_url:
         type: str
         default: https://galaxyproject.org/support/
         required: false
         desc: |
           The URL linked by the "Support" link in the "Help" menu.
-      
+
       mailing_join_addr:
         type: str
         default: galaxy-announce-join@bx.psu.edu
         required: false
         desc: |
           Address to join mailing list
-      
+
       use_heartbeat:
         type: bool
         default: true
@@ -345,34 +352,34 @@ mapping:
         desc: |
           Write thread status periodically to 'heartbeat.log' (careful, uses disk
            space rapidly!)
-      
+
       use_profile:
         type: bool
         default: true
         required: false
         desc: |
           Profiling middleware (cProfile based)
-      
+
       enable_galaxy_flavor_docker_image:
         type: bool
         default: false
         required: false
         desc: |
           Enable creation of Galaxy flavor Docker Image
-      
+
       message_box_visible:
         type: bool
         default: false
         required: false
         desc: |
           Show a message box under the masthead.
-      
+
       message_box_content:
         type: str
         required: false
         desc: |
           Show a message box under the masthead.
-      
+
       message_box_class:
         type: str
         default: info
@@ -380,49 +387,49 @@ mapping:
         desc: |
           Class of the message box under the masthead. Possible values are:
           'info' (the default), 'warning', 'error', 'done'.
-      
+
       static_enabled:
         type: bool
         default: true
         required: false
         desc: |
           Serving static files (needed if running standalone)
-      
+
       static_cache_time:
         type: int
         default: 360
         required: false
         desc: |
           Serving static files (needed if running standalone)
-      
+
       static_dir:
         type: str
         default: static/
         required: false
         desc: |
           Serving static files (needed if running standalone)
-      
+
       static_images_dir:
         type: str
         default: static/images
         required: false
         desc: |
           Serving static files (needed if running standalone)
-      
+
       static_favicon_dir:
         type: str
         default: static/favicon.ico
         required: false
         desc: |
           Serving static files (needed if running standalone)
-      
+
       static_scripts_dir:
         type: str
         default: static/scripts/
         required: false
         desc: |
           Serving static files (needed if running standalone)
-      
+
       static_style_dir:
         type: str
         default: static/style/blue
diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index 63841ad1d78..6f94f913ad2 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -900,7 +900,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                                        message=message,
                                        status=status)
         except Exception as e:
-            message = "Error displaying tool, probably due to a problem in the tool config.  The exception is: %s." % str(e)
+            message = "Error displaying tool, probably due to a problem in the tool config.  The exception is: %s." % util.unicodify(e)
         if trans.webapp.name == 'galaxy' or render_repository_actions_for == 'galaxy':
             return trans.response.send_redirect(web.url_for(controller='repository',
                                                             action='preview_tools_in_changeset',
@@ -1801,7 +1801,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                                        message=message,
                                        status='error')
         except Exception as e:
-            message = "Exception thrown attempting to display tool: %s." % str(e)
+            message = "Exception thrown attempting to display tool: %s." % util.unicodify(e)
         if trans.webapp.name == 'galaxy':
             return trans.response.send_redirect(web.url_for(controller='repository',
                                                             action='preview_tools_in_changeset',
@@ -2371,8 +2371,8 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                     try:
                         hg_util.remove_file(repo_dir, selected_file, force=True)
                     except Exception as e:
-                        log.debug("Error removing the following file using the mercurial API:\n %s" % str(selected_file))
-                        log.debug("The error was: %s" % str(e))
+                        log.debug("Error removing the following file using the mercurial API:\n %s", selected_file)
+                        log.debug("The error was: %s", util.unicodify(e))
                         log.debug("Attempting to remove the file using a different approach.")
                         relative_selected_file = selected_file.split('repo_%d' % repository.id)[1].lstrip('/')
                         repo.dirstate.remove(relative_selected_file)
@@ -2461,7 +2461,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                 message = "Your message has been sent"
                 status = "done"
             except Exception as e:
-                message = "An error occurred sending your message by email: %s" % str(e)
+                message = "An error occurred sending your message by email: %s" % util.unicodify(e)
                 status = "error"
         else:
             # Do all we can to eliminate spam.
diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py
index 57a7f8a5f7c..91bfadc6e68 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/upload.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py
@@ -75,7 +75,7 @@ class UploadController(BaseUIController):
                     stream = requests.get(url, stream=True)
                 except Exception as e:
                     valid_url = False
-                    message = 'Error uploading file via http: %s' % str(e)
+                    message = 'Error uploading file via http: %s' % util.unicodify(e)
                     status = 'error'
                     uploaded_file = None
                 if valid_url:
diff --git a/lib/galaxy/webapps/tool_shed/search/repo_search.py b/lib/galaxy/webapps/tool_shed/search/repo_search.py
index 9cc003b6f51..ce0a575070b 100644
--- a/lib/galaxy/webapps/tool_shed/search/repo_search.py
+++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py
@@ -1,11 +1,13 @@
 """Module for searching the toolshed repositories"""
 import logging
+import re
 import sys
 
 import whoosh.index
 from whoosh import scoring
-from whoosh.fields import Schema, STORED, TEXT
+from whoosh.fields import KEYWORD, Schema, STORED, TEXT
 from whoosh.qparser import MultifieldParser
+from whoosh.query import And, Term
 
 from galaxy import exceptions
 from galaxy.exceptions import ObjectNotFound
@@ -13,6 +15,7 @@ from galaxy.exceptions import ObjectNotFound
 if sys.version_info > (3,):
     long = int
 
+RESERVED_SEARCH_TERMS = ["category", "owner"]
 log = logging.getLogger(__name__)
 
 schema = Schema(
@@ -23,9 +26,11 @@ schema = Schema(
     homepage_url=TEXT(stored=True),
     remote_repository_url=TEXT(stored=True),
     repo_owner_username=TEXT(stored=True),
+    categories=KEYWORD(stored=True, commas=True, scorable=True),
     times_downloaded=STORED,
     approved=STORED,
     last_updated=STORED,
+    repo_lineage=STORED,
     full_last_updated=STORED)
 
 
@@ -66,8 +71,10 @@ class RepoSearch(object):
 
         :param search_term: unicode encoded string with the search term(s)
         :param boosts: namedtuple containing custom boosts for searchfields, see api/repositories.py
+        :param page_size: integer defining a length of one page
+        :param page: integer with the number of page requested
 
-        :returns results: dictionary containing number of hits, hits themselves and matched terms for each
+        :returns results: dictionary containing hits themselves and the number of hits
         """
         whoosh_index_dir = trans.app.config.whoosh_index_dir
         index_exists = whoosh.index.exists_in(whoosh_index_dir)
@@ -83,26 +90,30 @@ class RepoSearch(object):
                                                         'long_description_B' : boosts.repo_long_description_boost,
                                                         'homepage_url_B' : boosts.repo_homepage_url_boost,
                                                         'remote_repository_url_B' : boosts.repo_remote_repository_url_boost,
-                                                        'repo_owner_username' : boosts.repo_owner_username_boost})
+                                                        'repo_owner_username_B' : boosts.repo_owner_username_boost,
+                                                        'categories_B' : boosts.categories_boost})
 
                 searcher = index.searcher(weighting=repo_weighting)
 
+                allow_query, search_term_without_filters = self._parse_reserved_filters(search_term)
+
                 parser = MultifieldParser([
                     'name',
                     'description',
                     'long_description',
                     'homepage_url',
                     'remote_repository_url',
-                    'repo_owner_username'], schema=schema)
-
-                user_query = parser.parse('*' + search_term + '*')
+                    'repo_owner_username',
+                    'categories'], schema=schema)
+                user_query = parser.parse('*' + search_term_without_filters + '*')
 
                 try:
-                    hits = searcher.search_page(user_query, page, pagelen=page_size, terms=True)
+                    hits = searcher.search_page(user_query, page, pagelen=page_size, filter=allow_query, terms=True)
                 except ValueError:
                     raise ObjectNotFound('The requested page does not exist.')
 
-                log.debug('searching for: #' + str(search_term))
+                log.debug('user search query: #' + str(search_term))
+                log.debug('term without filters: #' + str(search_term_without_filters))
                 log.debug('total hits: ' + str(len(hits)))
                 log.debug('scored hits: ' + str(hits.scored_length()))
                 results = {}
@@ -111,6 +122,7 @@ class RepoSearch(object):
                 results['page_size'] = str(page_size)
                 results['hits'] = []
                 for hit in hits:
+                    log.debug('matched terms: ' + str(hit.matched_terms()))
                     hit_dict = {}
                     hit_dict['id'] = trans.security.encode_id(hit.get('id'))
                     hit_dict['repo_owner_username'] = hit.get('repo_owner_username')
@@ -121,11 +133,72 @@ class RepoSearch(object):
                     hit_dict['description'] = hit.get('description')
                     hit_dict['last_updated'] = hit.get('last_updated')
                     hit_dict['full_last_updated'] = hit.get('full_last_updated')
+                    hit_dict['repo_lineage'] = hit.get('repo_lineage')
+                    hit_dict['categories'] = hit.get('categories')
                     hit_dict['approved'] = hit.get('approved')
                     hit_dict['times_downloaded'] = hit.get('times_downloaded')
-                    results['hits'].append({'repository': hit_dict, 'matched_terms': hit.matched_terms(), 'score': hit.score})
+                    results['hits'].append({'repository': hit_dict, 'score': hit.score})
                 return results
             finally:
                 searcher.close()
         else:
             raise exceptions.InternalServerError('The search index file is missing.')
+
+    def _parse_reserved_filters(self, search_term):
+        """
+        Support github-like filters for narrowing the results.
+        Order of chunks does not matter, only recognized
+        filter names are allowed.
+
+        :param search_term: the original search str from user input
+
+        :returns allow_query: whoosh Query object used for filtering
+            results of searching in index
+        :returns search_term_without_filters: str that represents user's
+            search phrase without the wildcards
+
+        >>> rs = RepoSearch()
+        >>> rs._parse_reserved_filters("category:assembly")
+        (And([Term('categories', 'assembly')]), '')
+        >>> rs._parse_reserved_filters("category:assembly abyss")
+        (And([Term('categories', 'assembly')]), 'abyss')
+        >>> rs._parse_reserved_filters("category:'Climate Analysis' psy_maps")
+        (And([Term('categories', 'Climate Analysis')]), 'psy_maps')
+        >>> rs._parse_reserved_filters("climate category:'Climate Analysis' owner:'bjoern gruening' psy_maps")
+        (And([Term('categories', 'Climate Analysis'), Term('repo_owner_username', 'bjoern gruening')]), 'climate psy_maps')
+        >>> rs._parse_reserved_filters("abyss category:assembly")
+        (And([Term('categories', 'assembly')]), 'abyss')
+        >>> rs._parse_reserved_filters("abyss category:assembly greg")
+        (And([Term('categories', 'assembly')]), 'abyss greg')
+        >>> rs._parse_reserved_filters("owner:greg")
+        (And([Term('repo_owner_username', 'greg')]), '')
+        >>> rs._parse_reserved_filters("owner:greg category:assembly abyss")
+        (And([Term('repo_owner_username', 'greg'), Term('categories', 'assembly')]), 'abyss')
+        >>> rs._parse_reserved_filters("meaningoflife:42")
+        (None, 'meaningoflife:42')
+        """
+        allow_query = None
+        allow_terms = []
+        # Split query string on spaces that are not followed by <anytext>singlequote_space_
+        # to allow for quoting filtering values. Also unify double and single quotes into single quotes.
+        search_term_chunks = re.split(r"\s+(?!\w+'\s)", search_term.replace('"', "'"), re.MULTILINE)
+        reserved_terms = []
+        for term_chunk in search_term_chunks:
+            if ":" in term_chunk:
+                reserved_filter = term_chunk.split(":")[0]
+                # Remove the quotes used for delimiting values with space(s)
+                reserved_filter_value = term_chunk.split(":")[1].replace("'", "")
+                if reserved_filter in RESERVED_SEARCH_TERMS:
+                    reserved_terms.append(term_chunk)
+                    if reserved_filter == "category":
+                        allow_terms.append(Term('categories', reserved_filter_value))
+                    elif reserved_filter == "owner":
+                        allow_terms.append(Term('repo_owner_username', reserved_filter_value))
+                else:
+                    pass  # Treat unrecognized filter as normal search term.
+        if allow_terms:
+            allow_query = And(allow_terms)
+            search_term_without_filters = " ".join([chunk for chunk in search_term_chunks if chunk not in reserved_terms])
+        else:
+            search_term_without_filters = search_term
+        return allow_query, search_term_without_filters
diff --git a/lib/galaxy/webapps/tool_shed/search/tool_search.py b/lib/galaxy/webapps/tool_shed/search/tool_search.py
index ca4154961c3..bb67046974d 100644
--- a/lib/galaxy/webapps/tool_shed/search/tool_search.py
+++ b/lib/galaxy/webapps/tool_shed/search/tool_search.py
@@ -16,7 +16,7 @@ from galaxy.exceptions import ObjectNotFound
 
 log = logging.getLogger(__name__)
 
-tool_schema = Schema(
+schema = Schema(
     name=TEXT(stored=True),
     description=TEXT(stored=True),
     owner=TEXT(stored=True),
@@ -58,7 +58,7 @@ class ToolSearch(object):
                     'name',
                     'description',
                     'help',
-                    'repo_owner_username'], schema=tool_schema)
+                    'repo_owner_username'], schema=schema)
 
                 user_query = parser.parse('*' + search_term + '*')
 
diff --git a/lib/galaxy/webapps/tool_shed/util/hgweb_config.py b/lib/galaxy/webapps/tool_shed/util/hgweb_config.py
index 5a52d423c78..b38a72ff0dc 100644
--- a/lib/galaxy/webapps/tool_shed/util/hgweb_config.py
+++ b/lib/galaxy/webapps/tool_shed/util/hgweb_config.py
@@ -6,6 +6,8 @@ from datetime import date
 
 from six.moves import configparser
 
+from galaxy.util import unicodify
+
 log = logging.getLogger(__name__)
 
 new_hgweb_config_template = """
@@ -35,7 +37,7 @@ class HgWebConfigManager(object):
             # Persist our in-memory configuration.
             self.write_config()
         except Exception as e:
-            log.debug("Exception in HgWebConfigManager.add_entry(): %s" % str(e))
+            log.debug("Exception in HgWebConfigManager.add_entry(): %s", unicodify(e))
         finally:
             lock.release()
 
@@ -52,7 +54,7 @@ class HgWebConfigManager(object):
             # Persist our in-memory configuration.
             self.write_config()
         except Exception as e:
-            log.debug("Exception in HgWebConfigManager.change_entry(): %s" % str(e))
+            log.debug("Exception in HgWebConfigManager.change_entry(): %s", unicodify(e))
         finally:
             lock.release()
 
diff --git a/lib/galaxy/webapps/util.py b/lib/galaxy/webapps/util.py
index efc59361735..dd792ec5c3d 100644
--- a/lib/galaxy/webapps/util.py
+++ b/lib/galaxy/webapps/util.py
@@ -4,6 +4,8 @@ import logging
 
 import mako.exceptions
 
+from galaxy.util import unicodify
+
 
 log = logging.getLogger(__name__)
 
@@ -55,7 +57,7 @@ def wrap_if_allowed(app, stack, wrap, name=None, args=None, kwargs=None):
 
     :type   app:    :class:`galaxy.web.framework.webapp.WebApplication` subclass
     :param  app:    application to wrap
-    :type   stack:  :class:`galaxy.web.stack.ApplicationStack` subclass
+    :type   stack:  :class:`galaxy.web_stack.ApplicationStack` subclass
     :param  stack:  instance of application stack implementing `allowed_middleware()` method
     :type   wrap:   types.FunctionType or types.LambdaType
     :param  wrap:   function to wrap application with
@@ -71,5 +73,5 @@ def wrap_if_allowed(app, stack, wrap, name=None, args=None, kwargs=None):
     try:
         return wrap_if_allowed_or_fail(app, stack, wrap, name=name, args=args, kwargs=kwargs)
     except MiddlewareWrapUnsupported as exc:
-        log.warning(str(exc))
+        log.warning(unicodify(exc))
         return app
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index bf2f4165787..53e926ec9f7 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -4,6 +4,7 @@ histories.
 import logging
 
 from galaxy import exceptions, model
+from galaxy.tool_util.parser import ToolOutputCollectionPart
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
     DataToolParameter
@@ -13,7 +14,6 @@ from galaxy.tools.parameters.grouping import (
     Repeat,
     Section
 )
-from galaxy.tools.parser import ToolOutputCollectionPart
 from galaxy.util.odict import odict
 from .steps import (
     attach_ordered_steps,
@@ -141,7 +141,7 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
                 hid = None
                 for implicit_pair in jobs[job]:
                     query_assoc_name, dataset_collection = implicit_pair
-                    if query_assoc_name == assoc_name:
+                    if query_assoc_name == assoc_name or assoc_name.startswith("__new_primary_file_%s|" % query_assoc_name):
                         hid = dataset_collection.hid
                 if hid is None:
                     template = "Failed to find matching implicit job - job id is %s, implicit pairs are %s, assoc_name is %s."
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index d3a2c16617a..433f407800e 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1,9 +1,9 @@
 """
 Modules used in building workflows
 """
+import json
 import logging
 import re
-from json import loads
 from xml.etree.ElementTree import (
     Element,
     XML
@@ -18,6 +18,7 @@ from galaxy.exceptions import ToolMissingException
 from galaxy.jobs.actions.post import ActionBox
 from galaxy.model import PostJobAction
 from galaxy.model.dataset_collections import matching
+from galaxy.tool_util.parser.output_objects import ToolExpressionOutput
 from galaxy.tools import (
     DatabaseOperationTool,
     DefaultToolState,
@@ -31,6 +32,7 @@ from galaxy.tools.parameters import (
     visit_input_values
 )
 from galaxy.tools.parameters.basic import (
+    BaseDataToolParameter,
     BooleanToolParameter,
     ConnectedValue,
     DataCollectionToolParameter,
@@ -45,7 +47,7 @@ from galaxy.tools.parameters.basic import (
 )
 from galaxy.tools.parameters.history_query import HistoryQuery
 from galaxy.tools.parameters.wrapped import make_dict_copy
-from galaxy.tools.parser.output_objects import ToolExpressionOutput
+from galaxy.util import unicodify
 from galaxy.util.bunch import Bunch
 from galaxy.util.json import safe_loads
 from galaxy.util.odict import odict
@@ -424,6 +426,8 @@ class SubWorkflowModule(WorkflowModule):
                 )
                 if step.type == 'data_collection_input':
                     input['collection_type'] = step.tool_inputs.get('collection_type') if step.tool_inputs else None
+                if step_type == 'parameter_input':
+                    input['type'] = step.tool_inputs['parameter_type']
                 inputs.append(input)
         return inputs
 
@@ -993,7 +997,9 @@ class ToolModule(WorkflowModule):
                         params = make_dict_copy(self.state.inputs)
                         params['on_string'] = 'input dataset(s)'
                         params['tool'] = self.tool
-                        extra_kwds['label'] = fill_template(tool_output.label, context=params)
+                        extra_kwds['label'] = fill_template(tool_output.label,
+                                                            context=params,
+                                                            python_template_version=self.tool.python_template_version)
                     except Exception:
                         pass
                 data_outputs.append(
@@ -1157,7 +1163,7 @@ class ToolModule(WorkflowModule):
         if self.tool:
             state = super(ToolModule, self).decode_runtime_state(runtime_state)
             if RUNTIME_STEP_META_STATE_KEY in runtime_state:
-                self.__restore_step_meta_runtime_state(loads(runtime_state[RUNTIME_STEP_META_STATE_KEY]))
+                self.__restore_step_meta_runtime_state(json.loads(runtime_state[RUNTIME_STEP_META_STATE_KEY]))
             return state
         else:
             raise ToolMissingException("Tool %s missing. Cannot recover runtime state." % self.tool_id,
@@ -1202,11 +1208,13 @@ class ToolModule(WorkflowModule):
                 input_dict = all_inputs_by_name[prefixed_name]
 
                 replacement = NO_REPLACEMENT
+                dataset_instance = None
                 if iteration_elements and prefixed_name in iteration_elements:
-                    if isinstance(input, DataToolParameter) and hasattr(iteration_elements[prefixed_name], 'dataset_instance'):
+                    dataset_instance = getattr(iteration_elements[prefixed_name], 'dataset_instance', None)
+                    if isinstance(input, DataToolParameter) and dataset_instance:
                         # Pull out dataset instance (=HDA) from element and set a temporary element_identifier attribute
                         # See https://github.com/galaxyproject/galaxy/pull/1693 for context.
-                        replacement = iteration_elements[prefixed_name].dataset_instance
+                        replacement = dataset_instance
                         if hasattr(iteration_elements[prefixed_name], u'element_identifier') and iteration_elements[prefixed_name].element_identifier:
                             replacement.element_identifier = iteration_elements[prefixed_name].element_identifier
                     else:
@@ -1216,6 +1224,12 @@ class ToolModule(WorkflowModule):
                     replacement = progress.replacement_for_input(step, input_dict)
 
                 if replacement is not NO_REPLACEMENT:
+                    if not isinstance(input, BaseDataToolParameter):
+                        # Probably a parameter that can be replaced
+                        dataset = dataset_instance or replacement
+                        if getattr(dataset, 'extension', None) == 'expression.json':
+                            with open(dataset.file_name, 'r') as f:
+                                replacement = json.load(f)
                     found_replacement_keys.add(prefixed_name)
 
                 return replacement
@@ -1230,7 +1244,7 @@ class ToolModule(WorkflowModule):
 
             unmatched_input_connections = expected_replacement_keys - found_replacement_keys
             if unmatched_input_connections:
-                log.warn("Failed to use input connections for inputs [%s]" % unmatched_input_connections)
+                log.warning("Failed to use input connections for inputs [%s]" % unmatched_input_connections)
 
             param_combinations.append(execution_state.inputs)
 
@@ -1360,7 +1374,7 @@ class ToolModule(WorkflowModule):
         replacement_parameters = set()
         for pja in step.post_job_actions:
             for argument in pja.action_arguments.values():
-                for match in re.findall(r'\$\{(.+?)\}', argument):
+                for match in re.findall(r'\$\{(.+?)\}', unicodify(argument)):
                     replacement_parameters.add(match)
 
         return list(replacement_parameters)
diff --git a/lib/galaxy/workflow/resources/__init__.py b/lib/galaxy/workflow/resources/__init__.py
index a9bf1d07320..e9d9aabe28e 100644
--- a/lib/galaxy/workflow/resources/__init__.py
+++ b/lib/galaxy/workflow/resources/__init__.py
@@ -30,7 +30,7 @@ def get_resource_mapper_function(app):
     else:
         workflow_resource_params = _read_defined_parameter_definitions(config)
         with open(mapper, "r") as f:
-            mapper_definition = yaml.load(f)
+            mapper_definition = yaml.safe_load(f)
 
         if "by_group" in mapper_definition:
             by_group = mapper_definition["by_group"]
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 961a673e9f4..e9120f2529b 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -1,4 +1,3 @@
-import json
 import logging
 import uuid
 
@@ -369,15 +368,24 @@ class WorkflowProgress(object):
                 delayed_why = "dependent collection [%s] not yet populated with datasets" % replacement.id
                 raise modules.DelayedWorkflowEvaluation(why=delayed_why)
 
-        is_hda = isinstance(replacement, model.HistoryDatasetAssociation)
-        if not is_data and is_hda:
-            if replacement.is_ok:
-                with open(replacement.file_name, 'r') as f:
-                    replacement = json.load(f)
-            elif replacement.is_pending:
-                raise modules.DelayedWorkflowEvaluation()
+        data_inputs = (model.HistoryDatasetAssociation, model.HistoryDatasetCollectionAssociation, model.DatasetCollection)
+        if not is_data and isinstance(replacement, data_inputs):
+            if isinstance(replacement, model.HistoryDatasetAssociation):
+                if replacement.is_pending:
+                    raise modules.DelayedWorkflowEvaluation()
+                if not replacement.is_ok:
+                    raise modules.CancelWorkflowEvaluation()
             else:
-                raise modules.CancelWorkflowEvaluation()
+                if not replacement.collection.populated:
+                    raise modules.DelayedWorkflowEvaluation()
+                pending = False
+                for dataset_instance in replacement.dataset_instances:
+                    if dataset_instance.is_pending:
+                        pending = True
+                    elif not dataset_instance.is_ok:
+                        raise modules.CancelWorkflowEvaluation()
+                if pending:
+                    raise modules.DelayedWorkflowEvaluation()
 
         return replacement
 
diff --git a/lib/galaxy/workflow/scheduling_manager.py b/lib/galaxy/workflow/scheduling_manager.py
index f88e9b23e78..41ac0c45a30 100644
--- a/lib/galaxy/workflow/scheduling_manager.py
+++ b/lib/galaxy/workflow/scheduling_manager.py
@@ -8,8 +8,8 @@ from galaxy import model
 from galaxy.exceptions import HandlerAssignmentError
 from galaxy.util import plugin_config
 from galaxy.util.monitors import Monitors
-from galaxy.web.stack.handlers import ConfiguresHandlers, HANDLER_ASSIGNMENT_METHODS
-from galaxy.web.stack.message import WorkflowSchedulingMessage
+from galaxy.web_stack.handlers import ConfiguresHandlers, HANDLER_ASSIGNMENT_METHODS
+from galaxy.web_stack.message import WorkflowSchedulingMessage
 
 log = logging.getLogger(__name__)
 
@@ -47,7 +47,7 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
         self.handlers = {}
         self.handler_assignment_methods_configured = False
         self.handler_assignment_methods = None
-        self.handler_max_grab = 1
+        self.handler_max_grab = None
         self.default_handler_id = None
 
         self.__plugin_classes = self.__plugins_dict()
@@ -207,7 +207,8 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
                 self.__init_handlers(config_element)
 
                 # Determine the default handler(s)
-                self.default_handler_id = self._get_default(self.app.config, config_element, list(self.handlers.keys()))
+                self.default_handler_id = self._get_default(
+                    self.app.config, config_element, list(self.handlers.keys()), required=False)
             else:
                 plugin_type = config_element_tag
                 plugin_element = config_element
@@ -230,8 +231,9 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
 
     def __init_handlers(self, config_element=None):
         assert not self.__handlers_configured
-        self._init_handler_assignment_methods(config_element)
-        self._init_handlers(config_element)
+        handling_config_dict = ConfiguresHandlers.xml_to_dict(self.app.config, config_element)
+        self._init_handler_assignment_methods(handling_config_dict)
+        self._init_handlers(handling_config_dict)
         if not self.handler_assignment_methods_configured:
             self._set_default_handler_assignment_methods()
         else:
diff --git a/lib/galaxy_ext/metadata/_provided_metadata.py b/lib/galaxy_ext/metadata/_provided_metadata.py
deleted file mode 120000
index 6e81f9dc9f3..00000000000
--- a/lib/galaxy_ext/metadata/_provided_metadata.py
+++ /dev/null
@@ -1 +0,0 @@
-../../galaxy/tools/provided_metadata.py
\ No newline at end of file
diff --git a/lib/galaxy_ext/metadata/set_metadata.py b/lib/galaxy_ext/metadata/set_metadata.py
index a3f7ec9b844..380e3de3336 100644
--- a/lib/galaxy_ext/metadata/set_metadata.py
+++ b/lib/galaxy_ext/metadata/set_metadata.py
@@ -10,212 +10,13 @@ set to the path of the dataset on which metadata is being set
 (output_filename_override could previously be left empty and the path would be
 constructed automatically).
 """
-import json
-import logging
+
 import os
 import sys
 
 # insert *this* galaxy before all others on sys.path
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir)))
 
-from six.moves import cPickle
-from sqlalchemy.orm import clear_mappers
+from galaxy.metadata.set_metadata import set_metadata
 
-import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
-from galaxy.model.custom_types import total_size
-from galaxy.util import stringify_dictionary_keys
-from ._provided_metadata import parse_tool_provided_metadata
-
-# ensure supported version
-assert sys.version_info[:2] >= (2, 7), 'Python version must be at least 2.7, this is: %s' % sys.version
-
-logging.basicConfig()
-log = logging.getLogger(__name__)
-
-galaxy.model.Job()  # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
-
-
-def set_meta_with_tool_provided(dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size):
-    # This method is somewhat odd, in that we set the metadata attributes from tool,
-    # then call set_meta, then set metadata attributes from tool again.
-    # This is intentional due to interplay of overwrite kwd, the fact that some metadata
-    # parameters may rely on the values of others, and that we are accepting the
-    # values provided by the tool as Truth.
-    extension = dataset_instance.extension
-    if extension == "_sniff_":
-        try:
-            from galaxy.datatypes import sniff
-            extension = sniff.handle_uploaded_dataset_file(dataset_instance.dataset.external_filename, datatypes_registry)
-            # We need to both set the extension so it is available to set_meta
-            # and record it in the metadata so it can be reloaded on the server
-            # side and the model updated (see MetadataCollection.{from,to}_JSON_dict)
-            dataset_instance.extension = extension
-            # Set special metadata property that will reload this on server side.
-            setattr(dataset_instance.metadata, "__extension__", extension)
-        except Exception:
-            log.exception("Problem sniffing datatype.")
-
-    for metadata_name, metadata_value in file_dict.get('metadata', {}).items():
-        setattr(dataset_instance.metadata, metadata_name, metadata_value)
-    dataset_instance.datatype.set_meta(dataset_instance, **set_meta_kwds)
-    for metadata_name, metadata_value in file_dict.get('metadata', {}).items():
-        setattr(dataset_instance.metadata, metadata_name, metadata_value)
-
-    if max_metadata_value_size:
-        for k, v in list(dataset_instance.metadata.items()):
-            if total_size(v) > max_metadata_value_size:
-                log.info("Key %s too large for metadata, discarding" % k)
-                dataset_instance.metadata.remove_key(k)
-
-
-def set_metadata():
-    if len(sys.argv) == 1:
-        set_metadata_portable()
-    else:
-        set_metadata_legacy()
-
-
-def set_metadata_portable():
-    import galaxy.model
-    galaxy.model.metadata.MetadataTempFile.tmp_dir = tool_job_working_directory = os.path.abspath(os.getcwd())
-
-    metadata_params_path = os.path.join("metadata", "params.json")
-    try:
-        with open(metadata_params_path, "r") as f:
-            metadata_params = json.load(f)
-    except IOError:
-        raise Exception("Failed to find metadata/params.json from cwd [%s]" % tool_job_working_directory)
-    datatypes_config = metadata_params["datatypes_config"]
-    job_metadata = metadata_params["job_metadata"]
-    max_metadata_value_size = metadata_params.get("max_metadata_value_size") or 0
-    outputs = metadata_params["outputs"]
-
-    datatypes_registry = validate_and_load_datatypes_config(datatypes_config)
-    tool_provided_metadata = load_job_metadata(job_metadata)
-
-    def set_meta(new_dataset_instance, file_dict):
-        set_meta_with_tool_provided(new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)
-
-    for output_name, output_dict in outputs.items():
-        filename_in = os.path.join("metadata/metadata_in_%s" % output_name)
-        filename_kwds = os.path.join("metadata/metadata_kwds_%s" % output_name)
-        filename_out = os.path.join("metadata/metadata_out_%s" % output_name)
-        filename_results_code = os.path.join("metadata/metadata_results_%s" % output_name)
-        override_metadata = os.path.join("metadata/metadata_override_%s" % output_name)
-        dataset_filename_override = output_dict["filename_override"]
-
-        # Same block as below...
-        set_meta_kwds = stringify_dictionary_keys(json.load(open(filename_kwds)))  # load kwds; need to ensure our keywords are not unicode
-        try:
-            dataset = cPickle.load(open(filename_in, 'rb'))  # load DatasetInstance
-            dataset.dataset.external_filename = dataset_filename_override
-            store_by = metadata_params.get("object_store_store_by", "id")
-            extra_files_dir_name = "dataset_%s_files" % getattr(dataset.dataset, store_by)
-            files_path = os.path.abspath(os.path.join(tool_job_working_directory, extra_files_dir_name))
-            dataset.dataset.external_extra_files_path = files_path
-            file_dict = tool_provided_metadata.get_dataset_meta(output_name, dataset.dataset.id)
-            if 'ext' in file_dict:
-                dataset.extension = file_dict['ext']
-            # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
-            override_metadata = json.load(open(override_metadata))
-            for metadata_name, metadata_file_override in override_metadata:
-                if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value(metadata_file_override):
-                    metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON(metadata_file_override)
-                setattr(dataset.metadata, metadata_name, metadata_file_override)
-            set_meta(dataset, file_dict)
-            dataset.metadata.to_JSON_dict(filename_out)  # write out results of set_meta
-            json.dump((True, 'Metadata has been set successfully'), open(filename_results_code, 'wt+'))  # setting metadata has succeeded
-        except Exception as e:
-            json.dump((False, str(e)), open(filename_results_code, 'wt+'))  # setting metadata has failed somehow
-
-    write_job_metadata(tool_job_working_directory, job_metadata, set_meta, tool_provided_metadata)
-
-
-def set_metadata_legacy():
-    import galaxy.model
-    galaxy.model.metadata.MetadataTempFile.tmp_dir = tool_job_working_directory = os.path.abspath(os.getcwd())
-
-    # This is ugly, but to transition from existing jobs without this parameter
-    # to ones with, smoothly, it has to be the last optional parameter and we
-    # have to sniff it.
-    try:
-        max_metadata_value_size = int(sys.argv[-1])
-        sys.argv = sys.argv[:-1]
-    except ValueError:
-        max_metadata_value_size = 0
-        # max_metadata_value_size is unspecified and should be 0
-
-    # Set up datatypes registry
-    datatypes_config = sys.argv.pop(1)
-    datatypes_registry = validate_and_load_datatypes_config(datatypes_config)
-
-    job_metadata = sys.argv.pop(1)
-    tool_provided_metadata = load_job_metadata(job_metadata)
-
-    def set_meta(new_dataset_instance, file_dict):
-        set_meta_with_tool_provided(new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)
-
-    for filenames in sys.argv[1:]:
-        fields = filenames.split(',')
-        filename_in = fields.pop(0)
-        filename_kwds = fields.pop(0)
-        filename_out = fields.pop(0)
-        filename_results_code = fields.pop(0)
-        dataset_filename_override = fields.pop(0)
-        override_metadata = fields.pop(0)
-        set_meta_kwds = stringify_dictionary_keys(json.load(open(filename_kwds)))  # load kwds; need to ensure our keywords are not unicode
-        try:
-            dataset = cPickle.load(open(filename_in, 'rb'))  # load DatasetInstance
-            dataset.dataset.external_filename = dataset_filename_override
-            files_path = os.path.abspath(os.path.join(tool_job_working_directory, "dataset_%s_files" % (dataset.dataset.id)))
-            dataset.dataset.external_extra_files_path = files_path
-            file_dict = tool_provided_metadata.get_dataset_meta(None, dataset.dataset.id)
-            if 'ext' in file_dict:
-                dataset.extension = file_dict['ext']
-            # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
-            override_metadata = json.load(open(override_metadata))
-            for metadata_name, metadata_file_override in override_metadata:
-                if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value(metadata_file_override):
-                    metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON(metadata_file_override)
-                setattr(dataset.metadata, metadata_name, metadata_file_override)
-            set_meta(dataset, file_dict)
-            dataset.metadata.to_JSON_dict(filename_out)  # write out results of set_meta
-            json.dump((True, 'Metadata has been set successfully'), open(filename_results_code, 'wt+'))  # setting metadata has succeeded
-        except Exception as e:
-            json.dump((False, str(e)), open(filename_results_code, 'wt+'))  # setting metadata has failed somehow
-
-    write_job_metadata(tool_job_working_directory, job_metadata, set_meta, tool_provided_metadata)
-
-
-def validate_and_load_datatypes_config(datatypes_config):
-    galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir))
-
-    if not os.path.exists(datatypes_config):
-        print("Metadata setting failed because registry.xml could not be found. You may retry setting metadata.")
-        sys.exit(1)
-    import galaxy.datatypes.registry
-    datatypes_registry = galaxy.datatypes.registry.Registry()
-    datatypes_registry.load_datatypes(root_dir=galaxy_root, config=datatypes_config)
-    galaxy.model.set_datatypes_registry(datatypes_registry)
-    return datatypes_registry
-
-
-def load_job_metadata(job_metadata):
-    return parse_tool_provided_metadata(job_metadata)
-
-
-def write_job_metadata(tool_job_working_directory, job_metadata, set_meta, tool_provided_metadata):
-    for i, file_dict in enumerate(tool_provided_metadata.get_new_datasets_for_metadata_collection(), start=1):
-        filename = file_dict["filename"]
-        new_dataset_filename = os.path.join(tool_job_working_directory, "working", filename)
-        new_dataset = galaxy.model.Dataset(id=-i, external_filename=new_dataset_filename)
-        extra_files = file_dict.get('extra_files', None)
-        if extra_files is not None:
-            new_dataset._extra_files_path = os.path.join(tool_job_working_directory, "working", extra_files)
-        new_dataset.state = new_dataset.states.OK
-        new_dataset_instance = galaxy.model.HistoryDatasetAssociation(id=-i, dataset=new_dataset, extension=file_dict.get('ext', 'data'))
-        set_meta(new_dataset_instance, file_dict)
-        file_dict['metadata'] = json.loads(new_dataset_instance.metadata.to_JSON_dict())  # storing metadata in external form, need to turn back into dict, then later jsonify
-
-    tool_provided_metadata.rewrite()
-    clear_mappers()
+__all__ = ('set_metadata', )
diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py
index 0812a14ab05..e75d0e0930d 100644
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -10,7 +10,7 @@ from six import string_types
 from sqlalchemy import or_
 
 from galaxy import exceptions, util
-from galaxy.tools.deps import views
+from galaxy.tool_util.deps import views
 from tool_shed.galaxy_install.datatypes import custom_datatype_manager
 from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
 from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
index 3cfed4fdce2..a7e6b0f1d76 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
@@ -2,7 +2,7 @@ import logging
 import os
 import tempfile
 
-from galaxy.tools.deps.resolvers import NullDependency
+from galaxy.tool_util.deps.resolvers import NullDependency
 from galaxy.util import listify, url_get
 from tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
 from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
index be1b51994e8..ba664184fab 100644
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -364,10 +364,9 @@ class MatchedRepositoryGrid(grids.Grid):
         if match_tuples:
             for match_tuple in match_tuples:
                 repository_id, changeset_revision = match_tuple
-                clause_list.append("%s=%d and %s='%s'" % (model.RepositoryMetadata.table.c.repository_id,
-                                                          int(repository_id),
-                                                          model.RepositoryMetadata.table.c.changeset_revision,
-                                                          changeset_revision))
+                clause_list.append(and_(
+                    model.RepositoryMetadata.repository_id == int(repository_id),
+                    model.RepositoryMetadata.changeset_revision == changeset_revision))
             return trans.sa_session.query(model.RepositoryMetadata) \
                                    .join(model.Repository) \
                                    .filter(and_(model.Repository.table.c.deleted == false(),
diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py
index 6ab82b82761..7aa5b0007f6 100644
--- a/lib/tool_shed/metadata/metadata_generator.py
+++ b/lib/tool_shed/metadata/metadata_generator.py
@@ -6,9 +6,9 @@ import tempfile
 from sqlalchemy import and_
 
 from galaxy import util
+from galaxy.tool_util.parser.interface import TestCollectionDef
 from galaxy.tools.data_manager.manager import DataManager
 from galaxy.tools.loader_directory import looks_like_a_tool
-from galaxy.tools.parser.interface import TestCollectionDef
 from galaxy.tools.repositories import ValidationContext
 from galaxy.web import url_for
 from tool_shed.repository_types import util as rt_util
diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py
index 609186438d4..c844996de43 100644
--- a/lib/tool_shed/tools/tool_validator.py
+++ b/lib/tool_shed/tools/tool_validator.py
@@ -3,13 +3,13 @@ import logging
 import os
 import tempfile
 
+from galaxy.tool_util.fetcher import ToolLocationFetcher
 from galaxy.tools import (
     create_tool_from_source,
     get_tool_source,
     parameters,
     Tool
 )
-from galaxy.tools.fetcher import ToolLocationFetcher
 from galaxy.tools.parameters import dynamic_options
 from tool_shed.tools.data_table_manager import ShedToolDataTableManager
 from tool_shed.util import (
diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py
index 1268de69015..652d061e695 100644
--- a/lib/tool_shed/util/hg_util.py
+++ b/lib/tool_shed/util/hg_util.py
@@ -44,6 +44,9 @@ def clone_repository(repository_clone_url, repository_file_dir, ctx_rev=None):
     if ctx_rev:
         cmd.extend(['-r', ctx_rev])
     cmd.extend([repository_clone_url, repository_file_dir])
+    # Make sure the destination path actually exists before attempting to clone
+    if not os.path.exists(repository_file_dir):
+        os.makedirs(repository_file_dir)
     try:
         subprocess.check_output(cmd, stderr=subprocess.STDOUT)
         return True, None
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index a2bb858a632..b649f435760 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -8,7 +8,7 @@ import string
 import sqlalchemy.orm.exc
 from sqlalchemy import and_, false, true
 
-import galaxy.tools.deps.requirements
+import galaxy.tool_util.deps.requirements
 from galaxy import util
 from galaxy.util import checkers
 from galaxy.web import url_for
@@ -231,7 +231,7 @@ def get_tool_shed_repo_requirements(app, tool_shed_url, repositories=None, repo_
 
 
 def get_requirements_from_tools(tools):
-    return {tool['id']: galaxy.tools.deps.requirements.ToolRequirements.from_list(tool['requirements']) for tool in tools}
+    return {tool['id']: galaxy.tool_util.deps.requirements.ToolRequirements.from_list(tool['requirements']) for tool in tools}
 
 
 def get_requirements_from_repository(repository):
diff --git a/packages/build_scripts/commit_version.py b/packages/build_scripts/commit_version.py
new file mode 100644
index 00000000000..93a001f4886
--- /dev/null
+++ b/packages/build_scripts/commit_version.py
@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+# Modify version...
+import datetime
+import os
+import re
+import subprocess
+import sys
+
+
+DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
+PROJECT_DIRECTORY = os.getcwd()
+PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
+PROJECT_MODULE_FILENAME = "project_galaxy_%s.py" % PROJECT_DIRECTORY_NAME
+PROJECT_NAME = PROJECT_DIRECTORY_NAME.replace("_", "-")
+
+
+def main(argv):
+    source_dir = argv[1]
+    version = argv[2]
+    mod_path = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
+    if not DEV_RELEASE:
+        history_path = os.path.join(PROJECT_DIRECTORY, "HISTORY.rst")
+        history = open(history_path, "r").read()
+        today = datetime.datetime.today()
+        today_str = today.strftime('%Y-%m-%d')
+        history = history.replace(".dev0", " (%s)" % today_str)
+        open(history_path, "w").write(history)
+        mod = open(mod_path, "r").read()
+        mod = re.sub(r"__version__ = '[\d\.]*\.dev0'",
+                    "__version__ = '%s'" % version,
+                    mod)
+        mod = open(mod_path, "w").write(mod)
+    tag = "galaxy-%s-%s" % (PROJECT_NAME, version)
+    shell(["git", "commit", "-m", "Version %s of %s (tag %s)." % (version, PROJECT_NAME, tag),
+           "HISTORY.rst", mod_path])
+    shell(["git", "tag", tag])
+
+
+def shell(cmds, **kwds):
+    p = subprocess.Popen(cmds, **kwds)
+    return p.wait()
+
+
+if __name__ == "__main__":
+    main(sys.argv)
diff --git a/packages/build_scripts/new_version.py b/packages/build_scripts/new_version.py
new file mode 100644
index 00000000000..7de8a8c8ef7
--- /dev/null
+++ b/packages/build_scripts/new_version.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+# Modify version...
+import os
+import re
+import subprocess
+import sys
+from distutils.version import StrictVersion
+
+
+DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
+PROJECT_DIRECTORY = os.getcwd()
+PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
+PROJECT_MODULE_FILENAME = "project_galaxy_%s.py" % PROJECT_DIRECTORY_NAME
+PROJECT_NAME = PROJECT_DIRECTORY_NAME.replace("_", "-")
+
+
+def main(argv):
+    source_dir = argv[1]
+    version = argv[2]
+    if not DEV_RELEASE:
+        old_version = StrictVersion(version)
+        old_version_tuple = old_version.version
+        new_version_tuple = list(old_version_tuple)
+        new_version_tuple[1] = old_version_tuple[1] + 1
+        new_version_tuple[2] = 0
+        new_version = ".".join(map(str, new_version_tuple))
+        new_dev_version = 0
+    else:
+        dev_version = re.compile(r'dev([\d]+)').search(version).group(1)
+        new_dev_version = int(dev_version) + 1
+        new_version = version.replace("dev%s" % dev_version, "dev%s" % new_dev_version)
+
+    history_path = os.path.join(PROJECT_DIRECTORY, "HISTORY.rst")
+    if not DEV_RELEASE:
+        history = open(history_path, "r").read()
+
+        def extend(from_str, line):
+            from_str += "\n"
+            return history.replace(from_str, from_str + line + "\n")
+
+        history = extend(".. to_doc", """
+    ---------------------
+    %s.dev0
+    ---------------------
+
+""" % new_version)
+        open(history_path, "w").write(history)
+
+    mod_path = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
+    mod = open(mod_path, "r").read()
+    if not DEV_RELEASE:
+        mod = re.sub(r"__version__ = '[\d\.]+'",
+                    "__version__ = '%s.dev0'" % new_version,
+                    mod, 1)
+    else:
+        mod = re.sub("dev%s" % dev_version,
+                    "dev%s" % new_dev_version,
+                    mod, 1)
+    mod = open(mod_path, "w").write(mod)
+    shell(["git", "commit", "-m", "Starting work on %s %s" % (PROJECT_NAME, new_version),
+           "HISTORY.rst", mod_path])
+
+
+def shell(cmds, **kwds):
+    p = subprocess.Popen(cmds, **kwds)
+    return p.wait()
+
+
+if __name__ == "__main__":
+    main(sys.argv)
diff --git a/packages/build_scripts/print_version_for_release.py b/packages/build_scripts/print_version_for_release.py
new file mode 100644
index 00000000000..7fa53f94b53
--- /dev/null
+++ b/packages/build_scripts/print_version_for_release.py
@@ -0,0 +1,27 @@
+from __future__ import print_function
+
+import ast
+import os
+import re
+import sys
+from distutils.version import LooseVersion
+
+DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
+PROJECT_DIRECTORY = os.getcwd()
+PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
+PROJECT_MODULE_FILENAME = "project_galaxy_%s.py" % PROJECT_DIRECTORY_NAME
+
+source_dir = sys.argv[1]
+PROJECT_MODULE_PATH = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+with open(PROJECT_MODULE_PATH, 'rb') as f:
+    version = str(ast.literal_eval(_version_re.search(
+        f.read().decode('utf-8')).group(1)))
+
+if not DEV_RELEASE:
+    # Strip .devN
+    version_tuple = LooseVersion(version).version[0:3]
+    print(".".join(map(str, version_tuple)))
+else:
+    print(version)
diff --git a/packages/containers/HISTORY.rst b/packages/containers/HISTORY.rst
new file mode 100644
index 00000000000..ec2f0e746e9
--- /dev/null
+++ b/packages/containers/HISTORY.rst
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.9.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/containers/LICENSE b/packages/containers/LICENSE
new file mode 120000
index 00000000000..1ef648f64b3
--- /dev/null
+++ b/packages/containers/LICENSE
@@ -0,0 +1 @@
+../../LICENSE.txt
\ No newline at end of file
diff --git a/packages/containers/MANIFEST.in b/packages/containers/MANIFEST.in
new file mode 100644
index 00000000000..c74cefe0942
--- /dev/null
+++ b/packages/containers/MANIFEST.in
@@ -0,0 +1 @@
+include *.rst LICENSE
diff --git a/packages/containers/Makefile b/packages/containers/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/containers/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/containers/README.rst b/packages/containers/README.rst
new file mode 100644
index 00000000000..ed360aeef60
--- /dev/null
+++ b/packages/containers/README.rst
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-containers.svg
+   :target: https://pypi.python.org/pypi/galaxy-containers/
+
+
+Overview
+--------
+
+The Galaxy_ containers module - interfaces for modeling and interacting with container backends (docker and docker swarm currently).
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
diff --git a/packages/containers/dev-requirements.txt b/packages/containers/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/containers/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/containers/galaxy/__init__.py b/packages/containers/galaxy/__init__.py
new file mode 100644
index 00000000000..69e3be50dac
--- /dev/null
+++ b/packages/containers/galaxy/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/packages/containers/galaxy/containers b/packages/containers/galaxy/containers
new file mode 120000
index 00000000000..bc2353d5e12
--- /dev/null
+++ b/packages/containers/galaxy/containers
@@ -0,0 +1 @@
+../../../lib/galaxy/containers
\ No newline at end of file
diff --git a/packages/containers/galaxy/project_galaxy_containers.py b/packages/containers/galaxy/project_galaxy_containers.py
new file mode 100644
index 00000000000..6442c8261bb
--- /dev/null
+++ b/packages/containers/galaxy/project_galaxy_containers.py
@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev0'
+
+PROJECT_NAME = "galaxy-containers"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Container Modeling and Interaction Abstractions'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
diff --git a/packages/containers/requirements.txt b/packages/containers/requirements.txt
new file mode 100644
index 00000000000..3a4655d7abd
--- /dev/null
+++ b/packages/containers/requirements.txt
@@ -0,0 +1,3 @@
+galaxy-util
+requests
+
diff --git a/packages/containers/scripts b/packages/containers/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/containers/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/containers/setup.cfg b/packages/containers/setup.cfg
new file mode 120000
index 00000000000..eb7cf09393f
--- /dev/null
+++ b/packages/containers/setup.cfg
@@ -0,0 +1 @@
+../../setup.cfg
\ No newline at end of file
diff --git a/packages/containers/setup.py b/packages/containers/setup.py
new file mode 100644
index 00000000000..4d4fb9caec1
--- /dev/null
+++ b/packages/containers/setup.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import ast
+import os
+import re
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+SOURCE_DIR = "galaxy"
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+with open('%s/project_galaxy_containers.py' % SOURCE_DIR, 'rb') as f:
+    init_contents = f.read().decode('utf-8')
+
+    def get_var(var_name):
+        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        match = pattern.search(init_contents).group(1)
+        return str(ast.literal_eval(match))
+
+    version = get_var("__version__")
+    PROJECT_NAME = get_var("PROJECT_NAME")
+    PROJECT_URL = get_var("PROJECT_URL")
+    PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
+    PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.containers',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+    ],
+}
+PACKAGE_DIR = {
+    SOURCE_DIR: SOURCE_DIR,
+}
+
+readme = open('README.rst').read()
+history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+
+if os.path.exists("requirements.txt"):
+    requirements = open("requirements.txt").read().split("\n")
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+
+
+test_requirements = [
+    # TODO: put package test requirements here
+]
+
+
+setup(
+    name=PROJECT_NAME,
+    version=version,
+    description=PROJECT_DESCRIPTION,
+    long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
+    author=PROJECT_AUTHOR,
+    author_email=PROJECT_EMAIL,
+    url=PROJECT_URL,
+    packages=PACKAGES,
+    entry_points=ENTRY_POINTS,
+    package_data=PACKAGE_DATA,
+    package_dir=PACKAGE_DIR,
+    include_package_data=True,
+    install_requires=requirements,
+    extras_require={
+        'docker': ['docker'],
+    },
+    license="AFL",
+    zip_safe=False,
+    keywords='galaxy',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'Environment :: Console',
+        'License :: OSI Approved :: Academic Free License (AFL)',
+        'Operating System :: POSIX',
+        'Topic :: Software Development',
+        'Topic :: Software Development :: Code Generators',
+        'Topic :: Software Development :: Testing',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)
diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
index c49739afaf3..ec2f0e746e9 100644
--- a/packages/data/HISTORY.rst
+++ b/packages/data/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.5.0.dev0
+19.9.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.05 release cycle.
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/data/Makefile b/packages/data/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/data/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/data/README.rst b/packages/data/README.rst
index 962fa16e2ea..4deccf230e9 100644
--- a/packages/data/README.rst
+++ b/packages/data/README.rst
@@ -1,6 +1,6 @@
 
-.. image:: https://badge.fury.io/py/galaxy-datatypes.svg
-   :target: https://pypi.python.org/pypi/galaxy-datatypes/
+.. image:: https://badge.fury.io/py/galaxy-data.svg
+   :target: https://pypi.python.org/pypi/galaxy-data/
 
 
 Overview
diff --git a/packages/data/dev-requirements.txt b/packages/data/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/data/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py
index 2dc2d71d64d..b7c780d82ab 100644
--- a/packages/data/galaxy/project_galaxy_data.py
+++ b/packages/data/galaxy/project_galaxy_data.py
@@ -1,11 +1,12 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.5.0.dev0'
+__version__ = '19.9.0.dev1'
 
 PROJECT_NAME = "galaxy-data"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
 PROJECT_EMAIL = 'jmchilton@gmail.com'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
diff --git a/packages/data/requirements.txt b/packages/data/requirements.txt
index 0c13610d96a..f2b5c80f06e 100644
--- a/packages/data/requirements.txt
+++ b/packages/data/requirements.txt
@@ -1,7 +1,7 @@
 galaxy-objectstore
 galaxy-util
 bdbag
-bx
+bx-python
 h5py
 isa-rwval
 numpy
diff --git a/packages/data/scripts b/packages/data/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/data/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/data/setup.py b/packages/data/setup.py
index 9d63ce30e1c..38ec5a74e13 100644
--- a/packages/data/setup.py
+++ b/packages/data/setup.py
@@ -26,13 +26,14 @@ with open('%s/project_galaxy_data.py' % SOURCE_DIR, 'rb') as f:
     PROJECT_URL = get_var("PROJECT_URL")
     PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
     PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
 
 TEST_DIR = 'tests'
-PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
 PACKAGES = [
     'galaxy',
     'galaxy.datatypes',
     'galaxy.datatypes.dataproviders',
+    'galaxy.datatypes.display_applications',
     'galaxy.datatypes.util',
     'galaxy.datatypes.test',
     'galaxy.model',
@@ -77,6 +78,7 @@ setup(
     version=version,
     description=PROJECT_DESCRIPTION,
     long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
     author=PROJECT_AUTHOR,
     author_email=PROJECT_EMAIL,
     url=PROJECT_URL,
@@ -101,7 +103,6 @@ setup(
         'Natural Language :: English',
         "Programming Language :: Python :: 2",
         'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
diff --git a/packages/data/tests/unittest_utils b/packages/data/tests/unittest_utils
deleted file mode 120000
index 6b6233367e6..00000000000
--- a/packages/data/tests/unittest_utils
+++ /dev/null
@@ -1 +0,0 @@
-../../../test/unit/unittest_utils
\ No newline at end of file
diff --git a/packages/data/tests/unittest_utils/__init__.py b/packages/data/tests/unittest_utils/__init__.py
new file mode 120000
index 00000000000..2115ad35783
--- /dev/null
+++ b/packages/data/tests/unittest_utils/__init__.py
@@ -0,0 +1 @@
+../../test/unit/unittest_utils/__init__.py
\ No newline at end of file
diff --git a/packages/data/tests/unittest_utils/tempfilecache.py b/packages/data/tests/unittest_utils/tempfilecache.py
new file mode 120000
index 00000000000..93fb83f1df7
--- /dev/null
+++ b/packages/data/tests/unittest_utils/tempfilecache.py
@@ -0,0 +1 @@
+../../test/unit/unittest_utils/tempfilecache.py
\ No newline at end of file
diff --git a/packages/data/tests/unittest_utils/utility.py b/packages/data/tests/unittest_utils/utility.py
new file mode 120000
index 00000000000..54dd4ca7a3b
--- /dev/null
+++ b/packages/data/tests/unittest_utils/utility.py
@@ -0,0 +1 @@
+../../test/unit/unittest_utils/utility.py
\ No newline at end of file
diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
new file mode 100644
index 00000000000..ec2f0e746e9
--- /dev/null
+++ b/packages/job_execution/HISTORY.rst
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.9.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/job_execution/LICENSE b/packages/job_execution/LICENSE
new file mode 120000
index 00000000000..1ef648f64b3
--- /dev/null
+++ b/packages/job_execution/LICENSE
@@ -0,0 +1 @@
+../../LICENSE.txt
\ No newline at end of file
diff --git a/packages/job_execution/MANIFEST.in b/packages/job_execution/MANIFEST.in
new file mode 100644
index 00000000000..2bf148a5764
--- /dev/null
+++ b/packages/job_execution/MANIFEST.in
@@ -0,0 +1,2 @@
+include *.rst LICENSE
+
diff --git a/packages/job_execution/Makefile b/packages/job_execution/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/job_execution/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/job_execution/README.rst b/packages/job_execution/README.rst
new file mode 100644
index 00000000000..3a7574eab70
--- /dev/null
+++ b/packages/job_execution/README.rst
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-job-execution.svg
+   :target: https://pypi.python.org/pypi/galaxy-job-execution/
+
+
+Overview
+--------
+
+The Galaxy_ job execution runtime module.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
diff --git a/packages/job_execution/dev-requirements.txt b/packages/job_execution/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/job_execution/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/job_execution/galaxy/__init__.py b/packages/job_execution/galaxy/__init__.py
new file mode 100644
index 00000000000..69e3be50dac
--- /dev/null
+++ b/packages/job_execution/galaxy/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/packages/job_execution/galaxy/job_execution b/packages/job_execution/galaxy/job_execution
new file mode 120000
index 00000000000..4ef157cced2
--- /dev/null
+++ b/packages/job_execution/galaxy/job_execution
@@ -0,0 +1 @@
+../../../lib/galaxy/job_execution
\ No newline at end of file
diff --git a/packages/job_execution/galaxy/metadata b/packages/job_execution/galaxy/metadata
new file mode 120000
index 00000000000..668ce86f349
--- /dev/null
+++ b/packages/job_execution/galaxy/metadata
@@ -0,0 +1 @@
+../../../lib/galaxy/metadata
\ No newline at end of file
diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py
new file mode 100644
index 00000000000..a30f915133d
--- /dev/null
+++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py
@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev0'
+
+PROJECT_NAME = "galaxy-job-execution"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Job Execution Runtime Utilities'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
diff --git a/packages/job_execution/requirements.txt b/packages/job_execution/requirements.txt
new file mode 100644
index 00000000000..7dcf8f4def7
--- /dev/null
+++ b/packages/job_execution/requirements.txt
@@ -0,0 +1 @@
+galaxy-data
diff --git a/packages/job_execution/scripts b/packages/job_execution/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/job_execution/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg
new file mode 120000
index 00000000000..eb7cf09393f
--- /dev/null
+++ b/packages/job_execution/setup.cfg
@@ -0,0 +1 @@
+../../setup.cfg
\ No newline at end of file
diff --git a/packages/job_execution/setup.py b/packages/job_execution/setup.py
new file mode 100644
index 00000000000..e0d5cb5c879
--- /dev/null
+++ b/packages/job_execution/setup.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import ast
+import os
+import re
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+SOURCE_DIR = "galaxy"
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+with open('%s/project_galaxy_job_execution.py' % SOURCE_DIR, 'rb') as f:
+    init_contents = f.read().decode('utf-8')
+
+    def get_var(var_name):
+        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        match = pattern.search(init_contents).group(1)
+        return str(ast.literal_eval(match))
+
+    version = get_var("__version__")
+    PROJECT_NAME = get_var("PROJECT_NAME")
+    PROJECT_URL = get_var("PROJECT_URL")
+    PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
+    PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.job_execution',
+    'galaxy.metadata',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+        galaxy-set-metadata=galaxy.metadata.set_metadata:set_metadata
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+    ],
+}
+PACKAGE_DIR = {
+    SOURCE_DIR: SOURCE_DIR,
+}
+
+readme = open('README.rst').read()
+history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+
+if os.path.exists("requirements.txt"):
+    requirements = open("requirements.txt").read().split("\n")
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+
+
+test_requirements = [
+    # TODO: put package test requirements here
+]
+
+
+setup(
+    name=PROJECT_NAME,
+    version=version,
+    description=PROJECT_DESCRIPTION,
+    long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
+    author=PROJECT_AUTHOR,
+    author_email=PROJECT_EMAIL,
+    url=PROJECT_URL,
+    packages=PACKAGES,
+    entry_points=ENTRY_POINTS,
+    package_data=PACKAGE_DATA,
+    package_dir=PACKAGE_DIR,
+    include_package_data=True,
+    install_requires=requirements,
+    extras_require={},
+    license="AFL",
+    zip_safe=False,
+    keywords='galaxy',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'Environment :: Console',
+        'License :: OSI Approved :: Academic Free License (AFL)',
+        'Operating System :: POSIX',
+        'Topic :: Software Development',
+        'Topic :: Software Development :: Code Generators',
+        'Topic :: Software Development :: Testing',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)
diff --git a/packages/job_execution/tests/test_datasets.py b/packages/job_execution/tests/test_datasets.py
new file mode 120000
index 00000000000..8b6edf2669d
--- /dev/null
+++ b/packages/job_execution/tests/test_datasets.py
@@ -0,0 +1 @@
+../../../test/unit/jobs/test_datasets.py
\ No newline at end of file
diff --git a/packages/job_execution/tests/test_metadata.py b/packages/job_execution/tests/test_metadata.py
new file mode 120000
index 00000000000..9aa7e9cb83b
--- /dev/null
+++ b/packages/job_execution/tests/test_metadata.py
@@ -0,0 +1 @@
+../../../test/unit/tools/test_metadata.py
\ No newline at end of file
diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
new file mode 100644
index 00000000000..ec2f0e746e9
--- /dev/null
+++ b/packages/job_metrics/HISTORY.rst
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.9.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/job_metrics/LICENSE b/packages/job_metrics/LICENSE
new file mode 120000
index 00000000000..1ef648f64b3
--- /dev/null
+++ b/packages/job_metrics/LICENSE
@@ -0,0 +1 @@
+../../LICENSE.txt
\ No newline at end of file
diff --git a/packages/job_metrics/MANIFEST.in b/packages/job_metrics/MANIFEST.in
new file mode 100644
index 00000000000..c74cefe0942
--- /dev/null
+++ b/packages/job_metrics/MANIFEST.in
@@ -0,0 +1 @@
+include *.rst LICENSE
diff --git a/packages/job_metrics/Makefile b/packages/job_metrics/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/job_metrics/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/job_metrics/README.rst b/packages/job_metrics/README.rst
new file mode 100644
index 00000000000..65a810c4c24
--- /dev/null
+++ b/packages/job_metrics/README.rst
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-job-metrics.svg
+   :target: https://pypi.python.org/pypi/galaxy-job-metrics/
+
+
+Overview
+--------
+
+The Galaxy_ job metrics framework and default plugins.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
diff --git a/packages/job_metrics/dev-requirements.txt b/packages/job_metrics/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/job_metrics/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/job_metrics/galaxy/__init__.py b/packages/job_metrics/galaxy/__init__.py
new file mode 100644
index 00000000000..69e3be50dac
--- /dev/null
+++ b/packages/job_metrics/galaxy/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/packages/job_metrics/galaxy/job_metrics b/packages/job_metrics/galaxy/job_metrics
new file mode 120000
index 00000000000..a3831d64328
--- /dev/null
+++ b/packages/job_metrics/galaxy/job_metrics
@@ -0,0 +1 @@
+../../../lib/galaxy/job_metrics/
\ No newline at end of file
diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
new file mode 100644
index 00000000000..5c5c5411ab8
--- /dev/null
+++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev2'
+
+PROJECT_NAME = "galaxy-job-metrics"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Job Metrics'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
diff --git a/packages/job_metrics/requirements.txt b/packages/job_metrics/requirements.txt
new file mode 100644
index 00000000000..623c4906bb2
--- /dev/null
+++ b/packages/job_metrics/requirements.txt
@@ -0,0 +1 @@
+galaxy-util
diff --git a/packages/job_metrics/scripts b/packages/job_metrics/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/job_metrics/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg
new file mode 120000
index 00000000000..eb7cf09393f
--- /dev/null
+++ b/packages/job_metrics/setup.cfg
@@ -0,0 +1 @@
+../../setup.cfg
\ No newline at end of file
diff --git a/packages/job_metrics/setup.py b/packages/job_metrics/setup.py
new file mode 100644
index 00000000000..8970bc45aec
--- /dev/null
+++ b/packages/job_metrics/setup.py
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import ast
+import os
+import re
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+SOURCE_DIR = "galaxy"
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+with open('%s/project_galaxy_job_metrics.py' % SOURCE_DIR, 'rb') as f:
+    init_contents = f.read().decode('utf-8')
+
+    def get_var(var_name):
+        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        match = pattern.search(init_contents).group(1)
+        return str(ast.literal_eval(match))
+
+    version = get_var("__version__")
+    PROJECT_NAME = get_var("PROJECT_NAME")
+    PROJECT_URL = get_var("PROJECT_URL")
+    PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
+    PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.job_metrics',
+    'galaxy.job_metrics.instrumenters',
+    'galaxy.job_metrics.collectl',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+    ],
+}
+PACKAGE_DIR = {
+    SOURCE_DIR: SOURCE_DIR,
+}
+
+readme = open('README.rst').read()
+history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+
+if os.path.exists("requirements.txt"):
+    requirements = open("requirements.txt").read().split("\n")
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+
+
+test_requirements = [
+    # TODO: put package test requirements here
+]
+
+
+setup(
+    name=PROJECT_NAME,
+    version=version,
+    description=PROJECT_DESCRIPTION,
+    long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
+    author=PROJECT_AUTHOR,
+    author_email=PROJECT_EMAIL,
+    url=PROJECT_URL,
+    packages=PACKAGES,
+    entry_points=ENTRY_POINTS,
+    package_data=PACKAGE_DATA,
+    package_dir=PACKAGE_DIR,
+    include_package_data=True,
+    install_requires=requirements,
+    license="AFL",
+    zip_safe=False,
+    keywords='galaxy',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'Environment :: Console',
+        'License :: OSI Approved :: Academic Free License (AFL)',
+        'Operating System :: POSIX',
+        'Topic :: Software Development',
+        'Topic :: Software Development :: Code Generators',
+        'Topic :: Software Development :: Testing',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)
diff --git a/packages/job_metrics/tests/test_job_metrics.py b/packages/job_metrics/tests/test_job_metrics.py
new file mode 120000
index 00000000000..b3b70cbbe69
--- /dev/null
+++ b/packages/job_metrics/tests/test_job_metrics.py
@@ -0,0 +1 @@
+../../../test/unit/jobs/test_job_metrics.py
\ No newline at end of file
diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
index c49739afaf3..ec2f0e746e9 100644
--- a/packages/objectstore/HISTORY.rst
+++ b/packages/objectstore/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.5.0.dev0
+19.9.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.05 release cycle.
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/objectstore/Makefile b/packages/objectstore/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/objectstore/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/objectstore/dev-requirements.txt b/packages/objectstore/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/objectstore/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py
index f64be773ba9..825abc23062 100644
--- a/packages/objectstore/galaxy/project_galaxy_objectstore.py
+++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py
@@ -1,11 +1,12 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.5.0.dev0'
+__version__ = '19.9.0.dev2'
 
 PROJECT_NAME = "galaxy-objectstore"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Objectstore Framework and Plugins'
 PROJECT_EMAIL = 'jmchilton@gmail.com'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
diff --git a/packages/objectstore/scripts b/packages/objectstore/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/objectstore/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/objectstore/setup.py b/packages/objectstore/setup.py
index 3b3d519ec0b..444e4337388 100644
--- a/packages/objectstore/setup.py
+++ b/packages/objectstore/setup.py
@@ -26,9 +26,9 @@ with open('%s/project_galaxy_objectstore.py' % SOURCE_DIR, 'rb') as f:
     PROJECT_URL = get_var("PROJECT_URL")
     PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
     PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
 
 TEST_DIR = 'tests'
-PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
 PACKAGES = [
     'galaxy',
     'galaxy.objectstore',
@@ -65,6 +65,7 @@ setup(
     version=version,
     description=PROJECT_DESCRIPTION,
     long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
     author=PROJECT_AUTHOR,
     author_email=PROJECT_EMAIL,
     url=PROJECT_URL,
@@ -89,7 +90,6 @@ setup(
         'Natural Language :: English',
         "Programming Language :: Python :: 2",
         'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
diff --git a/packages/package-dev-requirements.txt b/packages/package-dev-requirements.txt
new file mode 100644
index 00000000000..034ad598066
--- /dev/null
+++ b/packages/package-dev-requirements.txt
@@ -0,0 +1,9 @@
+# For testing
+pytest
+
+# For dev
+sphinx
+
+# For release
+wheel
+twine
diff --git a/packages/package.Makefile b/packages/package.Makefile
new file mode 100644
index 00000000000..89536ddea59
--- /dev/null
+++ b/packages/package.Makefile
@@ -0,0 +1,89 @@
+# Location of virtualenv used for development.
+VENV?=.venv
+# Open resource on Mac OS X or Linux
+OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
+# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
+IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
+UPSTREAM?=galaxyproject
+SOURCE_DIR?=galaxy
+BUILD_SCRIPTS_DIR=scripts
+DEV_RELEASE?=0
+VERSION?=$(shell DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/print_version_for_release.py $(SOURCE_DIR) $(DEV_RELEASE))
+PROJECT_NAME?="galaxy-$(shell basename $(CURDIR))"
+PROJECT_NAME:=$(subst _,-,$(PROJECT_NAME))
+TEST_DIR?=test
+TESTS?=$(SOURCE_DIR) $(TEST_DIR)
+
+.PHONY: clean-pyc clean-build docs clean
+
+help:
+	@echo "clean - remove all build, test, coverage and Python artifacts"
+	@echo "clean-build - remove build artifacts"
+	@echo "clean-pyc - remove Python file artifacts"
+	@echo "clean-test - remove test and coverage artifacts"
+	@echo "setup-venv - setup a development virutalenv in current directory."
+	@echo "lint-dist - twine check dist results, including validating README content"
+	@echo "dist - package project for PyPI distribution"
+
+clean: clean-build clean-pyc clean-tests
+
+clean-build:
+	rm -fr build/
+	rm -fr dist/
+	rm -fr galaxy_*.egg-info
+
+clean-pyc:
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-tests:
+	rm -fr .tox/
+
+setup-venv:
+	if [ ! -d $(VENV) ]; then virtualenv $(VENV); exit; fi;
+	$(IN_VENV) pip install -r requirements.txt && pip install -r dev-requirements.txt
+
+test:
+	$(IN_VENV) pytest $(TESTS)
+
+develop:
+	python setup.py develop
+
+dist: clean
+	$(IN_VENV) python setup.py sdist bdist_wheel
+	ls -l dist
+
+lint-dist: dist
+	$(IN_VENV) twine check dist/*
+
+_release-test-artifacts:
+	$(IN_VENV) twine upload -r test dist/*
+	$(OPEN_RESOURCE) https://testpypi.python.org/pypi/$(PROJECT_NAME)
+
+release-test-artifacts: lint-dist _release-test-artifacts
+
+_release-artifacts:
+	@while [ -z "$$CONTINUE" ]; do \
+	  read -r -p "Have you executed release-test and reviewed results? [y/N]: " CONTINUE; \
+	done ; \
+	[ $$CONTINUE = "y" ] || [ $$CONTINUE = "Y" ] || (echo "Exiting."; exit 1;)
+	@echo "Releasing"
+	$(IN_VENV) twine upload dist/*
+
+release-artifacts: release-test-artifacts _release-artifacts
+
+commit-version:
+	$(IN_VENV) DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/commit_version.py $(SOURCE_DIR) $(VERSION)
+
+new-version:
+	$(IN_VENV) DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/new_version.py $(SOURCE_DIR) $(VERSION)
+
+release-local: commit-version release-artifacts new-version
+
+push-release:
+	git push $(UPSTREAM) dev
+	git push upstream $(UPSTREAM)/tags/galaxy-$(PROJECT_NAME)-$(VERSION)
+
+release: release-local push-release
diff --git a/packages/test.sh b/packages/test.sh
new file mode 100755
index 00000000000..aacfab67a3e
--- /dev/null
+++ b/packages/test.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+set -e
+
+# Change to packages directory.
+cd "$(dirname "$0")"
+
+# Use a throw-away virtualenv
+TEST_PYTHON=${TEST_PYTHON:-"python"}
+TEST_ENV_DIR=${TEST_ENV_DIR:-$(mktemp -d -t gxpkgtestenvXXXXXX)}
+
+virtualenv -p "$TEST_PYTHON" "$TEST_ENV_DIR"
+. "${TEST_ENV_DIR}/bin/activate"
+pip install pytest
+
+# ensure ordered by dependency dag
+PACKAGE_DIRS=(
+    util
+    objectstore
+    job_metrics
+    containers
+    tool_util
+    data
+    job_execution
+)
+# containers has no tests, tool_util not yet working 100%,
+# data has many problems quota, tool shed install database, etc..
+RUN_TESTS=(1 1 1 0 0 0 0 1)
+
+for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
+    package_dir=${PACKAGE_DIRS[$i]}
+    run_tests=${RUN_TESTS[$i]}
+
+    cd "$package_dir"
+    pip install -e .
+    if [ "$package_dir" = "util" ]; then
+        pip install -e '.[template,jstree]'
+    fi
+
+    if [[ "$run_tests" == "1" ]]; then
+        pytest --doctest-modules galaxy tests
+    fi
+    cd ..
+done
diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
new file mode 100644
index 00000000000..ec2f0e746e9
--- /dev/null
+++ b/packages/tool_util/HISTORY.rst
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.9.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/tool_util/LICENSE b/packages/tool_util/LICENSE
new file mode 120000
index 00000000000..1ef648f64b3
--- /dev/null
+++ b/packages/tool_util/LICENSE
@@ -0,0 +1 @@
+../../LICENSE.txt
\ No newline at end of file
diff --git a/packages/tool_util/MANIFEST.in b/packages/tool_util/MANIFEST.in
new file mode 100644
index 00000000000..baf7e4b1ce2
--- /dev/null
+++ b/packages/tool_util/MANIFEST.in
@@ -0,0 +1,4 @@
+include *.rst LICENSE
+include galaxy/tool_util/deps/mulled/invfile.lua
+include galaxy/tool_util/deps/resolvers/default_conda_mapping.yml
+include galaxy/tool_util/xsd/*
diff --git a/packages/tool_util/Makefile b/packages/tool_util/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/tool_util/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/tool_util/README.rst b/packages/tool_util/README.rst
new file mode 100644
index 00000000000..74c8c0f1f31
--- /dev/null
+++ b/packages/tool_util/README.rst
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-tool-util.svg
+   :target: https://pypi.python.org/pypi/galaxy-tool-util/
+
+
+Overview
+--------
+
+The Galaxy_ tool utilities.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
diff --git a/packages/tool_util/dev-requirements.txt b/packages/tool_util/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/tool_util/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/tool_util/galaxy/__init__.py b/packages/tool_util/galaxy/__init__.py
new file mode 100644
index 00000000000..69e3be50dac
--- /dev/null
+++ b/packages/tool_util/galaxy/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
new file mode 100644
index 00000000000..4f526958884
--- /dev/null
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev2'
+
+PROJECT_NAME = "galaxy-tool-util"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Tool and Tool Dependency Utilities'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
diff --git a/packages/tool_util/galaxy/tool_util b/packages/tool_util/galaxy/tool_util
new file mode 120000
index 00000000000..8997fb7715a
--- /dev/null
+++ b/packages/tool_util/galaxy/tool_util
@@ -0,0 +1 @@
+../../../lib/galaxy/tool_util
\ No newline at end of file
diff --git a/packages/tool_util/requirements.txt b/packages/tool_util/requirements.txt
new file mode 100644
index 00000000000..623c4906bb2
--- /dev/null
+++ b/packages/tool_util/requirements.txt
@@ -0,0 +1 @@
+galaxy-util
diff --git a/packages/tool_util/scripts b/packages/tool_util/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/tool_util/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
new file mode 120000
index 00000000000..eb7cf09393f
--- /dev/null
+++ b/packages/tool_util/setup.cfg
@@ -0,0 +1 @@
+../../setup.cfg
\ No newline at end of file
diff --git a/packages/tool_util/setup.py b/packages/tool_util/setup.py
new file mode 100644
index 00000000000..33bf10b7794
--- /dev/null
+++ b/packages/tool_util/setup.py
@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import ast
+import os
+import re
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+SOURCE_DIR = "galaxy"
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+with open('%s/project_galaxy_tool_util.py' % SOURCE_DIR, 'rb') as f:
+    init_contents = f.read().decode('utf-8')
+
+    def get_var(var_name):
+        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        match = pattern.search(init_contents).group(1)
+        return str(ast.literal_eval(match))
+
+    version = get_var("__version__")
+    PROJECT_NAME = get_var("PROJECT_NAME")
+    PROJECT_URL = get_var("PROJECT_URL")
+    PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
+    PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.tool_util',
+    'galaxy.tool_util.cwl',
+    'galaxy.tool_util.deps',
+    'galaxy.tool_util.deps.container_resolvers',
+    'galaxy.tool_util.deps.mulled',
+    'galaxy.tool_util.deps.resolvers',
+    'galaxy.tool_util.locations',
+    'galaxy.tool_util.parser',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+        mulled-build=galaxy.tool_util.deps.mulled.mulled_build:main
+        mulled-build-channel=galaxy.tool_util.deps.mulled.mulled_build_channel:main
+        mulled-search=galaxy.tool_util.deps.mulled.mulled_search:main
+        mulled-build-tool=galaxy.tool_util.deps.mulled.mulled_build_tool:main
+        mulled-build-files=galaxy.tool_util.deps.mulled.mulled_build_files:main
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+        'tool_util/deps/mulled/invfile.lua',
+        'tool_util/deps/resolvers/default_conda_mapping.yml',
+        'tool_util/xsd/galaxy.xsd',
+    ],
+}
+PACKAGE_DIR = {
+    SOURCE_DIR: SOURCE_DIR,
+}
+
+readme = open('README.rst').read()
+history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+
+if os.path.exists("requirements.txt"):
+    requirements = open("requirements.txt").read().split("\n")
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+
+
+test_requirements = [
+    # TODO: put package test requirements here
+]
+
+
+setup(
+    name=PROJECT_NAME,
+    version=version,
+    description=PROJECT_DESCRIPTION,
+    long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
+    author=PROJECT_AUTHOR,
+    author_email=PROJECT_EMAIL,
+    url=PROJECT_URL,
+    packages=PACKAGES,
+    entry_points=ENTRY_POINTS,
+    package_data=PACKAGE_DATA,
+    package_dir=PACKAGE_DIR,
+    include_package_data=True,
+    install_requires=requirements,
+    license="AFL",
+    zip_safe=False,
+    keywords='galaxy',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'Environment :: Console',
+        'License :: OSI Approved :: Academic Free License (AFL)',
+        'Operating System :: POSIX',
+        'Topic :: Software Development',
+        'Topic :: Software Development :: Code Generators',
+        'Topic :: Software Development :: Testing',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)
diff --git a/packages/tool_util/tests/test_conda_resolution.py b/packages/tool_util/tests/test_conda_resolution.py
new file mode 120000
index 00000000000..645faad4496
--- /dev/null
+++ b/packages/tool_util/tests/test_conda_resolution.py
@@ -0,0 +1 @@
+../../../test/unit/tools/test_conda_resolution.py
\ No newline at end of file
diff --git a/packages/tool_util/tests/test_output_checker.py b/packages/tool_util/tests/test_output_checker.py
new file mode 120000
index 00000000000..2a54b77ca94
--- /dev/null
+++ b/packages/tool_util/tests/test_output_checker.py
@@ -0,0 +1 @@
+../../../test/unit/tools/test_output_checker.py
\ No newline at end of file
diff --git a/packages/tool_util/tests/test_parsing.py b/packages/tool_util/tests/test_parsing.py
new file mode 120000
index 00000000000..b21638588e4
--- /dev/null
+++ b/packages/tool_util/tests/test_parsing.py
@@ -0,0 +1 @@
+../../../test/unit/tools/test_parsing.py
\ No newline at end of file
diff --git a/packages/tool_util/tests/test_tool_deps.py b/packages/tool_util/tests/test_tool_deps.py
new file mode 120000
index 00000000000..34701999330
--- /dev/null
+++ b/packages/tool_util/tests/test_tool_deps.py
@@ -0,0 +1 @@
+../../../test/unit/tools/test_tool_deps.py
\ No newline at end of file
diff --git a/packages/tool_util/tests/test_tool_loader.py b/packages/tool_util/tests/test_tool_loader.py
new file mode 120000
index 00000000000..572b75ae0a5
--- /dev/null
+++ b/packages/tool_util/tests/test_tool_loader.py
@@ -0,0 +1 @@
+../../../test/unit/tools/test_tool_loader.py
\ No newline at end of file
diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst
index c49739afaf3..ec2f0e746e9 100644
--- a/packages/util/HISTORY.rst
+++ b/packages/util/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.5.0.dev0
+19.9.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.05 release cycle.
+* Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/util/Makefile b/packages/util/Makefile
new file mode 120000
index 00000000000..37af8bae5ba
--- /dev/null
+++ b/packages/util/Makefile
@@ -0,0 +1 @@
+../package.Makefile
\ No newline at end of file
diff --git a/packages/util/dev-requirements.txt b/packages/util/dev-requirements.txt
new file mode 120000
index 00000000000..467b90d7a23
--- /dev/null
+++ b/packages/util/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
\ No newline at end of file
diff --git a/packages/util/galaxy/project_galaxy_util.py b/packages/util/galaxy/project_galaxy_util.py
index 770df42ba3d..c5a4d0ce99a 100644
--- a/packages/util/galaxy/project_galaxy_util.py
+++ b/packages/util/galaxy/project_galaxy_util.py
@@ -1,11 +1,12 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.5.0.dev0'
+__version__ = '19.9.0.dev3'
 
 PROJECT_NAME = "galaxy-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
 PROJECT_URL = "https://github.com/galaxyproject/galaxy"
 PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Generic Utilities'
 PROJECT_EMAIL = 'jmchilton@gmail.com'
 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
     PROJECT_USERAME, PROJECT_NAME
diff --git a/packages/util/requirements.txt b/packages/util/requirements.txt
index 3290e4ad496..e15e5db251e 100644
--- a/packages/util/requirements.txt
+++ b/packages/util/requirements.txt
@@ -1,7 +1,6 @@
 bleach
 boltons
 bz2file; python_version < '3.3'
-Cheetah3
 docutils
 markupsafe
 packaging
diff --git a/packages/util/scripts b/packages/util/scripts
new file mode 120000
index 00000000000..9aec9dc5a06
--- /dev/null
+++ b/packages/util/scripts
@@ -0,0 +1 @@
+../build_scripts
\ No newline at end of file
diff --git a/packages/util/setup.py b/packages/util/setup.py
index 212c29cfda4..1227150c7b1 100644
--- a/packages/util/setup.py
+++ b/packages/util/setup.py
@@ -26,11 +26,12 @@ with open('%s/project_galaxy_util.py' % SOURCE_DIR, 'rb') as f:
     PROJECT_URL = get_var("PROJECT_URL")
     PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
     PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
 
 TEST_DIR = 'tests'
-PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
 PACKAGES = [
     'galaxy',
+    'galaxy.exceptions',
     'galaxy.util',
     'galaxy.util.logging',
     'galaxy.util.path',
@@ -69,6 +70,7 @@ setup(
     version=version,
     description=PROJECT_DESCRIPTION,
     long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
     author=PROJECT_AUTHOR,
     author_email=PROJECT_EMAIL,
     url=PROJECT_URL,
@@ -78,6 +80,10 @@ setup(
     package_dir=PACKAGE_DIR,
     include_package_data=True,
     install_requires=requirements,
+    extras_require={
+        'template': ['future', 'Cheetah3'],
+        'jstree': ['dictobj'],
+    },
     license="AFL",
     zip_safe=False,
     keywords='galaxy',
@@ -93,7 +99,6 @@ setup(
         'Natural Language :: English',
         "Programming Language :: Python :: 2",
         'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
diff --git a/run_tests.sh b/run_tests.sh
index 5634c1d7793..1236e8742cc 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -1,7 +1,6 @@
 #!/bin/sh
 
-pwd_dir=$(pwd)
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 rm -f run_functional_tests.log
 
@@ -318,8 +317,8 @@ then
         -e "GALAXY_TEST_DATABASE_TYPE=$db_type" \
         -e "LC_ALL=C" \
         --rm \
-        -v `pwd`:/galaxy \
-        -v `pwd`/test/docker/base/run_test_wrapper.sh:/usr/local/bin/run_test_wrapper.sh $DOCKER_IMAGE "$@"
+        -v "$(pwd)":/galaxy \
+        -v "$(pwd)"/test/docker/base/run_test_wrapper.sh:/usr/local/bin/run_test_wrapper.sh "$DOCKER_IMAGE" "$@"
     exit $?
 fi
 
@@ -362,6 +361,8 @@ do
           fi
           ;;
       -a|-api|--api)
+          GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE="True"  # Run these tests with a non-trivial object store.
+          export GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE
           GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
           test_script="pytest"
           report_file="./run_api_tests.html"
@@ -372,7 +373,6 @@ do
               api_script="./test/api"
               shift 1
           fi
-          coverage_file="api_coverage.xml"
           ;;
       -selenium|--selenium)
           GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
@@ -410,15 +410,15 @@ do
           shift
           ;;
       --external_url)
-          GALAXY_TEST_EXTERNAL=$2
+          export GALAXY_TEST_EXTERNAL=$2
           shift 2
           ;;
       --external_master_key)
-          GALAXY_CONFIG_MASTER_KEY=$2
+          export GALAXY_CONFIG_MASTER_API_KEY=$2
           shift 2
           ;;
       --external_user_key)
-          GALAXY_TEST_USER_API_KEY=$2
+          export GALAXY_TEST_USER_API_KEY=$2
           shift 2
           ;;
       -f|-framework|--framework)
@@ -426,7 +426,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_framework_tests.html"
-          coverage_file="framework_coverage.xml"
           framework_test=1;
           shift 1
           ;;
@@ -435,7 +434,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_framework_tests.html"
-          coverage_file="main_tools_coverage.xml"
           framework_test=1;
           shift 1
           ;;
@@ -443,7 +441,6 @@ do
           marker="-m data_manager"
           test_script="pytest"
           report_file="run_data_managers_tests.html"
-          coverage_file="data_managers_coverage.xml"
           data_managers_test=1;
           shift 1
           ;;
@@ -452,7 +449,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_migrated_tests.html"
-          coverage_file="migrated_coverage.xml"
           migrated_test=1;
           shift
           ;;
@@ -461,7 +457,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_installed_tests.html"
-          coverage_file="installed_coverage.xml"
           installed_test=1;
           shift
           ;;
@@ -501,7 +496,6 @@ do
           # Must have coverage installed (try `which coverage`) - only valid with --unit
           # for now. Would be great to get this to work with functional tests though.
           coverage_arg="--with-coverage"
-          NOSE_WITH_COVERAGE=true
           shift
           ;;
       --debug)
@@ -513,7 +507,7 @@ do
       -u|-unit|--unit)
           report_file="run_unit_tests.html"
           test_script="pytest"
-          unit_extra='--doctest-modules --ignore lib/galaxy/web/proxy/js/node_modules/ --ignore lib/galaxy/webapps/tool_shed/controllers --ignore lib/galaxy/jobs/runners/chronos.py --ignore lib/galaxy/webapps/tool_shed/model/migrate --ignore lib/galaxy/util/jstree.py'
+          unit_extra='--doctest-modules --ignore lib/galaxy/web/proxy/js/node_modules/ --ignore lib/galaxy/webapps/tool_shed/controllers --ignore lib/galaxy/jobs/runners/chronos.py --ignore lib/galaxy/webapps/tool_shed/model/migrate'
           if [ $# -gt 1 ]; then
               unit_extra="$unit_extra $2"
               shift 2
@@ -521,7 +515,6 @@ do
               unit_extra="$unit_extra lib test/unit"
               shift 1
           fi
-          coverage_file="unit_coverage.xml"
           ;;
       -i|-integration|--integration)
           GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
@@ -533,7 +526,6 @@ do
           else
               integration_extra="./test/integration"
               shift 1
-          coverage_file="integration_coverage.xml"
           fi
           ;;
       --no_cleanup)
@@ -614,7 +606,7 @@ elif [ -n "$toolshed_script" ]; then
 elif [ -n "$api_script" ]; then
     extra_args="$api_script"
 elif [ -n "$section_id" ]; then
-    extra_args=`python tool_list.py $section_id`
+    extra_args=$(python tool_list.py "$section_id")
 elif [ -n "$unit_extra" ]; then
     extra_args="$unit_extra"
 elif [ -n "$integration_extra" ]; then
@@ -643,8 +635,8 @@ else
 fi
 export GALAXY_TEST_TOOL_CONF
 if [ "$test_script" = 'pytest' ]; then
-    if [ "$coverage_arg" = "--with_coverage" ]; then
-        coverage_arg="--cov-report term --cov-report xml:cov-unit.xml --cov=lib"
+    if [ "$coverage_arg" = '--with-coverage' ]; then
+        coverage_arg="--cov-report term --cov=lib"
     fi
     "$test_script" -v --html "$report_file" $coverage_arg  $xunit_args $extra_args "$@"
 else
diff --git a/scripts/api/fetch_to_library.py b/scripts/api/fetch_to_library.py
index 6c497bcb402..7a37701386b 100644
--- a/scripts/api/fetch_to_library.py
+++ b/scripts/api/fetch_to_library.py
@@ -13,7 +13,7 @@ def main():
                         help='file describing data library to fetch')
     args = parser.parse_args()
     with open(args.target, "r") as f:
-        target = yaml.load(f)
+        target = yaml.safe_load(f)
 
     histories_url = args.url + "/api/histories"
     new_history_response = requests.post(histories_url, data={'key': args.api_key})
diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 901c50aeb66..154b4e34de5 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -38,7 +38,7 @@ DEVTEAM = [
     "davebx", "martenson", "jmchilton",
     "tnabtaf", "natefoo", "jgoecks",
     "guerler", "jennaj", "nekrut", "jxtx",
-    "VJalili"
+    "VJalili", "WilliamHolden", "Nerdinacan"
 ]
 
 TEMPLATE = string.Template("""
@@ -143,15 +143,21 @@ Highlights
   Feature description.
 
 
-New Visualisations
+New Visualizations
 ===========================================================
 
+.. visualizations
+
 New Datatypes
 ===========================================================
 
+.. datatypes
+
 Builtin Tool Updates
 ===========================================================
 
+.. tools
+
 Release Notes
 ===========================================================
 
@@ -174,6 +180,9 @@ Schedule
  * Planned Release Date: ${release_date}
 """)
 
+PRS_TEMPLATE = """
+.. github_links
+"""
 
 RELEASE_ISSUE_TEMPLATE = string.Template("""
 
@@ -337,7 +346,7 @@ def do_release(argv):
         release=release_name
     )
     announce_file = _release_file(release_name + "_announce.rst")
-    open(announce_file, "w").write(announce_info.encode("utf-8"))
+    _write_file(announce_file, announce_info)
 
     announce_user_info = ANNOUNCE_USER_TEMPLATE.substitute(
         month_name=month_name,
@@ -345,7 +354,10 @@ def do_release(argv):
         release=release_name
     )
     announce_user_file = _release_file(release_name + "_announce_user.rst")
-    open(announce_user_file, "w").write(announce_user_info.encode("utf-8"))
+    _write_file(announce_user_file, announce_user_info)
+
+    prs_file = _release_file(release_name + "_prs.rst")
+    _write_file(prs_file, PRS_TEMPLATE)
 
     next_version_params = _next_version_params(release_name)
     next_version = next_version_params["version"]
@@ -354,10 +366,9 @@ def do_release(argv):
     next_announce = NEXT_TEMPLATE.substitute(**next_version_params)
     open(next_release_file, "w").write(next_announce.encode("utf-8"))
     releases_index = _release_file("index.rst")
-    releases_index_contents = open(releases_index, "r").read()
+    releases_index_contents = _read_file(releases_index)
     releases_index_contents = releases_index_contents.replace(".. announcements\n", ".. announcements\n   " + next_version + "_announce\n")
-    with open(releases_index, "w") as f:
-        f.write(releases_index_contents)
+    _write_file(releases_index, releases_index_contents)
 
     for pr in _get_prs(release_name):
         # 2015-06-29 18:32:13 2015-04-22 19:11:53 2015-08-12 21:15:45
@@ -365,15 +376,16 @@ def do_release(argv):
             "title": pr.title,
             "number": pr.number,
             "head": pr.head,
+            "labels": _pr_to_labels(pr),
         }
-        main([argv[0], "--release_file", "%s_prs.rst" % release_name, "--request", as_dict, "pr" + str(pr.number)])
+        main([argv[0], "--release_file", "%s.rst" % release_name, "--request", as_dict, "pr" + str(pr.number)])
 
 
 def check_release(argv):
     github = _github_client()
     release_name = argv[2]
     for pr in _get_prs(release_name):
-        _text_target(github, pr)
+        _text_target(github, pr, labels=_pr_to_labels(pr))
 
 
 def check_blocking_prs(argv):
@@ -451,8 +463,16 @@ def _get_prs(release_name, state="closed"):
         user=PROJECT_OWNER,
         repo=PROJECT_NAME,
     )
+    reached_old_prs = False
+
     for page in pull_requests:
+        if reached_old_prs:
+            break
+
         for pr in page:
+            if pr.created_at < datetime.datetime(2016, 11, 1, 0, 0):
+                reached_old_prs = True
+                pass
             merged_at = pr.merged_at
             milestone = pr.milestone
             proper_state = state != "closed" or merged_at
@@ -504,10 +524,15 @@ def main(argv):
     if newest_release is None:
         newest_release = sorted(os.listdir(RELEASES_PATH))[-1]
     history_path = os.path.join(RELEASES_PATH, newest_release)
-    history = open(history_path, "r").read().decode("utf-8")
+    user_announce_path = history_path[0:-len(".rst")] + "_announce_user.rst"
+    prs_path = history_path[0:-len(".rst")] + "_prs.rst"
 
-    def extend(from_str, line, source=history):
-        from_str += "\n"
+    history = _read_file(history_path)
+    user_announce = _read_file(user_announce_path)
+    prs_content = _read_file(prs_path)
+
+    def extend_target(target, line, source=history):
+        from_str = ".. %s\n" % target
         return source.replace(from_str, from_str + line + "\n")
 
     ident = argv[1]
@@ -548,48 +573,72 @@ def main(argv):
         if owner in DEVTEAM:
             owner = None
         text = ".. _Pull Request {0}: {1}/pull/{0}".format(pull_request, PROJECT_URL)
-        history = extend(".. github_links", text)
+        prs_content = extend_target("github_links", text, prs_content)
         if owner:
             to_doc += "\n(thanks to `@%s <https://github.com/%s>`__)." % (
                 owner, owner,
             )
         to_doc += "\n`Pull Request {0}`_".format(pull_request)
         if github:
-            text_target = _text_target(github, pull_request)
+            labels = None
+            if req and 'labels' in req:
+                labels = req['labels']
+            text_target = _text_target(github, pull_request, labels=labels)
     elif ident.startswith("issue"):
         issue = ident[len("issue"):]
         text = ".. _Issue {0}: {1}/issues/{0}".format(issue, PROJECT_URL)
-        history = extend(".. github_links", text)
+        prs_content = extend_target("github_links", text, prs_content)
         to_doc += "`Issue {0}`_".format(issue)
     else:
         short_rev = ident[:7]
         text = ".. _{0}: {1}/commit/{0}".format(short_rev, PROJECT_URL)
-        history = extend(".. github_links", text)
+        prs_content = extend_target("github_links", text, prs_content)
         to_doc += "{0}_".format(short_rev)
 
     to_doc = wrap(to_doc)
-    history = extend(".. %s\n" % text_target, to_doc, history)
-    open(history_path, "w").write(history.encode("utf-8"))
+    history = extend_target(text_target, to_doc, history)
+    if req and 'labels' in req:
+        labels = req['labels']
+        if 'area/datatypes' in labels:
+            user_announce = extend_target("datatypes", to_doc, user_announce)
+        if 'area/visualizations' in labels:
+            user_announce = extend_target("visualizations", to_doc, user_announce)
+        if 'area/tools' in labels:
+            user_announce = extend_target("tools", to_doc, user_announce)
+    _write_file(history_path, history)
+    _write_file(prs_path, prs_content)
+    _write_file(user_announce_path, user_announce)
 
 
-def _text_target(github, pull_request):
-    labels = []
+def _read_file(path):
+    with open(path, "r") as f:
+        return f.read().decode("utf-8")
+
+
+def _write_file(path, contents):
+    with open(path, "w") as f:
+        f.write(contents.encode("utf-8"))
+
+
+def _text_target(github, pull_request, labels=None):
     pr_number = None
     if isinstance(pull_request, string_types):
         pr_number = pull_request
     else:
         pr_number = pull_request.number
 
-    try:
-        labels = github.issues.labels.list_by_issue(int(pr_number), user=PROJECT_OWNER, repo=PROJECT_NAME)
-    except Exception as e:
-        print(e)
+    if labels is None:
+        labels = []
+        try:
+            labels = github.issues.labels.list_by_issue(int(pr_number), user=PROJECT_OWNER, repo=PROJECT_NAME)
+            labels = [l.name.lower() for l in labels]
+        except Exception as e:
+            print(e)
     is_bug = is_enhancement = is_feature = is_minor = is_major = is_merge = is_small_enhancement = False
     if len(labels) == 0:
         print('No labels found for %s' % pr_number)
         return None
-    for label in labels:
-        label_name = label.name.lower()
+    for label_name in labels:
         if label_name == "minor":
             is_minor = True
         elif label_name == "major":
@@ -604,11 +653,14 @@ def _text_target(github, pull_request):
             is_enhancement = True
         elif label_name in ["kind/testing", "kind/refactoring"]:
             is_small_enhancement = True
+        elif label_name == "procedures":
+            # Treat procedures as an implicit enhancement.
+            is_enhancement = True
 
     is_some_kind_of_enhancement = is_enhancement or is_feature or is_small_enhancement
 
     if not(is_bug or is_some_kind_of_enhancement or is_minor or is_merge):
-        print("No kind/ or minor or merge label found for %s" % _pr_to_str(pull_request))
+        print("No 'kind/*' or 'minor' or 'merge' or 'procedures' label found for %s" % _pr_to_str(pull_request))
         text_target = None
 
     if is_minor or is_merge:
@@ -632,6 +684,11 @@ def _text_target(github, pull_request):
     return text_target
 
 
+def _pr_to_labels(pr):
+    labels = [l["name"].lower() for l in pr.labels]
+    return labels
+
+
 def _previous_release(to):
     previous_release = None
     for release in _releases():
diff --git a/scripts/cleanup_datasets/delete_datasets.sh b/scripts/cleanup_datasets/delete_datasets.sh
index 501c234a8d5..e7dfb3f6874 100644
--- a/scripts/cleanup_datasets/delete_datasets.sh
+++ b/scripts/cleanup_datasets/delete_datasets.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -6 -r "$@" >> ./scripts/cleanup_datasets/delete_datasets.log
diff --git a/scripts/cleanup_datasets/delete_userless_histories.sh b/scripts/cleanup_datasets/delete_userless_histories.sh
index 72d68db72ec..9bb8c70882f 100644
--- a/scripts/cleanup_datasets/delete_userless_histories.sh
+++ b/scripts/cleanup_datasets/delete_userless_histories.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -1 "$@" >> ./scripts/cleanup_datasets/delete_userless_histories.log
diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index 35492e4c2f0..260b65f5d5a 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -635,6 +635,8 @@ class PurgeDeletedUsers(PurgesHDAs, RemovesMetadataFiles, Action):
         self.__zero_disk_usage_user_ids.add(row.zero_disk_usage_user_id)
 
     def zero_disk_usage(self):
+        if not self.__zero_disk_usage_user_ids:
+            return
         log.info('Zeroing disk usage for users who were purged')
         sql = """
             UPDATE galaxy_user
@@ -991,7 +993,7 @@ class Cleanup(object):
             # TODO: is this per session or cursor?
             if self.args.work_mem is not None:
                 log.info('Setting work_mem to %s' % self.args.work_mem)
-                self._conn.cursor().execute('SET work_mem TO %s', (self.args.work_mem,))
+                self.__conn.cursor().execute('SET work_mem TO %s', (self.args.work_mem,))
         return self.__conn
 
     def __parse_args(self):
diff --git a/scripts/cleanup_datasets/populate_uuid.sh b/scripts/cleanup_datasets/populate_uuid.sh
index ac2028462cf..c12c5240c19 100644
--- a/scripts/cleanup_datasets/populate_uuid.sh
+++ b/scripts/cleanup_datasets/populate_uuid.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
+cd "$(dirname "$0")"/../..
 export PYTHONPATH=./lib/
-python ./scripts/cleanup_datasets/populate_uuid.py ./config/galaxy.ini $@
+python ./scripts/cleanup_datasets/populate_uuid.py ./config/galaxy.ini "$@"
diff --git a/scripts/cleanup_datasets/purge_datasets.sh b/scripts/cleanup_datasets/purge_datasets.sh
index e4405015c50..6d5c12bb880 100644
--- a/scripts/cleanup_datasets/purge_datasets.sh
+++ b/scripts/cleanup_datasets/purge_datasets.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -3 -r "$@" >> ./scripts/cleanup_datasets/purge_datasets.log
diff --git a/scripts/cleanup_datasets/purge_folders.sh b/scripts/cleanup_datasets/purge_folders.sh
index ff970d0ac8e..d02b7671e6f 100644
--- a/scripts/cleanup_datasets/purge_folders.sh
+++ b/scripts/cleanup_datasets/purge_folders.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -5 -r "$@" >> ./scripts/cleanup_datasets/purge_folders.log
diff --git a/scripts/cleanup_datasets/purge_histories.sh b/scripts/cleanup_datasets/purge_histories.sh
index 66e9f3d285f..8c7ff274d4a 100644
--- a/scripts/cleanup_datasets/purge_histories.sh
+++ b/scripts/cleanup_datasets/purge_histories.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -2 -r "$@" >> ./scripts/cleanup_datasets/purge_histories.log
diff --git a/scripts/cleanup_datasets/purge_libraries.sh b/scripts/cleanup_datasets/purge_libraries.sh
index 6a96b30268d..9e66e05cb5c 100644
--- a/scripts/cleanup_datasets/purge_libraries.sh
+++ b/scripts/cleanup_datasets/purge_libraries.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -4 -r "$@" >> ./scripts/cleanup_datasets/purge_libraries.log
diff --git a/scripts/cleanup_datasets/update_metadata.sh b/scripts/cleanup_datasets/update_metadata.sh
index 7933a0d9ebb..a78325d8ee7 100644
--- a/scripts/cleanup_datasets/update_metadata.sh
+++ b/scripts/cleanup_datasets/update_metadata.sh
@@ -6,4 +6,4 @@
 . ./scripts/get_python.sh
 . ./setup_paths.sh
 
-$GALAXY_PYTHON ./scripts/cleanup_datasets/update_metadata.py ./config/galaxy.ini $@
+"$GALAXY_PYTHON" ./scripts/cleanup_datasets/update_metadata.py ./config/galaxy.ini "$@"
diff --git a/scripts/db_shell.py b/scripts/db_shell.py
index 2ec27eb2db4..ddf85059796 100644
--- a/scripts/db_shell.py
+++ b/scripts/db_shell.py
@@ -58,8 +58,7 @@ def printquery(statement, bind=None):
     import sqlalchemy.orm
     if isinstance(statement, sqlalchemy.orm.Query):
         if bind is None:
-            bind = statement.session.get_bind(
-                statement._mapper_zero_or_none())
+            bind = statement.session.get_bind()
         statement = statement.statement
     elif bind is None:
         bind = statement.bind
diff --git a/scripts/extract_toolbox_sections.py b/scripts/extract_toolbox_sections.py
index cc0a49bd28d..20e3e5a2675 100644
--- a/scripts/extract_toolbox_sections.py
+++ b/scripts/extract_toolbox_sections.py
@@ -14,18 +14,18 @@ def main():
 
     # index range 1-1000, current sections/tools divided between 250-750
     sectionindex = 250
-    sectionfactor = int(500 / len(root.getchildren()))
+    sectionfactor = int(500 / len(root))
 
-    for rootchild in root.getchildren():
+    for rootchild in root:
         currentsectionlabel = ""
         if (rootchild.tag == "section"):
             sectionname = rootchild.attrib['name']
             # per section tool index range 1-1000, current labels/tools
             # divided between 20 and 750
             toolindex = 250
-            toolfactor = int(500 / len(rootchild.getchildren()))
+            toolfactor = int(500 / len(rootchild))
             currentlabel = ""
-            for sectionchild in rootchild.getchildren():
+            for sectionchild in rootchild:
                 if (sectionchild.tag == "tool"):
                     addToToolDict(sectionchild, sectionname, sectionindex, toolindex, currentlabel)
                     toolindex += toolfactor
diff --git a/scripts/galaxy-main b/scripts/galaxy-main
index 5943cc709ab..c51ae7f6329 100755
--- a/scripts/galaxy-main
+++ b/scripts/galaxy-main
@@ -54,7 +54,7 @@ except Exception:
     log.exception("Failed to add Galaxy to sys.path")
     raise
 from galaxy.util import unicodify
-from galaxy.web.stack import get_app_kwds
+from galaxy.web_stack import get_app_kwds
 
 REQUIRES_DAEMONIZE_MESSAGE = "Attempted to use Galaxy in daemon mode, but daemonize is unavailable."
 
diff --git a/scripts/grt/export.py b/scripts/grt/export.py
index 24e5f447ce0..0a8c3f9e2b2 100644
--- a/scripts/grt/export.py
+++ b/scripts/grt/export.py
@@ -49,7 +49,10 @@ def kw_metrics(job):
 
 
 def round_to_2sd(number):
-    return str(int(float('%.2g' % number)))
+    if number:
+        return str(int(float('%.2g' % number)))
+    else:
+        return '-1'
 
 
 def main(argv):
@@ -289,11 +292,15 @@ def main(argv):
 
     # Now on to outputs.
     with tarfile.open(REPORT_BASE + '.tar.gz', 'w:gz') as handle:
-        for name in ('jobs', 'metric_num', 'params', 'datasets'):
-            handle.add(REPORT_BASE + '.' + name + '.tsv')
+        for name in ('jobs', 'metric_num', 'datasets'):
+            path = REPORT_BASE + '.' + name + '.tsv'
+            if os.path.exists(path):
+                handle.add(path)
 
-    for name in ('jobs', 'metric_num', 'params', 'datasets'):
-        os.unlink(REPORT_BASE + '.' + name + '.tsv')
+    for name in ('jobs', 'metric_num', 'datasets'):
+        path = REPORT_BASE + '.' + name + '.tsv'
+        if os.path.exists(path):
+            os.unlink(REPORT_BASE + '.' + name + '.tsv')
 
     _times.append(('job_finish', time.time() - _start_time))
     sha = hash_util.memory_bound_hexdigest(hash_util.sha256, REPORT_BASE + ".tar.gz")
diff --git a/scripts/grt/upload.py b/scripts/grt/upload.py
index aa978456bf6..eb411ca66f7 100644
--- a/scripts/grt/upload.py
+++ b/scripts/grt/upload.py
@@ -33,9 +33,8 @@ def main(argv):
         with open(args.grt_config) as handle:
             config = yaml.safe_load(handle)
     except Exception:
-        logging.warning('Using default GRT configuration')
-        with open(sample_config) as handle:
-            config = yaml.safe_load(handle)
+        logging.exception('Could not parse GRT configuration')
+        sys.exit(1)
 
     REPORT_DIR = args.report_directory
     GRT_URL = config['grt']['url'].rstrip('/') + '/'
diff --git a/scripts/maintenance.sh b/scripts/maintenance.sh
index 8ca4771ed54..e45d11bb603 100755
--- a/scripts/maintenance.sh
+++ b/scripts/maintenance.sh
@@ -6,7 +6,7 @@
 set -e
 
 display_help(){
-  scriptname=`basename $0`
+  scriptname=$(basename "$0")
   printf "./$scriptname [--help] [--no-dry-run] [--days 10] 
 Will run the galaxy cleanup scripts in the recommend order. By default a 'dry-run' is started. Specify --no-dry-run to do the actual cleanup.
 
@@ -52,7 +52,7 @@ do
   esac
 done
 
-cd "$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)"/../
+cd "$(dirname "$0")"/..
 
 . scripts/common_startup_functions.sh
 
diff --git a/scripts/manage_tool_dependencies.py b/scripts/manage_tool_dependencies.py
index 0ff3a6b6a5c..e1de8bcf562 100644
--- a/scripts/manage_tool_dependencies.py
+++ b/scripts/manage_tool_dependencies.py
@@ -9,7 +9,7 @@ from galaxy.config import (
     find_root,
     parse_dependency_options,
 )
-from galaxy.tools.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
+from galaxy.tool_util.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
 from galaxy.util.script import main_factory
 
 DESCRIPTION = "Script to manage tool dependencies (with focus on a Conda environments)."
@@ -21,7 +21,7 @@ def _init_if_needed(args, kwargs):
 
 
 def _build_dependency_manager_no_config(kwargs):
-    """Simplified variant of build_dependency_manager from galaxy.tools.deps.
+    """Simplified variant of build_dependency_manager from galaxy.tool_util.deps.
 
     The canonical factory method requires a full Galaxy configuration object
     which we do not have available in this script (an optimization).
diff --git a/scripts/migrate_tools/0002_tools.sh b/scripts/migrate_tools/0002_tools.sh
index 926aba9529d..7262196b5a9 100644
--- a/scripts/migrate_tools/0002_tools.sh
+++ b/scripts/migrate_tools/0002_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml "$@"
diff --git a/scripts/migrate_tools/0003_tools.sh b/scripts/migrate_tools/0003_tools.sh
index dfc3bde56b3..f8a1ba8bb16 100644
--- a/scripts/migrate_tools/0003_tools.sh
+++ b/scripts/migrate_tools/0003_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml "$@"
diff --git a/scripts/migrate_tools/0004_tools.sh b/scripts/migrate_tools/0004_tools.sh
index 40b76956fa2..7ae608f3683 100644
--- a/scripts/migrate_tools/0004_tools.sh
+++ b/scripts/migrate_tools/0004_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml "$@"
diff --git a/scripts/migrate_tools/0005_tools.sh b/scripts/migrate_tools/0005_tools.sh
index c9f1f3c61d6..da7f9c09098 100644
--- a/scripts/migrate_tools/0005_tools.sh
+++ b/scripts/migrate_tools/0005_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml "$@"
diff --git a/scripts/migrate_tools/0006_tools.sh b/scripts/migrate_tools/0006_tools.sh
index 1f000ebeca6..ff85522a5f9 100644
--- a/scripts/migrate_tools/0006_tools.sh
+++ b/scripts/migrate_tools/0006_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml "$@"
diff --git a/scripts/migrate_tools/0007_tools.sh b/scripts/migrate_tools/0007_tools.sh
index a6cf948593d..8a88f44420c 100644
--- a/scripts/migrate_tools/0007_tools.sh
+++ b/scripts/migrate_tools/0007_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml "$@"
diff --git a/scripts/migrate_tools/0008_tools.sh b/scripts/migrate_tools/0008_tools.sh
index 50cafd19936..d312237023b 100644
--- a/scripts/migrate_tools/0008_tools.sh
+++ b/scripts/migrate_tools/0008_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml "$@"
diff --git a/scripts/migrate_tools/0009_tools.sh b/scripts/migrate_tools/0009_tools.sh
index 36f162b141c..78242fe2422 100644
--- a/scripts/migrate_tools/0009_tools.sh
+++ b/scripts/migrate_tools/0009_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml "$@"
diff --git a/scripts/migrate_tools/0010_tools.sh b/scripts/migrate_tools/0010_tools.sh
index fde17704dd3..03c65dd9973 100644
--- a/scripts/migrate_tools/0010_tools.sh
+++ b/scripts/migrate_tools/0010_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml "$@"
diff --git a/scripts/migrate_tools/0011_tools.sh b/scripts/migrate_tools/0011_tools.sh
index a31365804fd..e06a6be40b3 100644
--- a/scripts/migrate_tools/0011_tools.sh
+++ b/scripts/migrate_tools/0011_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml "$@"
diff --git a/scripts/migrate_tools/0012_tools.sh b/scripts/migrate_tools/0012_tools.sh
index 97fbe354d04..2df312f980a 100644
--- a/scripts/migrate_tools/0012_tools.sh
+++ b/scripts/migrate_tools/0012_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml "$@"
diff --git a/scripts/pages_identifier_conversion.py b/scripts/pages_identifier_conversion.py
index ce914938f21..b9cec401071 100644
--- a/scripts/pages_identifier_conversion.py
+++ b/scripts/pages_identifier_conversion.py
@@ -9,12 +9,12 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
 import galaxy
 import galaxy.app
 import galaxy.config
+from galaxy.managers.pages import PageContentProcessor, placeholderRenderForSave
 from galaxy.objectstore import build_object_store_from_config
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util import unicodify
 from galaxy.util.bunch import Bunch
 from galaxy.util.script import app_properties_from_args, populate_config_args
-from galaxy.webapps.galaxy.controllers.page import _PageContentProcessor, _placeholderRenderForSave
 
 
 def main(argv):
@@ -37,7 +37,7 @@ def main(argv):
     mock_trans = Bunch(app=Bunch(security=security_helper), model=model, user_is_admin=lambda: True, sa_session=session)
     for p in pagerevs:
         try:
-            processor = _PageContentProcessor(mock_trans, _placeholderRenderForSave)
+            processor = PageContentProcessor(mock_trans, placeholderRenderForSave)
             processor.feed(p.content)
             newcontent = unicodify(processor.output(), 'utf-8')
             if p.content != newcontent:
diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py
index 1f2f875db37..41ce98e83ce 100644
--- a/scripts/tool_shed/build_ts_whoosh_index.py
+++ b/scripts/tool_shed/build_ts_whoosh_index.py
@@ -17,8 +17,8 @@ import os
 import sys
 from optparse import OptionParser
 
+from mercurial import hg, ui
 from six.moves import configparser
-from whoosh.fields import Schema, STORED, TEXT
 from whoosh.filedb.filestore import FileStorage
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
@@ -31,38 +31,17 @@ from galaxy.util import (
     unicodify
 )
 from galaxy.webapps.tool_shed import config, model
+from galaxy.webapps.tool_shed.search.repo_search import schema as repo_schema
+from galaxy.webapps.tool_shed.search.tool_search import schema as tool_schema
+from galaxy.webapps.tool_shed.util.hgweb_config import HgWebConfigManager
 
 if sys.version_info > (3,):
     long = int
 
 logging.basicConfig(level='DEBUG')
 
-repo_schema = Schema(
-    id=STORED,
-    name=TEXT(stored=True),
-    description=TEXT(stored=True),
-    long_description=TEXT(stored=True),
-    homepage_url=TEXT(stored=True),
-    remote_repository_url=TEXT(stored=True),
-    repo_owner_username=TEXT(stored=True),
-    times_downloaded=STORED,
-    approved=STORED,
-    last_updated=STORED,
-    full_last_updated=STORED)
 
-tool_schema = Schema(
-    name=TEXT(stored=True),
-    description=TEXT(stored=True),
-    owner=TEXT(stored=True),
-    id=TEXT(stored=True),
-    help=TEXT(stored=True),
-    version=TEXT(stored=True),
-    repo_name=TEXT(stored=True),
-    repo_owner_username=TEXT(stored=True),
-    repo_id=STORED)
-
-
-def build_index(sa_session, whoosh_index_dir, path_to_repositories):
+def build_index(sa_session, whoosh_index_dir, path_to_repositories, hgweb_config_dir):
     """
     Build the search indexes. One for repositories and another for tools within.
     """
@@ -85,7 +64,7 @@ def build_index(sa_session, whoosh_index_dir, path_to_repositories):
     repos_indexed = 0
     tools_indexed = 0
 
-    for repo in get_repos(sa_session, path_to_repositories):
+    for repo in get_repos(sa_session, path_to_repositories, hgweb_config_dir):
 
         repo_index_writer.add_document(id=repo.get('id'),
                              name=unicodify(repo.get('name')),
@@ -94,10 +73,12 @@ def build_index(sa_session, whoosh_index_dir, path_to_repositories):
                              homepage_url=unicodify(repo.get('homepage_url')),
                              remote_repository_url=unicodify(repo.get('remote_repository_url')),
                              repo_owner_username=unicodify(repo.get('repo_owner_username')),
+                             categories=unicodify(repo.get('categories')),
                              times_downloaded=repo.get('times_downloaded'),
                              approved=repo.get('approved'),
                              last_updated=repo.get('last_updated'),
-                             full_last_updated=repo.get('full_last_updated'))
+                             full_last_updated=repo.get('full_last_updated'),
+                             repo_lineage=unicodify(repo.get('repo_lineage')))
         #  Tools get their own index
         for tool in repo.get('tools_list'):
             tool_index_writer.add_document(id=unicodify(tool.get('id')),
@@ -121,13 +102,19 @@ def build_index(sa_session, whoosh_index_dir, path_to_repositories):
     print("TOTAL tools indexed: ", tools_indexed)
 
 
-def get_repos(sa_session, path_to_repositories):
+def get_repos(sa_session, path_to_repositories, hgweb_config_dir):
     """
     Load repos from DB and included tools from .xml configs.
     """
+    hgwcm = HgWebConfigManager()
+    hgwcm.hgweb_config_dir = hgweb_config_dir
     results = []
     for repo in sa_session.query(model.Repository).filter_by(deleted=False).filter_by(deprecated=False).filter(model.Repository.type != 'tool_dependency_definition'):
-
+        category_names = []
+        for rca in sa_session.query(model.RepositoryCategoryAssociation).filter(model.RepositoryCategoryAssociation.repository_id == repo.id):
+            for category in sa_session.query(model.Category).filter(model.Category.id == rca.category.id):
+                category_names.append(category.name)
+        categories = (",").join(category_names)
         repo_id = repo.id
         name = repo.name
         description = repo.description
@@ -154,6 +141,14 @@ def get_repos(sa_session, path_to_repositories):
         last_updated = pretty_print_time_interval(repo.update_time)
         full_last_updated = repo.update_time.strftime("%Y-%m-%d %I:%M %p")
 
+        # load all changesets of the repo
+        repo_path = hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name))
+        hg_repo = hg.repository(ui.ui(), repo_path)
+        lineage = []
+        for changeset in hg_repo.changelog:
+            lineage.append(str(changeset) + ":" + str(hg_repo.changectx(changeset)))
+        repo_lineage = str(lineage)
+
         #  Parse all the tools within repo for separate index.
         tools_list = []
         path = os.path.join(path_to_repositories, *directory_hash_id(repo.id))
@@ -178,7 +173,9 @@ def get_repos(sa_session, path_to_repositories):
                             approved=approved,
                             last_updated=last_updated,
                             full_last_updated=full_last_updated,
-                            tools_list=tools_list))
+                            tools_list=tools_list,
+                            repo_lineage=repo_lineage,
+                            categories=categories))
     return results
 
 
@@ -218,9 +215,11 @@ def get_sa_session_and_needed_config_settings(path_to_tool_shed_config):
 if __name__ == "__main__":
     parser = OptionParser()
     parser.add_option("-c", "--config", dest="path_to_tool_shed_config", default="config/tool_shed.ini", help="specify tool_shed.ini location")
+    parser.add_option("-r", "--hgweb", dest="hgweb_config_dir", default=".", help="specify hgweb.config location")
     (options, args) = parser.parse_args()
     path_to_tool_shed_config = options.path_to_tool_shed_config
+    hgweb_config_dir = options.hgweb_config_dir
     sa_session, config_settings = get_sa_session_and_needed_config_settings(path_to_tool_shed_config)
     whoosh_index_dir = config_settings.get('whoosh_index_dir', None)
     path_to_repositories = config_settings.get('file_path', 'database/community_files')
-    build_index(sa_session, whoosh_index_dir, path_to_repositories)
+    build_index(sa_session, whoosh_index_dir, path_to_repositories, hgweb_config_dir)
diff --git a/scripts/tool_shed/migrate_tools_to_repositories.sh b/scripts/tool_shed/migrate_tools_to_repositories.sh
index e1108e20307..bbab9b1b333 100644
--- a/scripts/tool_shed/migrate_tools_to_repositories.sh
+++ b/scripts/tool_shed/migrate_tools_to_repositories.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
+cd "$(dirname "$0")"/../..
 python ./scripts/tool_shed/migrate_tools_to_repositories.py ./community_wsgi.ini >> ./scripts/tool_shed/migrate_tools_to_repositories.log
diff --git a/scripts/validate_tools.sh b/scripts/validate_tools.sh
index df7bfdeae45..f57c1cb814a 100755
--- a/scripts/validate_tools.sh
+++ b/scripts/validate_tools.sh
@@ -1,33 +1,31 @@
 #!/bin/sh
 
-cd `dirname $0`/..
+cd "$(dirname "$0")"/..
 
-./scripts/common_startup.sh
+GALAXY_SKIP_CLIENT_BUILD=1 ./scripts/common_startup.sh
 GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
-if [ -d "$GALAXY_VIRTUAL_ENV" ];
-then
+if [ -d "$GALAXY_VIRTUAL_ENV" ]; then
     printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
     . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
-xsd_path="lib/galaxy/tools/xsd/galaxy.xsd"
+xsd_path="lib/galaxy/tool_util/xsd/galaxy.xsd"
 
-err_tmp=`mktemp`
+err_tmp=$(mktemp)
 count=0
 exit=0
 for p in "$@"; do
     count=$((count+1))
     path="$p"
-    echo $path
+    echo "$path"
     PYTHONPATH=lib:$PYTHONPATH
     export PYTHONPATH
-    result=`python -c "import galaxy.tools.loader; import xml.etree; xml.etree.ElementTree.dump(galaxy.tools.loader.load_tool('$path').getroot())" | xmllint --nowarning --noout --schema "$xsd_path" - 2> "$err_tmp"`
-    if [ $? -eq 0 ]
-    then
+    python -c "import galaxy.tool_util.loader; import xml.etree; xml.etree.ElementTree.dump(galaxy.tool_util.loader.load_tool('$path').getroot())" | xmllint --nowarning --noout --schema "$xsd_path" - 2> "$err_tmp"
+    if [ $? -eq 0 ]; then
         echo "ok $count";
     else
         echo "not ok $count $path";
-        cat "$err_tmp" | sed 's/^/    /'
+        sed 's/^/    /' "$err_tmp"
         exit=1
     fi
 done
diff --git a/setup.cfg b/setup.cfg
index 9f71b41c5cb..4eafad8d715 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,3 +1,6 @@
+[wheel]
+universal = 1
+
 [flake8]
 # These are exceptions allowed by Galaxy style guidelines.
 # E128 continuation line under-indented for visual indent
diff --git a/static/images/delete.gif b/static/images/delete.gif
new file mode 120000
index 00000000000..97ee732f75b
--- /dev/null
+++ b/static/images/delete.gif
@@ -0,0 +1 @@
+../../client/galaxy/images/delete.gif
\ No newline at end of file
diff --git a/static/images/star.gif b/static/images/star.gif
new file mode 120000
index 00000000000..e3e3d574f9f
--- /dev/null
+++ b/static/images/star.gif
@@ -0,0 +1 @@
+../../client/galaxy/images/star.gif
\ No newline at end of file
diff --git a/static/welcome.html.sample b/static/welcome.html.sample
index c3ef6200153..711e83b7d2b 100644
--- a/static/welcome.html.sample
+++ b/static/welcome.html.sample
@@ -5,13 +5,13 @@
         <link rel="stylesheet" href="style/base.css" type="text/css" />
     </head>
     <body class="m-0">
-        <div class="jumbotron rounded-0">
+        <div class="py-4">
             <div class="container">
                 <h2>Hello, <strong>Galaxy</strong> is running!</h2>
                 To customize this page edit <code>static/welcome.html</code>
                 <br>
-                <a target="_blank" href="https://docs.galaxyproject.org/en/latest/admin/config.html" class="btn btn-primary btn-lg">Configuring Galaxy »</a>
-                <a target="_blank" href="https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/" class="btn btn-primary btn-lg">Installing Tools »</a>
+                <a target="_blank" href="https://docs.galaxyproject.org/en/latest/admin/config.html" class="btn btn-primary">Configuring Galaxy »</a>
+                <a target="_blank" href="https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/" class="btn btn-primary">Installing Tools »</a>
             </div>
             <br>
             <div class="container">
@@ -23,7 +23,7 @@
             </div>
         </div>
         <div class="container">
-            <p class="lead">
+            <p>
                 <a target="_blank" class="reference" href="http://galaxyproject.org/">
                 Galaxy</a> is an open platform for supporting data intensive
                 research. Galaxy is developed by <a target="_blank" class="reference" href="https://galaxyproject.org/galaxy-team/">The Galaxy Team</a>
diff --git a/templates/admin/jobs.mako b/templates/admin/jobs.mako
deleted file mode 100644
index 36a372044f9..00000000000
--- a/templates/admin/jobs.mako
+++ /dev/null
@@ -1,209 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    <script type="text/javascript">
-        function toggle_all(source) {
-            // sets all checkboxes in source's parent form to match source element.
-            $.each($(source).closest("form").find(":checkbox"), function(i, v){
-                v.checked = source.checked;
-            });
-        }
-    </script>
-</%def>
-
-<%def name="title()">Jobs</%def>
-
-<h2>Jobs</h2>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<p>
-    Unfinished and recently finished jobs are displayed on this page.  The
-    'cutoff' input box will do two things -- it will limit the display of
-    unfinished jobs to only those jobs that have not had their job state
-    updated recently, and it will limit the recently finished jobs list to only
-    displaying jobs that have finished since the cutoff.
-</p>
-<p>
-    If any jobs are displayed, you may choose to stop them.  Your stop message
-    will be displayed to the user as: "This job was stopped by an
-    administrator: <b>&lt;YOUR MESSAGE&gt;</b>  For more information or help,
-    report this error".
-</p>
-
-%if jobs:
-<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST">
-    <h4>
-        Unfinished Jobs: These jobs are unfinished and have had their state updated in the previous ${cutoff} seconds.
-    </h4>
-    <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-        <tr class="header">
-            <td><input type="checkbox" onClick="toggle_all(this)"/></td>
-            <td>Job ID</td>
-            <td>User</td>
-            <td>Last Update</td>
-            <td>Tool</td>
-            <td>State</td>
-            <td>Inputs</td>
-            <td>Command Line</td>
-            <td>Job Runner</td>
-            <td>PID/Cluster ID</td>
-        </tr>
-        %for job in jobs:
-                <td>
-                    <input type="checkbox" name="stop" value="${job.id}"/>
-                </td>
-                <td>${job.id}</td>
-                %if job.history and job.history.user:
-                    <td>${job.history.user.email|h}</td>
-                %else:
-                    <td>anonymous</td>
-                %endif
-                <td>${last_updated[job.id]} ago</td>
-                <td>${job.tool_id|h}</td>
-                <td>${job.state}</td>
-                <%
-                    try:
-                        inputs = ", ".join( [ '%s&nbsp;%s' % ( da.dataset.id, da.dataset.state ) for da in job.input_datasets ] )
-                    except:
-                        inputs = 'Unable to determine inputs'
-                %>
-                <td>${inputs}</td>
-                <td>${job.command_line|h}</td>
-                <td>${job.job_runner_name|h}</td>
-                <td>${job.job_runner_external_id}</td>
-            </tr>
-        %endfor
-    </table>
-    <p/>
-    <div class="card">
-        <div class="card-header">
-            Stop Jobs
-        </div>
-        <div class="card-body">
-            <div class="form-row">
-                <label>
-                    Stop message:
-                </label>
-                <div class="form-row-input">
-                    <input type="text" name="stop_msg" size="40"/>
-                </div>
-                <div class="toolParamHelp" style="clear: both;">
-                    to be displayed to the user
-                </div>
-            </div>
-            <div class="form-row">
-                <input type="submit" class="primary-button" name="submit" value="Submit">
-            </div>
-        </div>
-    </div>
-    <p/>
-</form>
-%else:
-    <div class="infomessage">There are no unfinished jobs to show with current cutoff time.</div>
-    <p/>
-%endif
-
-%if recent_jobs:
-    <h4>
-        Recent Jobs: These jobs have completed in the previous ${cutoff} seconds.
-    </h4>
-    <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-        <tr class="header">
-            <td>Job ID</td>
-            <td>User</td>
-            <td>Finished</td>
-            <td>Tool</td>
-            <td>State</td>
-            <td>Inputs</td>
-            <td>Command Line</td>
-            <td>Job Runner</td>
-            <td>PID/Cluster ID</td>
-        </tr>
-        %for job in recent_jobs:
-                <td><a href="${h.url_for( controller="admin", action="job_info" )}?jobid=${job.id}">${job.id}</a></td>
-                %if job.history and job.history.user:
-                    <td>${job.history.user.email|h}</td>
-                %else:
-                    <td>anonymous</td>
-                %endif
-                <td>${finished[job.id]} ago</td>
-                <td>${job.tool_id|h}</td>
-                <td>${job.state}</td>
-                <%
-                    try:
-                        inputs = ", ".join( [ '%s&nbsp;%s' % ( da.dataset.id, da.dataset.state ) for da in job.input_datasets ] )
-                    except:
-                        inputs = 'Unable to determine inputs'
-                %>
-                <td>${inputs}</td>
-                <td>${job.command_line|h}</td>
-                <td>${job.job_runner_name|h}</td>
-                <td>${job.job_runner_external_id|h}</td>
-            </tr>
-        %endfor
-    </table>
-    <p/>
-%else:
-    <div class="infomessage">There are no recently finished jobs to show with current cutoff time.</div>
-    <p/>
-%endif
-
-<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST">
-    <div class="card">
-        <div class="card-header">
-            Update Jobs
-        </div>
-        <div class="card-body">
-
-            <div class="form-row">
-                <label>
-                    Cutoff:
-                </label>
-                <div class="form-row-input">
-                    <input type="text" name="cutoff" size="4" value="${cutoff}"/>
-                </div>
-                <div class="toolParamHelp" style="clear: both;">
-                    In seconds
-                </div>
-            </div>
-            <div class="form-row">
-                <input type="submit" class="primary-button" name="submit" value="Refresh">
-            </div>
-        </div>
-    </div>
-</form>
-
-<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST">
-    <p/>
-    <div class="card">
-        <div class="card-header">
-            Administrative Job Lock
-        </div>
-        <div class="card-body">
-            <div class="form-row">
-                <input type="hidden" name="ajl_submit" value="True"/>
-    %if job_lock==True:
-                <p>Job dispatching is currently <strong>locked</strong>.</p>
-                <label>
-                    <input type='checkbox' name='job_lock' checked='checked' />
-                    Prevent jobs from dispatching.
-                </label>
-    %else:
-                <p>Job dispatching is currently <strong>unlocked</strong>.</p>
-                <label>
-                    <input type='checkbox' name='job_lock' />
-                    Prevent jobs from dispatching.
-                </label>
-    %endif
-            </div>
-            <div class="form-row">
-                <input type="submit" class="primary-button" name="submit" value="Update">
-            </div>
-        </div>
-    </div>
-</form>
diff --git a/templates/base.mako b/templates/base.mako
index f14ee5fbb4a..8c6e3f2ba1d 100644
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -51,7 +51,6 @@
 <%def name="javascripts()">
     ## TODO: remove when all libs are required directly in modules
     ${h.js(
-        'libs/require',
         'bundled/libs.chunk',
         'bundled/base.chunk'
     )}
@@ -66,7 +65,9 @@
 
     ${ galaxy_client.load( app=self.js_app ) }
     ${ galaxy_client.config_sentry( app=self.js_app ) }
-    ${ galaxy_client.config_google_analytics( app=self.js_app ) }
+    %if self.js_app and self.js_app.config and self.js_app.config.ga_code:
+        ${ galaxy_client.config_google_analytics(self.js_app.config.ga_code) }
+    %endif
 
     %if not form_input_auto_focus is UNDEFINED and form_input_auto_focus:
         <script type="text/javascript">
diff --git a/templates/base/base_panels.mako b/templates/base/base_panels.mako
index eb967f3e17d..b82f2dea88c 100644
--- a/templates/base/base_panels.mako
+++ b/templates/base/base_panels.mako
@@ -70,7 +70,7 @@
     </script>
 
     %if t.webapp.name == 'galaxy' and app.config.ga_code:
-        ${galaxy_client.config_google_analytics(app)}
+        ${galaxy_client.config_google_analytics(app.config.ga_code)}
     %endif
 
 </%def>
@@ -195,7 +195,7 @@
                     <div id="left">
                         ${self.left_panel()}
                         <div class="unified-panel-footer">
-                            <div id="left-panel-collapse" class="panel-collapse"></div>
+                            <div id="left-panel-collapse" class="panel-collapse left"></div>
                             <div id="left-panel-drag" class="drag"></div>
                         </div>
                     </div><!--end left-->
diff --git a/templates/display_common.mako b/templates/display_common.mako
index 937da544531..ee5aadb1485 100644
--- a/templates/display_common.mako
+++ b/templates/display_common.mako
@@ -114,6 +114,8 @@
             return "datasets"
         elif controller == "page":
             return "pages"
+        elif controller == "visualization":
+            return "visualizations"
         else:
             return controller
     %>
diff --git a/templates/embed_base.mako b/templates/embed_base.mako
index 1e7c74b2622..163f293392a 100644
--- a/templates/embed_base.mako
+++ b/templates/embed_base.mako
@@ -11,7 +11,6 @@
         ${self.render_title( item )}
     </div>
     <div class='summary-content'>
-        ${self.render_summary_content( item, item_data )}
     </div>
     <div class='expanded-content'>
         <div class='item-content'></div>
@@ -42,7 +41,7 @@
         display_href = h.url_for( controller=item_controller, action='display_by_username_and_slug', username=item_user.username, slug=item_slug )
     %>
     <div style="float: left">
-        <a class="display_in_embed icon-button toggle-expand" item_id="${trans.security.encode_id( item.id )}" item_class="$item.__class__.__name__" href="${display_href}"
+        <a class="display_in_embed icon-button toggle-expand" item_id="${trans.security.encode_id( item.id )}" item_class="${item.__class__.__name__}" href="${display_href}"
             title="Show ${item_display_name} content"></a>
         <a class="toggle icon-button" href="${display_href}" title="Hide ${item_display_name} content"></a>
     </div>
@@ -57,7 +56,3 @@
     ## Use a hidden var to store the ajax URL for getting an item's content.
     <input type="hidden" name="ajax-item-content-url" value="${h.url_for( controller=item_controller, action='get_item_content_async', id=trans.security.encode_id( item.id ) )}"/>
 </%def>
-
-## Methods to override to render summary content.
-<%def name="render_summary_content( item, item_data )">
-</%def>
diff --git a/templates/galaxy_client_app.mako b/templates/galaxy_client_app.mako
index 4b4cb51d032..7c22f5d77fa 100644
--- a/templates/galaxy_client_app.mako
+++ b/templates/galaxy_client_app.mako
@@ -39,8 +39,6 @@ ${ h.dumps( dictionary, indent=( 2 if trans.debug else 0 ) ) }
     %if app and app.config:
         <script type="text/javascript">
 
-            // TODO: make this work the same in all places, maybe 
-            // make a global func in galaxy_client_app?
             var sentry = {};
             %if app.config.sentry_dsn:
                 sentry.sentry_dsn_public = "${app.config.sentry_dsn_public}"
@@ -57,17 +55,20 @@ ${ h.dumps( dictionary, indent=( 2 if trans.debug else 0 ) ) }
     %endif
 </%def>
 
-<%def name="config_google_analytics(app)">
-    %if app and app.config and app.config.ga_code:
-        <script>
+<%def name="config_google_analytics(ga_code)">
+    <script>
+        console.log("config_google_analytics ga_code:", '${ga_code}');
+        %if ga_code:
             (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
             (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
             m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
             })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-            ga('create', '${app.config.ga_code}', 'auto');
+            ga('create', '${ga_code}', 'auto');
             ga('send', 'pageview');
-        </script>
-    %endif
+        %else:
+            console.warn("Missing google analytics code");
+        %endif
+    </script>
 </%def>
 
 
diff --git a/templates/js-app.mako b/templates/js-app.mako
index 71d78bb471a..f606b272ba2 100644
--- a/templates/js-app.mako
+++ b/templates/js-app.mako
@@ -37,7 +37,6 @@
 
 <%def name="javascripts()">
     ${ h.js(
-        'libs/require',
         'bundled/libs.chunk',
         'bundled/base.chunk'
     )}
@@ -75,8 +74,10 @@
     </script>
     %endif
 
-    ## ${ galaxy_client.config_sentry(app)}
-    ## ${ galaxy_client.config_google_analytics(app)}
+    ${ galaxy_client.config_sentry(app) }
+    %if app.config.ga_code:
+        ${ galaxy_client.config_google_analytics(app.config.ga_code) }
+    %endif
 
 </%def>
 
diff --git a/templates/show_params.mako b/templates/show_params.mako
index daeeb837d84..2a4e8f3549c 100644
--- a/templates/show_params.mako
+++ b/templates/show_params.mako
@@ -9,133 +9,8 @@
         text-align: center;
         background-color: #eee;
     }
-
-    table.info_data_table {
-        table-layout: fixed;
-        word-break: break-word;
-    }
-    table.info_data_table td:nth-child(1) {
-        width: 25%;
-    }
-
 </style>
 
-<%def name="inputs_recursive( input_params, param_values, depth=1, upgrade_messages=None )">
-    <%
-        from galaxy.util import listify
-        if upgrade_messages is None:
-            upgrade_messages = {}
-    %>
-    %for input_index, input in enumerate( input_params.values() ):
-        %if input.name in param_values:
-            %if input.type == "repeat":
-                %for i in range( len(param_values[input.name]) ):
-                    ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) }
-                %endfor
-            %elif input.type == "section":
-                <tr>
-                    ##<!-- Get the value of the current Section parameter -->
-                    ${inputs_recursive_indent( text=input.name, depth=depth )}
-                    <td></td>
-                </tr>
-                ${ inputs_recursive( input.inputs, param_values[input.name], depth=depth+1, upgrade_messages=upgrade_messages.get( input.name ) ) }
-            %elif input.type == "conditional":
-                <%
-                try:
-                    current_case = param_values[input.name]['__current_case__']
-                    is_valid = True
-                except:
-                    current_case = None
-                    is_valid = False
-                %>
-                %if is_valid:
-                    <tr>
-                        ${ inputs_recursive_indent( text=input.test_param.label, depth=depth )}
-                        ##<!-- Get the value of the current Conditional parameter -->
-                        <td>${input.cases[current_case].value | h}</td>
-                        <td></td>
-                    </tr>
-                    ${ inputs_recursive( input.cases[current_case].inputs, param_values[input.name], depth=depth+1, upgrade_messages=upgrade_messages.get( input.name ) ) }
-                %else:
-                    <tr>
-                        ${ inputs_recursive_indent( text=input.name, depth=depth )}
-                        <td><em>The previously used value is no longer valid</em></td>
-                        <td></td>
-                    </tr>
-                %endif
-            %elif input.type == "upload_dataset":
-                    <tr>
-                        ${inputs_recursive_indent( text=input.group_title( param_values ), depth=depth )}
-                        <td>${ len( param_values[input.name] ) } uploaded datasets</td>
-                        <td></td>
-                    </tr>
-            ## files used for inputs
-            %elif input.type == "data":
-                    <tr>
-                        ${inputs_recursive_indent( text=input.label, depth=depth )}
-                        <td>
-                        %for i, element in enumerate(listify(param_values[input.name])):
-                            %if i > 0:
-                            ,
-                            %endif
-                            %if element.history_content_type == "dataset":
-                                <%
-                                    hda = element
-                                    encoded_id = trans.security.encode_id( hda.id )
-                                    show_params_url = h.url_for( controller='dataset', action='show_params', dataset_id=encoded_id )
-                                %>
-                                <a class="input-dataset-show-params" data-hda-id="${encoded_id}"
-                                       href="${show_params_url}">${hda.hid}: ${hda.name | h}</a>
-
-                            %else:
-                                ${element.hid}: ${element.name | h}
-                            %endif
-                        %endfor
-                        </td>
-                        <td></td>
-                    </tr>
-             %elif input.visible:
-                <%
-                if  hasattr( input, "label" ) and input.label:
-                    label = input.label
-                else:
-                    #value for label not required, fallback to input name (same as tool panel)
-                    label = input.name
-                %>
-                <tr>
-                    ${inputs_recursive_indent( text=label, depth=depth )}
-                    <td>${input.value_to_display_text( param_values[input.name] ) | h}</td>
-                    <td>${ upgrade_messages.get( input.name, '' ) | h }</td>
-                </tr>
-            %endif
-        %else:
-            ## Parameter does not have a stored value.
-            <tr>
-                <%
-                    # Get parameter label.
-                    if input.type == "conditional":
-                        label = input.test_param.label
-                    elif input.type == "repeat":
-                        label = input.label()
-                    else:
-                        label = input.label or input.name
-                %>
-                ${inputs_recursive_indent( text=label, depth=depth )}
-                <td><em>not used (parameter was added after this job was run)</em></td>
-                <td></td>
-            </tr>
-        %endif
-
-    %endfor
-</%def>
-
- ## function to add a indentation depending on the depth in a <tr>
-<%def name="inputs_recursive_indent( text, depth )">
-    <td style="padding-left: ${ ( depth - 1 ) * 10 }px">
-        ${text | h}
-    </td>
-</%def>
-
 <h2>
 % if tool:
     ${tool.name | h}
@@ -212,31 +87,13 @@
     </tbody>
 </table>
 
-<h3>Tool Parameters</h3>
-<table class="tabletip" id="tool-parameters">
-    <thead>
-        <tr>
-            <th>Input Parameter</th>
-            <th>Value</th>
-            <th>Note for rerun</th>
-        </tr>
-    </thead>
-    <tbody>
-        % if params_objects and tool:
-            ${ inputs_recursive( tool.inputs, params_objects, depth=1, upgrade_messages=upgrade_messages ) }
-        %elif params_objects is None:
-            <tr><td colspan="3">Unable to load parameters.</td></tr>
-        % else:
-            <tr><td colspan="3">No parameters.</td></tr>
-        % endif
-    </tbody>
-</table>
-%if has_parameter_errors:
-    <br />
-    ${ render_msg( 'One or more of your original parameters may no longer be valid or displayed properly.', status='warning' ) }
+%if job:
+<div class="job-parameters" dataset_id="${encoded_hda_id}" dataset_type="hda">
+</div>
 %endif
 
 
+
 <h3>Inheritance Chain</h3>
 <div class="inherit" style="background-color: #fff; font-weight:bold;">${hda.name | h}</div>
 
@@ -256,26 +113,8 @@ ${ job.command_line | h }</pre>
 %endif
 
 %if job and (trans.user_is_admin or trans.app.config.expose_potentially_sensitive_job_metrics):
-<h3>Job Metrics</h3>
-<% job_metrics = trans.app.job_metrics %>
-<% plugins = set([metric.plugin for metric in job.metrics]) %>
-    %for plugin in sorted(plugins):
-    %if trans.user_is_admin or plugin != 'env':
-    <h4>${ plugin | h }</h4>
-    <table class="tabletip info_data_table">
-        <tbody>
-        <%
-            plugin_metrics = filter(lambda x: x.plugin == plugin, job.metrics)
-            plugin_metric_displays = [job_metrics.format( metric.plugin, metric.metric_name, metric.metric_value ) for metric in plugin_metrics]
-            plugin_metric_displays = sorted(plugin_metric_displays, key=lambda pair: pair[0])  # Sort on displayed title
-        %>
-            %for metric_title, metric_value in plugin_metric_displays:
-                <tr><td>${ metric_title | h }</td><td>${ metric_value | h }</td></tr>
-            %endfor
-        </tbody>
-    </table>
-    %endif
-    %endfor
+<div class="job-metrics" dataset_id="${encoded_hda_id}" dataset_type="hda">
+</div>
 %endif
 
 %if trans.user_is_admin:
@@ -352,5 +191,7 @@ $(function(){
             window.parent.Galaxy.currHistoryPanel.scrollToId( 'dataset-' + $( this ).data( 'hda-id' ) );
         }
     })
+    window.bundleEntries.mountJobMetrics();
+    window.bundleEntries.mountJobParameters();
 });
 </script>
diff --git a/templates/tagging_common.mako b/templates/tagging_common.mako
index 97ecbd272d9..a4d95adf1cd 100644
--- a/templates/tagging_common.mako
+++ b/templates/tagging_common.mako
@@ -1,6 +1,6 @@
-<%namespace file="/display_common.mako" import="get_controller_name" />
+<%namespace file="/display_common.mako" import="get_controller_name, modern_route_for_controller" />
 <%!
-from cgi import escape
+from markupsafe import escape
 %>
 
 ## Render a tagging element if there is a tagged_item.
@@ -32,7 +32,7 @@ from cgi import escape
     <%
         tagged_item_id = str( trans.security.encode_id ( tagged_item.id ) )
         controller_name = get_controller_name(tagged_item)
-        click_url = h.url_for( controller='/' + controller_name , action='list_published')
+        click_url = h.url_for( controller='/' + modern_route_for_controller(controller_name) , action='list_published')
         community_tags = trans.app.tag_handler.get_community_tags( item=tagged_item, limit=5 )
 
         ## Having trouble converting list of tags into a plain array, this just
diff --git a/templates/webapps/galaxy/dataset/embed.mako b/templates/webapps/galaxy/dataset/embed.mako
index b31c04e2f27..74948f29527 100644
--- a/templates/webapps/galaxy/dataset/embed.mako
+++ b/templates/webapps/galaxy/dataset/embed.mako
@@ -1,8 +1,4 @@
 <%inherit file="/embed_base.mako"/>
-<%!
-    from galaxy.web.framework.helpers import iff
-%>
-
 <%def name="render_item_links( dataset )">
     <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}"
        title="Save dataset" class="icon-button disk"></a>
@@ -11,12 +7,4 @@
        title="Import dataset" class="icon-button import"></a>
     <a href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}"
        title="Go to dataset" class="icon-button go-to-full-screen"></a>
-    
-</%def>
-
-<%def name="render_summary_content( dataset, data )">
-##    <ul>
-##        <li>Format : ${dataset.extension}
-##        <pre>${dataset.peek}</pre>
-##    </ul>
 </%def>
diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako
index 473a68a3e92..15230baf84f 100644
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -26,7 +26,6 @@
             'logo_src'                  : h.url_for( app.config.get( 'logo_src', '/static/images/galaxyIcon_noText.png' ) ),
             'is_admin_user'             : trans.user_is_admin,
             'active_view'               : active_view,
-            'ftp_upload_dir'            : app.config.get("ftp_upload_dir",  None),
             'ftp_upload_site'           : app.config.get("ftp_upload_site",  None),
             'datatypes_disable_auto'    : app.config.get_bool("datatypes_disable_auto",  False),
             'user_json'                 : get_user_dict()
diff --git a/templates/webapps/galaxy/galaxy.panels.mako b/templates/webapps/galaxy/galaxy.panels.mako
index 324ca1d25d8..39fc84ec0e7 100644
--- a/templates/webapps/galaxy/galaxy.panels.mako
+++ b/templates/webapps/galaxy/galaxy.panels.mako
@@ -225,7 +225,7 @@
     </script>
 
     ${ galaxy_client.load() }
-    ## ${ galaxy_client.config_sentry(app) }
+    ${ galaxy_client.config_sentry(app) }
 
 </%def>
 
diff --git a/templates/webapps/galaxy/page/display.mako b/templates/webapps/galaxy/page/display.mako
index 1ed74810217..5d3d29f613c 100644
--- a/templates/webapps/galaxy/page/display.mako
+++ b/templates/webapps/galaxy/page/display.mako
@@ -7,80 +7,8 @@
     <script type="text/javascript">
         config.addInitialization(function() {
             console.log("page/display.mako, javascript_app", "Setup embedded content");
-            // Setup embedded content:
-            //  (a) toggles for showing/hiding embedded content;
-            //  (b) ...
-            $('.embedded-item').each( function() {
-                var container = $(this);
-                if( container.hasClass( 'history' ) ){ return; }
-                //note: we can't do the same override for visualizations
-                // bc builtins (like trackster) need the handlers/ajax below to work.
-                // instead: (for registry visualizations) we'll clear the handlers below
-                //  and add new ones (in embed_in_frame.mako) ...ugh.
-            
-                // Show embedded item.
-                var show_embedded_item = function() {
-                    var ajax_url = container.find("input[type=hidden]").val();
-                    // Only get item content if it's not already there.
-                    var item_content = $.trim(container.find(".item-content").text());
-                    if (!item_content) {
-                        $.ajax({
-                            type: "GET",
-                            url: ajax_url,
-                            error: function() { alert("Getting item content failed."); },
-                            success: function( item_content ) {
-                                container.find(".summary-content").hide("fast");
-                                container.find(".item-content").html(item_content);
-                                container.find(".expanded-content").show("fast");
-                                container.find(".toggle-expand").hide();
-                                container.find(".toggle").show();
-
-                                window.bundleEntries.make_popup_menus();
-                            }
-                        });
-                    } else {
-                        container.find(".summary-content").hide("fast");
-                        container.find(".expanded-content").show("fast");
-                        container.find(".toggle-expand").hide();
-                        container.find(".toggle").show();
-                    }
-                };
-            
-                // Hide embedded item.
-                var hide_embedded_item = function() {
-                    container.find(".expanded-content").hide("fast");
-                    container.find(".summary-content").show("fast");
-                    container.find(".toggle").hide();
-                    container.find(".toggle-expand").show();
-                };
-            
-                // Setup toggle expand.
-                var toggle_expand = $(this).find('.toggle-expand');
-                toggle_expand.click( function() {
-                    show_embedded_item();
-                    return false;
-                });
-            
-                // Setup toggle contract.
-                var toggle_contract = $(this).find('.toggle');
-                toggle_contract.click( function() {
-                    hide_embedded_item();
-                    return false;
-                });
-            
-                // Setup toggle embed.
-                var toggle_embed = $(this).find('.toggle-embed');
-                toggle_embed.click( function() {
-                    if (container.find(".expanded-content").is(":visible")) {
-                        hide_embedded_item();
-                    } else {
-                        show_embedded_item();
-                    }
-                    return false;
-                });
-            });
+            window.bundleEntries.render_embedded_items();
         });
-    
     </script>
 </%def>
 
diff --git a/templates/webapps/galaxy/page/editor.mako b/templates/webapps/galaxy/page/editor.mako
index 27e2eb0307f..858774b54ef 100644
--- a/templates/webapps/galaxy/page/editor.mako
+++ b/templates/webapps/galaxy/page/editor.mako
@@ -16,46 +16,15 @@
         // Apparently pages() relies on these variables being defined
         // in window. 
         config.addInitialization(function(){
-            var pagesConfig = {
-                page_id: "${trans.security.encode_id(page.id)}",
-                page_list_url: '${h.url_for( controller='pages', action='list' )}',
-                list_objects_url: "${h.url_for(controller='page', action='LIST_ACTION' )}",
-                set_accessible_url: "${h.url_for( controller='ITEM_CONTROLLER', action='set_accessible_async' )}",
-                get_name_and_link_url: "${h.url_for( controller='ITEM_CONTROLLER', action='get_name_and_link_async' )}?id=",
-                editor_base_path: "${h.url_for('/static/wymeditor')}/",
-                iframe_base_path: "${h.url_for('/static/wymeditor/iframe/galaxy')}/",
-                save_url: "${h.url_for(controller='page', action='save' )}"
-            };
             console.log("editor.mako, javascript_app", "define variables needed by galaxy.pages script");
-            window.bundleEntries.pages(pagesConfig);
+            window.bundleEntries.pages();
         });
     </script>
 </%def>
 
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "base", "embed_item" )}
-    <style type='text/css'>
-        .galaxy-page-editor-button
-        {
-            position: relative;
-            float: left;
-            padding: 0.2em;
-        }
-    </style>
-</%def>
-
 <%def name="center_panel()">
 
-    <div class="unified-panel-header" unselectable="on">
-        <div class="unified-panel-header-inner">
-            Page Editor: ${page.title | h}
-            <a id="save-button" class="btn btn-secondary fa fa-save float-right"></a>
-        </div>
-    </div>
-
-    <div class="unified-panel-body">
-        <textarea name="page_content">${ content }</textarea>
-    </div>
+    <span id="page-editor-content" class="inbound" page_id="${trans.security.encode_id(page.id)}">
+    </span>
 
 </%def>
diff --git a/templates/webapps/galaxy/visualization/embed.mako b/templates/webapps/galaxy/visualization/embed.mako
index 242d6df7eea..9a6037dcfae 100644
--- a/templates/webapps/galaxy/visualization/embed.mako
+++ b/templates/webapps/galaxy/visualization/embed.mako
@@ -1,4 +1 @@
 <%inherit file="/embed_base.mako"/>
-
-<%def name="render_summary_content( workflow, steps )">
-</%def>
diff --git a/templates/webapps/galaxy/visualization/embed_in_frame.mako b/templates/webapps/galaxy/visualization/embed_in_frame.mako
index b239bc1ba3a..2bd7d24c5ec 100644
--- a/templates/webapps/galaxy/visualization/embed_in_frame.mako
+++ b/templates/webapps/galaxy/visualization/embed_in_frame.mako
@@ -24,10 +24,6 @@
         <div class="annotation">${item.annotation}</div>
         %endif
     </div>
-    ##<div class='summary-content'>
-        ## currently, no summary content for visualization
-        ## could do the title or caption, whatever...
-    ##</div>
     <div class='expanded-content'>
         <div class='item-content'>
         </div>
diff --git a/templates/webapps/galaxy/workflow/display.mako b/templates/webapps/galaxy/workflow/display.mako
index 68265cfcfea..1bd5fac5e50 100644
--- a/templates/webapps/galaxy/workflow/display.mako
+++ b/templates/webapps/galaxy/workflow/display.mako
@@ -2,9 +2,9 @@
 <%namespace file="/display_common.mako" import="render_message" />
 
 <%!
+    import markupsafe
     from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter, RuntimeValue
     from galaxy.web import form_builder
-    import cgi
 %>
 
 <%def name="stylesheets()">
@@ -64,7 +64,7 @@
                     <i>select at runtime</i>
                 %endif
             %else:
-                ${cgi.escape( param.value_to_display_text( value ) or 'Unavailable.' )}
+                ${markupsafe.escape( param.value_to_display_text( value ) or 'Unavailable.' )}
             %endif
         </div>
         %if hasattr( step, 'upgrade_messages' ) and step.upgrade_messages and param.name in step.upgrade_messages:
diff --git a/templates/webapps/galaxy/workflow/editor.mako b/templates/webapps/galaxy/workflow/editor.mako
index aa55bfbd47b..09f66de636d 100644
--- a/templates/webapps/galaxy/workflow/editor.mako
+++ b/templates/webapps/galaxy/workflow/editor.mako
@@ -57,6 +57,9 @@
     ${parent.stylesheets()}
 
     <style type="text/css">
+    #center {
+        z-index: 0;
+    }
     canvas { position: absolute; z-index: 10; }
     canvas.dragging { position: absolute; z-index: 1000; }
     </style>
@@ -225,10 +228,18 @@
 <%def name="center_panel()">
 
     <div class="unified-panel-header" unselectable="on">
-        <div class="panel-header-buttons">
-            <a id="workflow-options-button" class="panel-header-button" href="#"><span class="fa fa-cog"></span></a>
-        </div>
         <div class="unified-panel-header-inner">
+            <div class="panel-header-buttons">
+                <a id="workflow-run-button" class="panel-header-button" href="#" title="Run" style="display: inline-block;" aria-label="Run">
+                    <span class="fa fa-play"></span>
+                </a>
+                <a id="workflow-save-button" class="panel-header-button" href="#" title="Save" style="display: inline-block;" aria-label="Save">
+                    <span class="fa fa-floppy-o"></span>
+                </a>
+                <a id="workflow-options-button" class="panel-header-button" href="#" title="Workflow options" style="display: inline-block;" aria-label="Workflow options">
+                    <span class="fa fa-cog"></span>
+                </a>
+            </div>
             ${h.to_unicode( stored.name ) | h}
         </div>
     </div>
diff --git a/templates/webapps/galaxy/workflow/embed.mako b/templates/webapps/galaxy/workflow/embed.mako
index 2297b99c5fc..dee48db4490 100644
--- a/templates/webapps/galaxy/workflow/embed.mako
+++ b/templates/webapps/galaxy/workflow/embed.mako
@@ -1,24 +1,6 @@
 <%inherit file="/embed_base.mako"/>
-<%!
-    from galaxy.web.framework.helpers import iff
-%>
-
 <%def name="render_item_links( workflow )">
 	<a href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username,
                           slug=item.slug, format='json-download' )}" title="Save Worflow" class="icon-button disk">
-	## FIXME: find and set appropriate icon for linking to workflow.
-	<!--
-	<a href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username,
-                          slug=item.slug, format='json' )}" title="Worflow Link for Import" class="icon-button TODO ">
-	-->
 	${parent.render_item_links( workflow )}
 </%def>
-
-<%def name="render_summary_content( workflow, steps )">
-
-##    <ul>
-##        <% num_steps = len ( steps ) %>
-##        <li>${num_steps} step${iff( num_steps != 1, "s", "" )}
-##        <li>Operations: ...
-##    </ul>
-</%def>
diff --git a/templates/webapps/tool_shed/base_panels.mako b/templates/webapps/tool_shed/base_panels.mako
index 295f897679f..dd4c983abe4 100644
--- a/templates/webapps/tool_shed/base_panels.mako
+++ b/templates/webapps/tool_shed/base_panels.mako
@@ -46,7 +46,7 @@
 <%def name="masthead()">
 
     %if app.config.ga_code:
-        ${galaxy_client.config_google_analytics(app)}
+        ${ galaxy_client.config_google_analytics(app.config.ga_code)}
     %endif
 
     ## start main tag
diff --git a/test-data/groupby_out1.dat b/test-data/groupby_out1.dat
deleted file mode 100644
index f822b20ca1a..00000000000
--- a/test-data/groupby_out1.dat
+++ /dev/null
@@ -1,20 +0,0 @@
-chr1	1.48053e+08
-chr10	5.52516e+07
-chr11	8.75888e+07
-chr12	3.84401e+07
-chr13	1.12382e+08
-chr14	9.87102e+07
-chr15	4.16664e+07
-chr16	206638
-chr18	5.05624e+07
-chr19	5.92262e+07
-chr2	1.69276e+08
-chr20	3.35042e+07
-chr21	3.31607e+07
-chr22	3.04712e+07
-chr5	1.31612e+08
-chr6	1.08564e+08
-chr7	1.15958e+08
-chr8	1.18881e+08
-chr9	1.28843e+08
-chrx	1.45195e+08
diff --git a/test-data/groupby_out2.dat b/test-data/groupby_out2.dat
deleted file mode 100644
index f89d723ab44..00000000000
--- a/test-data/groupby_out2.dat
+++ /dev/null
@@ -1,3 +0,0 @@
-	
-chr10	chr10
-chr22	chr22
diff --git a/test-data/groupby_out3.tabular b/test-data/groupby_out3.tabular
deleted file mode 100644
index cc5214529db..00000000000
--- a/test-data/groupby_out3.tabular
+++ /dev/null
@@ -1,20 +0,0 @@
-chr1	1.48053e+08	1.48031e+08	-,+	1.48185e+08	1.47962e+08	5.9221e+08	4	1	chr1,chr1,chr1,chr1	+,-	148185136	88085.9
-chr10	5.52516e+07	5.52516e+07	-	5.52516e+07	5.52516e+07	5.52516e+07	1	1	chr10	-	55251623	0
-chr11	8.75888e+07	1.16165e+08	-,+	1.16212e+08	1.81238e+06	3.50355e+08	4	1	chr11,chr11,chr11,chr11	+,-	1812377	4.9523e+07
-chr12	3.84401e+07	3.84401e+07	-	3.84401e+07	3.84401e+07	3.84401e+07	1	1	chr12	-	38440094	0
-chr13	1.12382e+08	1.12382e+08	+	1.12382e+08	1.12382e+08	1.12382e+08	1	1	chr13	+	112381694	0
-chr14	9.87102e+07	9.87102e+07	-	9.87102e+07	9.87102e+07	9.87102e+07	1	1	chr14	-	98710240	0
-chr15	4.16664e+07	4.16764e+07	-,+	4.1826e+07	4.14869e+07	1.66666e+08	4	1	chr15,chr15,chr15,chr15	+,-	41673708	120341
-chr16	206638	212188	+,-	259268	142908	826552	4	1	chr16,chr16,chr16,chr16	+,-	244413	47354.9
-chr18	5.05624e+07	5.94314e+07	-,+	5.96006e+07	2.37861e+07	2.0225e+08	4	1	chr18,chr18,chr18,chr18	+,-	23786114	1.54594e+07
-chr19	5.92262e+07	5.9267e+07	+,-	5.93022e+07	5.90686e+07	2.36905e+08	4	1	chr19,chr19,chr19,chr19	+,-	59236026	94686.3
-chr2	1.69276e+08	1.69292e+08	+,-	2.2023e+08	1.18289e+08	6.77103e+08	4	1	chr2,chr2,chr2,chr2	+,-	220190202	5.09343e+07
-chr20	3.35042e+07	3.35466e+07	-,+	3.35933e+07	3.33304e+07	1.34017e+08	4	1	chr20,chr20,chr20,chr20	+,-	33579500	104752
-chr21	3.31607e+07	3.30953e+07	+,-	3.3745e+07	3.2707e+07	1.32643e+08	4	1	chr21,chr21,chr21,chr21	+,-	33321040	405475
-chr22	3.04712e+07	3.04128e+07	+,-	3.09391e+07	3.01202e+07	1.21885e+08	4	1	chr22,chr22,chr22,chr22	+,-	30120223	345080
-chr5	1.31612e+08	1.31589e+08	+,-	1.31848e+08	1.31424e+08	5.2645e+08	4	1	chr5,chr5,chr5,chr5	+,-	131556601	153188
-chr6	1.08564e+08	1.08617e+08	-,+	1.08723e+08	1.083e+08	4.34257e+08	4	1	chr6,chr6,chr6,chr6	+,-	108640045	159611
-chr7	1.15958e+08	1.16613e+08	+,-	1.16946e+08	1.13661e+08	4.63832e+08	4	1	chr7,chr7,chr7,chr7	+,-	113660517	1.33533e+06
-chr8	1.18881e+08	1.18881e+08	-	1.18881e+08	1.18881e+08	1.18881e+08	1	1	chr8	-	118881131	0
-chr9	1.28843e+08	1.28835e+08	+,-	1.28937e+08	1.28764e+08	5.15371e+08	4	1	chr9,chr9,chr9,chr9	+,-	128787519	70228.2
-chrX	1.45195e+08	1.5267e+08	+,-	1.52694e+08	1.22745e+08	5.80779e+08	4	1	chrX,chrX,chrX,chrX	+,-	152648964	1.29614e+07
diff --git a/test-data/groupby_out4.tabular b/test-data/groupby_out4.tabular
deleted file mode 100644
index 3a9115ca22c..00000000000
--- a/test-data/groupby_out4.tabular
+++ /dev/null
@@ -1,3 +0,0 @@
-	1600
-chr10	1133.33
-chr22	1500
diff --git a/test-data/new_tags_1.txt b/test-data/new_tags_1.txt
index 91caa6c4fae..4dbd9d7a001 100644
--- a/test-data/new_tags_1.txt
+++ b/test-data/new_tags_1.txt
@@ -1,2 +1,2 @@
-forward	orientation:forward	alias:r1	alias:f
-reverse	orientation:reverse	alias:r2	alias:r
+forward	orientation:forward	alias:r1	alias:f	#forward
+reverse	orientation:reverse	alias:r2	alias:r	#reverse
diff --git a/test/api/test_configuration.py b/test/api/test_configuration.py
index 30e45d8663f..91e192ba621 100644
--- a/test/api/test_configuration.py
+++ b/test/api/test_configuration.py
@@ -10,7 +10,6 @@ from base.populators import (
 TEST_KEYS_FOR_ALL_USERS = [
     'enable_unique_workflow_defaults',
     'ftp_upload_site',
-    'ftp_upload_dir',
     'wiki_url',
     'support_url',
     'logo_url',
diff --git a/test/api/test_datasets.py b/test/api/test_datasets.py
index ab4df66bc5d..013fcf2d10b 100644
--- a/test/api/test_datasets.py
+++ b/test/api/test_datasets.py
@@ -3,21 +3,101 @@ from __future__ import print_function
 import textwrap
 
 from base import api
-from base.populators import TestsDatasets
+from base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+)
 
 
-class DatasetsApiTestCase(api.ApiTestCase, TestsDatasets):
+class DatasetsApiTestCase(api.ApiTestCase):
 
     def setUp(self):
         super(DatasetsApiTestCase, self).setUp()
-        self.history_id = self._new_history()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
+        self.history_id = self.dataset_populator.new_history()
 
     def test_index(self):
         index_response = self._get("datasets")
-        self._assert_status_code_is(index_response, 501)
+        self._assert_status_code_is(index_response, 200)
+
+    def test_search_datasets(self):
+        hda_id = self.dataset_populator.new_dataset(self.history_id)['id']
+        payload = {'limit': 1, 'offset': 0}
+        index_response = self._get("datasets", payload).json()
+        assert len(index_response) == 1
+        assert index_response[0]['id'] == hda_id
+        hdca_id = self.dataset_collection_populator.create_list_in_history(self.history_id,
+                                                                           contents=["1\n2\n3"]).json()['id']
+        payload = {'limit': 3, 'offset': 0}
+        index_response = self._get("datasets", payload).json()
+        assert len(index_response) == 3
+        assert index_response[0]['id'] == hdca_id
+        assert index_response[0]['history_content_type'] == 'dataset_collection'
+        assert index_response[2]['id'] == hda_id
+        assert index_response[2]['history_content_type'] == 'dataset'
+        payload = {'limit': 2, 'offset': 0, 'q': ['history_content_type'], 'qv': ['dataset']}
+        index_response = self._get("datasets", payload).json()
+        assert index_response[1]['id'] == hda_id
+
+    def test_search_by_tag(self):
+        hda_id = self.dataset_populator.new_dataset(self.history_id)['id']
+        update_payload = {
+            'tags': ['cool:new_tag', 'cool:another_tag'],
+        }
+        updated_hda = self._put(
+            "histories/{history_id}/contents/{hda_id}".format(history_id=self.history_id, hda_id=hda_id),
+            update_payload).json()
+        assert 'cool:new_tag' in updated_hda['tags']
+        assert 'cool:another_tag' in updated_hda['tags']
+        payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag'], 'qv': ['dataset', 'cool:new_tag']}
+        index_response = self._get("datasets", payload).json()
+        assert len(index_response) == 1
+        payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag-contains'],
+                   'qv': ['dataset', 'new_tag']}
+        index_response = self._get("datasets", payload).json()
+        assert len(index_response) == 1
+        payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag-contains'], 'qv': ['dataset', 'notag']}
+        index_response = self._get("datasets", payload).json()
+        assert len(index_response) == 0
+
+    def test_search_by_tool_id(self):
+        self.dataset_populator.new_dataset(self.history_id)
+        payload = {'limit': 1, 'offset': 0, 'q': ['history_content_type', 'tool_id'], 'qv': ['dataset', 'upload1']}
+        assert len(self._get("datasets", payload).json()) == 1
+        payload = {'limit': 1, 'offset': 0, 'q': ['history_content_type', 'tool_id'], 'qv': ['dataset', 'uploadX']}
+        assert len(self._get("datasets", payload).json()) == 0
+        payload = {'limit': 1, 'offset': 0, 'q': ['history_content_type', 'tool_id-contains'], 'qv': ['dataset', 'pload1']}
+        assert len(self._get("datasets", payload).json()) == 1
+        self.dataset_collection_populator.create_list_in_history(self.history_id,
+                                                                 name="search by tool id",
+                                                                 contents=["1\n2\n3"]).json()
+        self.dataset_populator.wait_for_history(self.history_id)
+        payload = {'limit': 10, 'offset': 0, 'history_id': self.history_id, 'q': ['name', 'tool_id'],
+                   'qv': ['search by tool id', 'upload1']}
+        result = self._get("datasets", payload).json()
+        assert result[0]['name'] == 'search by tool id', result
+        payload = {'limit': 1, 'offset': 0, 'q': ['history_content_type', 'tool_id'],
+                   'qv': ['dataset_collection', 'uploadX']}
+        result = self._get("datasets", payload).json()
+        assert len(result) == 0
+
+    def test_invalid_search(self):
+        payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag-invalid_op'], 'qv': ['dataset', 'notag']}
+        index_response = self._get("datasets", payload)
+        self._assert_status_code_is(index_response, 400)
+        assert index_response.json()['err_msg'] == 'bad op in filter'
+
+    def test_search_returns_only_accessible(self):
+        hda_id = self.dataset_populator.new_dataset(self.history_id)['id']
+        with self._different_user():
+            payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type'], 'qv': ['dataset']}
+            index_response = self._get("datasets", payload).json()
+            for item in index_response:
+                assert hda_id != item['id']
 
     def test_show(self):
-        hda1 = self._new_dataset(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
         show_response = self._get("datasets/%s" % (hda1["id"]))
         self._assert_status_code_is(show_response, 200)
         self.__assert_matches_hda(hda1, show_response.json())
@@ -33,8 +113,8 @@ class DatasetsApiTestCase(api.ApiTestCase, TestsDatasets):
         A   B   C   D
         10  20  30  40
         """)
-        hda1 = self._new_dataset(self.history_id, content=contents)
-        self._wait_for_history(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id, content=contents)
+        self.dataset_populator.wait_for_history(self.history_id)
         display_response = self._get("histories/%s/contents/%s/display" % (self.history_id, hda1["id"]), {
             'raw': 'True'
         })
diff --git a/test/api/test_libraries.py b/test/api/test_libraries.py
index 8535511e480..a9f8d5f4f05 100644
--- a/test/api/test_libraries.py
+++ b/test/api/test_libraries.py
@@ -101,7 +101,7 @@ class LibrariesApiTestCase(api.ApiTestCase, TestsDatasets):
 
     def test_fetch_upload_to_folder(self):
         history_id, library, destination = self._setup_fetch_to_folder("flat_zip")
-        items = [{"src": "files", "dbkey": "hg19", "info": "my cool bed"}]
+        items = [{"src": "files", "dbkey": "hg19", "info": "my cool bed", "created_from_basename": "4.bed"}]
         targets = [{
             "destination": destination,
             "items": items
@@ -117,6 +117,7 @@ class LibrariesApiTestCase(api.ApiTestCase, TestsDatasets):
         assert dataset["genome_build"] == "hg19", dataset
         assert dataset["misc_info"] == "my cool bed", dataset
         assert dataset["file_ext"] == "bed", dataset
+        assert dataset["created_from_basename"] == "4.bed"
 
     def test_fetch_zip_to_folder(self):
         history_id, library, destination = self._setup_fetch_to_folder("flat_zip")
diff --git a/test/api/test_page_revisions.py b/test/api/test_page_revisions.py
index 33d29d74fe6..fb89c90d680 100644
--- a/test/api/test_page_revisions.py
+++ b/test/api/test_page_revisions.py
@@ -28,8 +28,8 @@ class PageRevisionsApiTestCase(BasePageApiTestCase):
         revisions_json = revisions_response.json()
         assert len(revisions_json) == 2  # Original revision and new one
 
-    def test_404_if_index_unknown_page(self):
+    def test_malformed_id_if_index_unknown_page(self):
         revisions_url = "pages/%s/revisions" % self._random_key()
         revisions_response = self._get(revisions_url)
-        self._assert_status_code_is(revisions_response, 404)
-        self._assert_error_code_is(revisions_response, error_codes.USER_OBJECT_NOT_FOUND)
+        self._assert_status_code_is(revisions_response, 400)
+        self._assert_error_code_is(revisions_response, error_codes.MALFORMED_ID)
diff --git a/test/api/test_pages.py b/test/api/test_pages.py
index 6cabf05526a..4126fa0a46e 100644
--- a/test/api/test_pages.py
+++ b/test/api/test_pages.py
@@ -1,6 +1,7 @@
 from requests import delete
 
 from base import api  # noqa: I100,I202
+from base.populators import DatasetPopulator
 from galaxy.exceptions import error_codes  # noqa: I201
 
 
@@ -53,7 +54,7 @@ class PageApiTestCase(BasePageApiTestCase):
         self._assert_error_code_is(page_response_2, error_codes.USER_SLUG_DUPLICATE)
 
     def test_page_requires_name(self):
-        page_request = self._test_page_payload()
+        page_request = self._test_page_payload(slug="requires-name")
         del page_request['title']
         page_response = self._post("pages", page_request)
         self._assert_status_code_is(page_response, 400)
@@ -70,10 +71,10 @@ class PageApiTestCase(BasePageApiTestCase):
         delete_response = delete(self._api_url("pages/%s" % response_json['id'], use_key=True))
         self._assert_status_code_is(delete_response, 200)
 
-    def test_404_on_delete_unknown_page(self):
+    def test_400_on_delete_invalid_page_id(self):
         delete_response = delete(self._api_url("pages/%s" % self._random_key(), use_key=True))
-        self._assert_status_code_is(delete_response, 404)
-        self._assert_error_code_is(delete_response, error_codes.USER_OBJECT_NOT_FOUND)
+        self._assert_status_code_is(delete_response, 400)
+        self._assert_error_code_is(delete_response, error_codes.MALFORMED_ID)
 
     def test_403_on_delete_unowned_page(self):
         page_response = self._create_valid_page_as("others_page@bx.psu.edu", "otherspage")
@@ -81,6 +82,23 @@ class PageApiTestCase(BasePageApiTestCase):
         self._assert_status_code_is(delete_response, 403)
         self._assert_error_code_is(delete_response, error_codes.USER_DOES_NOT_OWN_ITEM)
 
+    def test_400_on_invalid_id_encoding(self):
+        page_request = self._test_page_payload(slug="invalid-id-encding")
+        page_request["content"] = '''<p>Page!<div class="embedded-item" id="History-invaidencodedid"></div></p>'''
+        page_response = self._post("pages", page_request)
+        self._assert_status_code_is(page_response, 400)
+        self._assert_error_code_is(page_response, error_codes.MALFORMED_ID)
+
+    def test_400_on_invalid_embedded_content(self):
+        dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        valid_id = dataset_populator.new_history()
+        page_request = self._test_page_payload(slug="invalid-id-encding")
+        page_request["content"] = '''<p>Page!<div class="embedded-item" id="CoolObject-%s"></div></p>''' % valid_id
+        page_response = self._post("pages", page_request)
+        self._assert_status_code_is(page_response, 400)
+        self._assert_error_code_is(page_response, error_codes.USER_REQUEST_INVALID_PARAMETER)
+        assert "embedded HTML content" in page_response.content
+
     def test_show(self):
         response_json = self._create_valid_page_with_slug("pagetoshow")
         show_response = self._get("pages/%s" % response_json['id'])
@@ -95,7 +113,7 @@ class PageApiTestCase(BasePageApiTestCase):
         response_json = self._create_valid_page_as("others_page_show@bx.psu.edu", "otherspageshow")
         show_response = self._get("pages/%s" % response_json['id'])
         self._assert_status_code_is(show_response, 403)
-        self._assert_error_code_is(show_response, error_codes.USER_DOES_NOT_OWN_ITEM)
+        self._assert_error_code_is(show_response, error_codes.USER_CANNOT_ACCESS_ITEM)
 
     def _users_index_has_page_with_id(self, id):
         index_response = self._get("pages")
diff --git a/test/api/test_users.py b/test/api/test_users.py
index aaf8d091b11..f1a98a121e5 100644
--- a/test/api/test_users.py
+++ b/test/api/test_users.py
@@ -121,8 +121,7 @@ class UsersApiTestCase(api.ApiTestCase):
 
     @skip_without_tool("cat1")
     def test_search_favorites(self):
-        user = self._setup_user(TEST_USER_EMAIL)
-        user_key = self._setup_user_get_key(TEST_USER_EMAIL)
+        user, user_key = self._setup_user_get_key(TEST_USER_EMAIL)
         url = self._api_url("users/%s/favorites/tools" % user["id"], params=dict(key=user_key))
         fav_response = put(url, data=json.dumps({"object_id" : "cat1"}))
         self._assert_status_code_is_ok(fav_response)
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 17f99df00e5..7608c3c0de2 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -1924,6 +1924,13 @@ input1:
 
     @skip_without_tool("cat")
     def test_pause_outputs_with_deleted_inputs(self):
+        self._deleted_inputs_workflow(purge=False)
+
+    @skip_without_tool("cat")
+    def test_error_outputs_with_purged_inputs(self):
+        self._deleted_inputs_workflow(purge=True)
+
+    def _deleted_inputs_workflow(self, purge):
         # We run a workflow on a collection with a deleted element.
         with self.dataset_populator.test_history() as history_id:
             workflow_id = self._upload_yaml_workflow("""
@@ -1948,7 +1955,8 @@ steps:
             hdca1 = self.dataset_collection_populator.create_list_in_history(history_id,
                                                                              contents=[("sample1-1", "1 2 3")]).json()
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-            r = self._delete("histories/%s/contents/%s" % (history_id, hdca1['elements'][DELETED]['object']['id']))
+            deleted_id = hdca1['elements'][DELETED]['object']['id']
+            r = self._delete("histories/%s/contents/%s?purge=%s" % (history_id, deleted_id, purge))
             label_map = {"input1": self._ds_entry(hdca1)}
             workflow_request = dict(
                 history="hist_id=%s" % history_id,
@@ -1962,7 +1970,8 @@ steps:
             self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=False)
             contents = self.__history_contents(history_id)
             assert contents[DELETED]['deleted']
-            assert contents[PAUSED_1]['state'] == 'paused'
+            state = 'error' if purge else 'paused'
+            assert contents[PAUSED_1]['state'] == state
             assert contents[PAUSED_2]['state'] == 'paused'
 
     def test_run_with_implicit_connection(self):
@@ -2111,6 +2120,46 @@ test_data: {}
         assert int(str_43) == 43
         assert abs(float(str_4point14) - 4.14) < .0001
 
+    @skip_without_tool("param_value_from_file")
+    def test_expression_tool_map_over(self):
+        history_id = self.dataset_populator.new_history()
+        self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  text_input1: collection
+steps:
+- label: param_out
+  tool_id: param_value_from_file
+  in:
+     input1: text_input1
+- label: consume_expression_parameter
+  tool_id: validation_default
+  in:
+    input1: param_out#text_param
+  outputs:
+    out_file1:
+      rename: "replaced_param_collection"
+test_data:
+  text_input1:
+    type: list
+    elements:
+      - identifier: A
+        content: A
+      - identifier: B
+        content: B
+""", history_id=history_id)
+        history_contents = self._get('histories/{history_id}/contents'.format(history_id=history_id)).json()
+        collection = [c for c in history_contents if c['history_content_type'] == 'dataset_collection' and c['name'] == 'replaced_param_collection'][0]
+        collection_details = self._get(collection['url']).json()
+        assert collection_details['element_count'] == 2
+        elements = collection_details['elements']
+        assert elements[0]['element_identifier'] == 'A'
+        assert elements[1]['element_identifier'] == 'B'
+        element_a_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=elements[0]['object'])
+        element_b_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=elements[1]['object'])
+        assert element_a_content.strip() == 'A'
+        assert element_b_content.strip() == 'B'
+
     @skip_without_tool('cat1')
     def test_workflow_rerun_with_use_cached_job(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_run")
@@ -2892,6 +2941,35 @@ input1:
             assert details1["history_content_type"] == "dataset_collection"
             assert details1["tags"][0] == "name:foo", details1
 
+    @skip_without_tool("cat")
+    def test_assign_column_pja(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  input1: data
+steps:
+  first_cat:
+    tool_id: cat
+    in:
+      input1: input1
+    outputs:
+      out_file1:
+        change_datatype: bed
+        set_columns:
+          chromCol: 1
+          endCol: 2
+          startCol: 3
+""", test_data="""
+input1:
+  value: 1.bed
+  type: File
+""", history_id=history_id)
+            details_dataset_new_col = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=True)
+            assert details_dataset_new_col["history_content_type"] == "dataset", details_dataset_new_col
+            assert details_dataset_new_col['metadata_endCol'] == 2
+            assert details_dataset_new_col['metadata_startCol'] == 3
+
     @skip_without_tool("collection_creates_pair")
     @skip_without_tool("cat")
     def test_run_remove_tag_on_collection_output(self):
diff --git a/test/api/test_workflows_from_yaml.py b/test/api/test_workflows_from_yaml.py
index f6b7d1e54de..c3ebec9a02f 100644
--- a/test/api/test_workflows_from_yaml.py
+++ b/test/api/test_workflows_from_yaml.py
@@ -306,7 +306,7 @@ test_data:
 """, history_id=history_id)
 
         content = self.dataset_populator.get_history_dataset_content(history_id)
-        self.assertEquals(content, "hello world\nhello world 2\n")
+        self.assertEqual(content, "hello world\nhello world 2\n")
 
     def test_workflow_import_tool(self):
         history_id = self.dataset_populator.new_history()
@@ -321,7 +321,7 @@ test_data:
             history_id=history_id
         )
         content = self.dataset_populator.get_history_dataset_content(history_id)
-        self.assertEquals(content, "hello world\nhello world 2\n")
+        self.assertEqual(content, "hello world\nhello world 2\n")
 
     def _steps_by_label(self, workflow_as_dict):
         by_label = {}
diff --git a/test/base/api.py b/test/base/api.py
index 8b98da97abf..c6d99404a5c 100644
--- a/test/base/api.py
+++ b/test/base/api.py
@@ -1,3 +1,4 @@
+import os
 from contextlib import contextmanager
 
 from six.moves.urllib.parse import urlencode
@@ -22,6 +23,12 @@ from .testcase import FunctionalTestCase
 
 class UsesApiTestCaseMixin(object):
 
+    def tearDown(self):
+        if os.environ.get('GALAXY_TEST_EXTERNAL') is None:
+            # Only kill running jobs after test for managed test instances
+            for job in self.galaxy_interactor.get('jobs?state=running&?user_details=true').json():
+                self._delete("jobs/%s" % job['id'])
+
     def _api_url(self, path, params=None, use_key=None, use_admin_key=None):
         if not params:
             params = {}
@@ -40,17 +47,15 @@ class UsesApiTestCaseMixin(object):
         self.master_api_key = get_master_api_key()
         self.galaxy_interactor = ApiTestInteractor(self)
 
-    def _setup_user(self, email, password=None):
+    def _setup_user(self, email, password=None, is_admin=True):
         self.galaxy_interactor.ensure_user_with_email(email, password=password)
-        users = self._get("users", admin=True).json()
+        users = self._get("users", admin=is_admin).json()
         user = [user for user in users if user["email"] == email][0]
         return user
 
-    def _setup_user_get_key(self, email):
-        self.galaxy_interactor.ensure_user_with_email(email)
-        users = self._get("users", admin=True).json()
-        user = [user for user in users if user["email"] == email][0]
-        return self._post("users/%s/api_key" % user["id"], admin=True).json()
+    def _setup_user_get_key(self, email, password=None, is_admin=True):
+        user = self._setup_user(email, password, is_admin)
+        return user, self._post("users/%s/api_key" % user["id"], admin=True).json()
 
     @contextmanager
     def _different_user(self, email=OTHER_USER):
@@ -61,7 +66,7 @@ class UsesApiTestCaseMixin(object):
         """
         original_api_key = self.user_api_key
         original_interactor_key = self.galaxy_interactor.api_key
-        new_key = self._setup_user_get_key(email)
+        user, new_key = self._setup_user_get_key(email)
         try:
             self.user_api_key = new_key
             self.galaxy_interactor.api_key = new_key
diff --git a/test/base/driver_util.py b/test/base/driver_util.py
index 42b275cb9b0..c828c848389 100644
--- a/test/base/driver_util.py
+++ b/test/base/driver_util.py
@@ -172,6 +172,8 @@ def setup_galaxy_config(
             default_data_manager_config = data_manager_config
     data_manager_config_file = "%s,test/functional/tools/sample_data_manager_conf.xml" % default_data_manager_config
     master_api_key = get_master_api_key()
+    cleanup_job = 'never' if ("GALAXY_TEST_NO_CLEANUP" in os.environ or
+                              "TOOL_SHED_TEST_NO_CLEANUP" in os.environ) else 'onsuccess'
 
     # Data Manager testing temp path
     # For storing Data Manager outputs and .loc files so that real ones don't get clobbered
@@ -204,7 +206,7 @@ def setup_galaxy_config(
         conda_prefix=conda_prefix,
         conda_auto_init=conda_auto_init,
         conda_auto_install=conda_auto_install,
-        cleanup_job='onsuccess',
+        cleanup_job=cleanup_job,
         data_manager_config_file=data_manager_config_file,
         enable_beta_tool_formats=True,
         expose_dataset_path=True,
@@ -238,6 +240,36 @@ def setup_galaxy_config(
     )
     config.update(database_conf(tmpdir, prefer_template_database=prefer_template_database))
     config.update(install_database_conf(tmpdir, default_merged=default_install_db_merged))
+    if asbool(os.environ.get("GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE")):
+        object_store_config = os.path.join(tmpdir, "object_store_conf.yml")
+        with open(object_store_config, "w") as f:
+            contents = """
+type: hierarchical
+backends:
+   - id: files1
+     type: disk
+     weight: 1
+     files_dir: "${temp_directory}/files1"
+     extra_dirs:
+     - type: temp
+       path: "${temp_directory}/tmp1"
+     - type: job_work
+       path: "${temp_directory}/job_working_directory1"
+   - id: files2
+     type: disk
+     weight: 1
+     files_dir: "${temp_directory}/files2"
+     extra_dirs:
+     - type: temp
+       path: "${temp_directory}/tmp2"
+     - type: job_work
+       path: "${temp_directory}/job_working_directory2"
+"""
+            contents_template = string.Template(contents)
+            expanded_contents = contents_template.safe_substitute(temp_directory=tmpdir)
+            f.write(expanded_contents)
+        config["object_store_config_file"] = object_store_config
+
     if datatypes_conf is not None:
         config['datatypes_config_file'] = datatypes_conf
     if enable_tool_shed_check:
diff --git a/test/base/integration_util.py b/test/base/integration_util.py
index 36e9aa44b0c..24724825829 100644
--- a/test/base/integration_util.py
+++ b/test/base/integration_util.py
@@ -9,7 +9,7 @@ from unittest import skip, SkipTest, TestCase
 
 import pytest
 
-from galaxy.tools.deps.commands import which
+from galaxy.tool_util.deps.commands import which
 from galaxy.tools.verify.test_data import TestDataResolver
 from .api import UsesApiTestCaseMixin
 from .driver_util import GalaxyTestDriver
@@ -17,8 +17,11 @@ from .driver_util import GalaxyTestDriver
 NO_APP_MESSAGE = "test_case._app called though no Galaxy has been configured."
 
 
-def skip_if_jenkins(cls):
+def _identity(func):
+    return func
 
+
+def skip_if_jenkins(cls):
     if os.environ.get("BUILD_NUMBER", ""):
         return skip
 
@@ -27,7 +30,7 @@ def skip_if_jenkins(cls):
 
 def skip_unless_executable(executable):
     if which(executable):
-        return lambda func: func
+        return _identity
     return skip("PATH doesn't contain executable %s" % executable)
 
 
@@ -39,6 +42,17 @@ def skip_unless_kubernetes():
     return skip_unless_executable("kubectl")
 
 
+def k8s_config_path():
+    return os.environ.get('GALAXY_TEST_KUBE_CONFIG_PATH', '~/.kube/config')
+
+
+def skip_unless_fixed_port():
+    if os.environ.get("GALAXY_TEST_PORT"):
+        return _identity
+
+    return skip("GALAXY_TEST_PORT must be set for this test.")
+
+
 class IntegrationInstance(UsesApiTestCaseMixin):
     """Unit test case with utilities for spinning up Galaxy."""
 
diff --git a/test/base/populators.py b/test/base/populators.py
index 60621657961..0ee8b19d416 100644
--- a/test/base/populators.py
+++ b/test/base/populators.py
@@ -1292,11 +1292,13 @@ class DatasetCollectionPopulator(BaseDatasetCollectionPopulator):
 
 def load_data_dict(history_id, test_data, dataset_populator, dataset_collection_populator):
 
-    def read_test_data(test_dict):
+    def open_test_data(test_dict, mode="rb"):
         test_data_resolver = TestDataResolver()
         filename = test_data_resolver.get_filename(test_dict["value"])
-        content = open(filename, "r").read()
-        return content
+        return open(filename, mode)
+
+    def read_test_data(test_dict):
+        return open_test_data(test_dict, mode="r").read()
 
     inputs = {}
     label_map = {}
@@ -1342,7 +1344,7 @@ def load_data_dict(history_id, test_data, dataset_populator, dataset_collection_
         elif is_dict and "type" in value:
             input_type = value["type"]
             if input_type == "File":
-                content = read_test_data(value)
+                content = open_test_data(value)
                 new_dataset_kwds = {
                     "content": content
                 }
@@ -1370,7 +1372,7 @@ def load_data_dict(history_id, test_data, dataset_populator, dataset_collection_
 def wait_on_state(state_func, desc="state", skip_states=["running", "queued", "new", "ready"], assert_ok=False, timeout=DEFAULT_TIMEOUT):
     def get_state():
         response = state_func()
-        assert response.status_code == 200, "Failed to fetch state update while waiting."
+        assert response.status_code == 200, "Failed to fetch state update while waiting. [%s]" % response.content
         state = response.json()["state"]
         if state in skip_states:
             return None
diff --git a/test/docker/base/Dockerfile b/test/docker/base/Dockerfile
index cc917f67f8e..6da7bea3101 100644
--- a/test/docker/base/Dockerfile
+++ b/test/docker/base/Dockerfile
@@ -1,5 +1,5 @@
 FROM ubuntu:16.04
-MAINTAINER John Chilton <jmchilton@gmail.com>
+LABEL maintainer="John Chilton <jmchilton@gmail.com>"
 
 ARG CHROME_VERSION="google-chrome-beta"
 ARG CHROME_DRIVER_VERSION="2.38"
@@ -79,7 +79,7 @@ RUN cd $GALAXY_ROOT && \
 RUN for VENV in $GALAXY_VIRTUAL_ENV_3 $GALAXY_VIRTUAL_ENV_2; do \
         export GALAXY_VIRTUAL_ENV=$VENV && \
         . $GALAXY_VIRTUAL_ENV/bin/activate && \
-        pip install psycopg2; done && \
+        pip install psycopg2-binary; done && \
     cd $GALAXY_ROOT && \
     echo "Prepopulating postgres database" && \
     su -c '/usr/lib/postgresql/${POSTGRES_MAJOR}/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \
@@ -156,8 +156,8 @@ USER root
 
 ADD run_test_wrapper.sh /usr/local/bin/run_test_wrapper.sh
 
-EXPOSE :9009
-EXPOSE :8080
-EXPOSE :80
+EXPOSE 9009
+EXPOSE 8080
+EXPOSE 80
 
 ENTRYPOINT ["/bin/bash", "/usr/local/bin/run_test_wrapper.sh"]
diff --git a/test/docker/base/run_test_wrapper.sh b/test/docker/base/run_test_wrapper.sh
index 26b6de3df3a..46295549ef0 100644
--- a/test/docker/base/run_test_wrapper.sh
+++ b/test/docker/base/run_test_wrapper.sh
@@ -28,8 +28,8 @@ then
     su -c '/usr/lib/postgresql/9.5/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
     sleep 3
     GALAXY_TEST_INSTALL_DB_MERGED="true"
-    GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy?client_encoding=utf8"
-    TOOL_SHED_TEST_DBURI="postgres://root@localhost:5930/toolshed?client_encoding=utf8"
+    GALAXY_TEST_DBURI="postgresql://root@localhost:5930/galaxy?client_encoding=utf8"
+    TOOL_SHED_TEST_DBURI="postgresql://root@localhost:5930/toolshed?client_encoding=utf8"
     export GALAXY_CONFIG_OVERRIDE_DATABASE_ENCODING="UTF-8"
 elif [ "$GALAXY_TEST_DATABASE_TYPE" = "sqlite" ];
 then
diff --git a/test/functional/tool-data/testbeta.loc b/test/functional/tool-data/testbeta.loc
index e69de29bb2d..35c31b7e60a 100644
--- a/test/functional/tool-data/testbeta.loc
+++ b/test/functional/tool-data/testbeta.loc
@@ -0,0 +1 @@
+newvalue	/private/var/folders/_g/g4jwh5zn7tqfkvzprm2l3p7r0000gn/T/tmpgIldpH/tmp1_p5YA/tmpYyEtCB/database/data_manager_tool-dataP247gI/testbeta/newvalue/newvalue.txt
diff --git a/test/functional/tools/composite_shapefile.xml b/test/functional/tools/composite_shapefile.xml
new file mode 100644
index 00000000000..34caff62a46
--- /dev/null
+++ b/test/functional/tools/composite_shapefile.xml
@@ -0,0 +1,39 @@
+<tool id="shapefile_composite" name="composite shapefile tool" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="1.8.6">fiona</requirement>
+    </requirements>
+    <command><![CDATA[
+        mkdir '$output_shapefile.extra_files_path' &&
+        python -c "import fiona; shape = fiona.open('$input.extra_files_path/shapefile.shp'); print(shape.schema)" > '$output' &&
+        cp '$input.extra_files_path'/* '$output_shapefile.extra_files_path'
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="shp" label="Shapefile" help="Used in GIS applications"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" label="${tool.name} on ${on_string}: Shapefile test" />
+        <data name="output_shapefile" format="shp" label="${tool.name} on ${on_string}: Shapefile test - shp" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="" ftype="shp" >
+                <composite_data value="shapefile/shapefile.shp"/>
+                <composite_data value="shapefile/shapefile.shx"/>
+                <composite_data value="shapefile/shapefile.dbf"/>
+                <composite_data value="shapefile/shapefile.prj"/>
+            </param>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="{'properties': OrderedDict([('FIPS', 'str:2'), ('ISO2', 'str:2'), ('ISO3', 'str:3'), ('UN', 'int:3')," />
+                </assert_contents>
+            </output>
+            <output name="output_shapefile" file="shapefile/output.html">
+                <extra_files type="file" name="shapefile.shp" value="shapefile/shapefile.shp" md5="ae4648a8a6be706e910e46607f261317" />
+                <extra_files type="file" name="shapefile.shx" value="shapefile/shapefile.shx" md5="6321ef787b7826afe06e9cf3eb20e656" />
+                <extra_files type="file" name="shapefile.dbf" value="shapefile/shapefile.dbf" md5="d65d87e1570510af8a81d7d174ea361a" />
+                <extra_files type="file" name="shapefile.prj" value="shapefile/shapefile.prj" lines_diff="2" />
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/output_format.xml b/test/functional/tools/output_format.xml
index 4f95a20f238..8c5005879ef 100644
--- a/test/functional/tools/output_format.xml
+++ b/test/functional/tools/output_format.xml
@@ -32,11 +32,13 @@
       <param name="input_text" value="foo" />
       <output name="direct_output" ftype="txt">
         <assert_contents><has_line line="test" /></assert_contents>
+        <metadata name="created_from_basename" value="1" />
       </output>
       <!-- In this case input_based_output ftype is "randomly" either
            fastqsanger or fastqsolexa -->
       <output name="format_source_1_output" ftype="fastqsanger">
         <assert_contents><has_line line="test" /></assert_contents>
+        <metadata name="created_from_basename" value="3" />
       </output>
       <output name="format_source_2_output" ftype="fastqsolexa">
         <assert_contents><has_line line="test" /></assert_contents>
diff --git a/test/functional/tools/parse_values_from_file.xml b/test/functional/tools/parse_values_from_file.xml
new file mode 120000
index 00000000000..0e5b50fda34
--- /dev/null
+++ b/test/functional/tools/parse_values_from_file.xml
@@ -0,0 +1 @@
+../../../tools/expression_tools/parse_values_from_file.xml
\ No newline at end of file
diff --git a/test/functional/tools/sample_datatypes_conf.xml b/test/functional/tools/sample_datatypes_conf.xml
index 6b9c6d5326c..ba5dbdcf9cb 100644
--- a/test/functional/tools/sample_datatypes_conf.xml
+++ b/test/functional/tools/sample_datatypes_conf.xml
@@ -42,6 +42,7 @@
     <datatype extension="data_manager_json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
     <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
     <datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
+    <datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true">
     </datatype>
     <datatype extension="tar" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 28798011dcb..493582f31ff 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -52,7 +52,9 @@
   <tool file="detect_errors_aggressive.xml" />
   <tool file="md5sum.xml" />
   <tool file="checksum.xml" />
+  <tool file="composite_shapefile.xml" />
   <tool file="is_valid_xml.xml" />
+  <tool file="param_value_from_file.xml"/>
   <!--
   TODO: Figure out why this transiently fails on Jenkins.
   <tool file="maxseconds.xml" />
diff --git a/test/functional/tools/tool_provided_metadata_9.xml b/test/functional/tools/tool_provided_metadata_9.xml
index 797ede1c871..285d5c88089 100644
--- a/test/functional/tools/tool_provided_metadata_9.xml
+++ b/test/functional/tools/tool_provided_metadata_9.xml
@@ -10,7 +10,8 @@
   "name": "my dynamic name",
   "ext": "txt",
   "info": "my dynamic info",
-  "dbkey": "cust1"
+  "dbkey": "cust1",
+  "created_from_basename": "my name.txt"
 }}
 </configfile>
     </configfiles>
@@ -29,6 +30,7 @@
           <metadata name="name" value="my dynamic name" />
           <metadata name="info" value="my dynamic info" />
           <metadata name="dbkey" value="cust1" />
+          <metadata name="created_from_basename" value="my name.txt" />
         </output>
       </test>
     </tests>
diff --git a/test/functional/tools/unicode_stream.xml b/test/functional/tools/unicode_stream.xml
index 7fb2b00a30d..623b83a61be 100644
--- a/test/functional/tools/unicode_stream.xml
+++ b/test/functional/tools/unicode_stream.xml
@@ -1,21 +1,26 @@
 <tool id="unicode_stream" name="unicode_stream" version="0.1.0">
     <description>
     </description>
+    <version_command>echo "\x00"</version_command>
     <command detect_errors="exit_code"><![CDATA[
-echo '$input1' > '$out_file1';
+#if $include_null:
+    echo "\x00" > $out_file1;
+#end if
+echo '$input1' >> '$out_file1';
 cat '$cf';
+echo "\x00";
 >&2 cat '$cf';
 sh -c "exit $exit"
     ]]></command>
     <configfiles>
-        <configfile name="cf">ვეპხის ტყ��ს�ნი შ�თ� რუსთ�ველი
-</configfile>
+        <configfile name="cf">ვეპხის ტყ��ს�ნი შ�თ� რუსთ�ველი</configfile>
     </configfiles>
     <inputs>
         <param name="input1" type="text" label="Input">
             <sanitizer sanitize="False" />
         </param>
         <param name="exit" type="integer" value="0" label="Exit Code" />
+        <param name="include_null" type="boolean" label="Include unicode null in output?"/>
     </inputs>
     <outputs>
         <data name="out_file1" format="txt" />
@@ -34,6 +39,10 @@ sh -c "exit $exit"
             <param name="input1" value="ვვვვვ"/>
             <param name="exit" value="0" />
         </test>
+        <test expect_exit_code="0" expect_failure="false">
+            <param name="include_null" value="true"/>
+            <param name="exit" value="0" />
+        </test>
     </tests>
     <help>
     </help>
diff --git a/test/functional/tools/validation_hdf5.xml b/test/functional/tools/validation_hdf5.xml
index f66fa618835..d3cd9f9175b 100644
--- a/test/functional/tools/validation_hdf5.xml
+++ b/test/functional/tools/validation_hdf5.xml
@@ -13,7 +13,7 @@
             <param name="input" value="matrix.cool" />
             <output name="output">
                 <assert_contents>
-                    <has_h5_keys keys="bins, chroms,indexes,pixels" />
+                    <has_h5_keys keys="bins, chroms,indexes,pixels,chroms/length" />
                     <has_h5_attribute key="nbins" value="33754" />
                     <has_h5_attribute key="nchroms" value="15" />
                 </assert_contents>
diff --git a/test/galaxy_selenium/navigates_galaxy.py b/test/galaxy_selenium/navigates_galaxy.py
index 10ab5a61429..a38b2a4fd80 100644
--- a/test/galaxy_selenium/navigates_galaxy.py
+++ b/test/galaxy_selenium/navigates_galaxy.py
@@ -331,6 +331,23 @@ class NavigatesGalaxy(HasDriver):
             raise self.prepend_timeout_message(e, message)
         return history_item_selector_state
 
+    def click_grid_popup_option(self, item_name, option_label):
+        item_button = None
+        grid = self.components.grids.body.wait_for_visible()
+        for row in grid.find_elements_by_tag_name('tr'):
+            name_cell = row.find_elements_by_tag_name('td')[1]
+            if name_cell.text == item_name:
+                item_button = name_cell
+                break
+
+        if item_button is None:
+            raise AssertionError('Failed to find item with name [%s]' % item_name)
+
+        popup_menu_button = item_button.find_element_by_css_selector('.dropdown-toggle')
+        popup_menu_button.click()
+        popup_option = self.driver.find_element_by_link_text(option_label)
+        popup_option.click()
+
     def published_grid_search_for(self, search_term=None):
         return self._inline_search_for(
             '#input-free-text-search-filter',
@@ -800,6 +817,13 @@ class NavigatesGalaxy(HasDriver):
     def workflow_editor_options_menu_element(self):
         return self.wait_for_selector_visible("#workflow-options-button-menu")
 
+    def workflow_editor_click_run(self):
+        return self.wait_for_and_click_selector("#workflow-run-button")
+
+    def workflow_editor_click_save(self):
+        self.wait_for_and_click_selector("#workflow-save-button")
+        self.sleep_for(self.wait_types.DATABASE_OPERATION)
+
     def admin_open(self):
         self.components.masthead.admin.wait_for_and_click()
 
@@ -830,10 +854,10 @@ class NavigatesGalaxy(HasDriver):
 
     def libraries_index_create(self, name):
         self.libraries_index_click_create_new()
-        name_text_box = self.wait_for_selector_clickable("input[name='Name']")
+        name_text_box = self.wait_for_selector_visible("textarea[name='input_library_name']")
         name_text_box.send_keys(name)
 
-        self.wait_for_and_click_selector("#button-0")
+        self.wait_for_and_click_selector(".save_library_btn")
 
     def libraries_index_click_search(self):
         self.sleep_for(WAIT_TYPES.UX_RENDER)
@@ -861,10 +885,10 @@ class NavigatesGalaxy(HasDriver):
     def libraries_folder_create(self, name):
         self.components.libraries.folder.add_folder.wait_for_and_click()
 
-        name_text_box = self.wait_for_selector_clickable("input[name='Name']")
+        name_text_box = self.wait_for_selector_visible("textarea[name='input_folder_name']")
         name_text_box.send_keys(name)
 
-        create_button = self.wait_for_selector_clickable("#button-0")
+        create_button = self.wait_for_selector_clickable(".save_folder_btn")
         create_button.click()
 
     def libraries_click_dataset_import(self):
@@ -1079,7 +1103,7 @@ class NavigatesGalaxy(HasDriver):
 
         # Click labelled option
         self.wait_for_visible(self.navigation.history_panel.options_menu)
-        menu_item_sizzle_selector = '#history-options-button-menu > li > a:contains("%s")' % option_label
+        menu_item_sizzle_selector = '#history-options-button-menu > a:contains("%s")' % option_label
         menu_selection_element = self.wait_for_sizzle_selector_clickable(menu_item_sizzle_selector)
         menu_selection_element.click()
 
diff --git a/test/galaxy_selenium/navigation.yml b/test/galaxy_selenium/navigation.yml
index 57395ed628f..eae430b7eed 100644
--- a/test/galaxy_selenium/navigation.yml
+++ b/test/galaxy_selenium/navigation.yml
@@ -59,7 +59,8 @@ masthead:
     # user menu
     logout: 'Logout'
     custom_builds: 'Custom Builds'
-    saved_histories: 'Saved Histories'
+    histories: 'Histories'
+    pages: 'Pages'
 
     # Shared data
     libraries: 'Data Libraries'
@@ -102,7 +103,7 @@ history_panel:
     selectors:
       show_button: '#current-history-panel .actions .show-selectors-btn'
       action_button: '#current-history-panel .list-action-menu .list-action-menu-btn'
-      action_menu: '.list-action-menu ul.dropdown-menu'
+      action_menu: '.list-action-menu div.dropdown-menu'
 
     labels:
       build_pair: "Build Dataset Pair"
@@ -201,6 +202,21 @@ histories:
     labels:
       unshare: 'Unshare'
 
+pages:
+  selectors:
+    create: '.manage-table-actions .action-button'
+    submit: '#submit'
+  editor:
+    selectors:
+      wym_iframe: 'div.wym_iframe iframe'
+      wym_iframe_content: '.text-content'
+      save: '#save-button'
+      embed_button: '#embed-galaxy-object'
+      dataset_selector: '.saved-datasets'
+      embed_dialog_add_button: '.pages-embed .buttons #button-0'
+
+    labels:
+      embed_dataset: 'Embed Dataset'
 
 login:
   selectors:
@@ -338,7 +354,7 @@ libraries:
     selectors:
       add_items_button: '.add-library-items-datasets'
       add_items_menu: '.add-library-items-datasets .dropdown-menu'
-      add_items_options: '.add-library-items-datasets .dropdown-menu li a'
+      add_items_options: '.add-library-items-datasets .dropdown-menu div a'
 
       add_folder: '.add-library-items-folder'
 
@@ -352,7 +368,7 @@ libraries:
       import_datasets_cancel_button: '.modal-footer .buttons #button-1'
       import_progress_bar: '.progress-bar-import'
       import_history_content: '.library_selected_history_content'
-      import_history_contents_items: '.library_selected_history_content ul li'
+      import_history_contents_items: '.library_selected_history_content tbody > tr'
       import_from_path_textarea: '#import_paths'
       select_all: '#select-all-checkboxes'
 
@@ -365,9 +381,10 @@ libraries:
       table: '.dataset_table'
       table_rows: '.dataset_table table tbody tr'
 
-published_grids:
+grids:
   selectors:
-    search: '#input-free-text-search-filter'
+    body: '#grid-table-body'
+    free_text_search: '#input-free-text-search-filter'
 
 gies:
   jupyter:
diff --git a/test/integration/chained_dyndest_job_conf.xml b/test/integration/chained_dyndest_job_conf.xml
index 5fc420259ed..a8d8deee901 100644
--- a/test/integration/chained_dyndest_job_conf.xml
+++ b/test/integration/chained_dyndest_job_conf.xml
@@ -1,16 +1,12 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="dynamic" type="runner">
             <param id="rules_module">integration.chained_dyndest_rules.module1</param>
         </plugin>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="dyn_dest1">
         <destination id="dyn_dest1" runner="dynamic">
             <param id="type">python</param>
diff --git a/test/integration/delay_job_conf.xml b/test/integration/delay_job_conf.xml
deleted file mode 100644
index 76c68373506..00000000000
--- a/test/integration/delay_job_conf.xml
+++ /dev/null
@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<!-- 
-    Delay non-upload jobs indefinitely.
--->
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
-        <plugin id="dynamic" type="runner">
-            <param id="rules_module">integration.delay_rules</param>
-        </plugin>
-    </plugins>
-
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
-    <destinations default="local_dest">
-
-        <destination id="local_dest" runner="dynamic">
-            <param id="type">python</param>
-            <param id="function">delay</param>
-        </destination>
-
-        <destination id="upload_dest" runner="local">
-        </destination>
-
-    </destinations>
-
-    <tools>
-        <tool id="upload1" destination="upload_dest" />
-    </tools>
-
-</job_conf>
diff --git a/test/integration/delay_job_conf.yml b/test/integration/delay_job_conf.yml
new file mode 100644
index 00000000000..61021c1fe5e
--- /dev/null
+++ b/test/integration/delay_job_conf.yml
@@ -0,0 +1,18 @@
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+  dynamic:
+    rules_module: integration.delay_rules
+execution:
+  default: local_dest
+  environments:
+    local_dest:
+      runner: dynamic
+      type: python
+      function: delay
+    upload_dest:
+      runner: local
+tools:
+  - id: upload1
+    destination: upload_dest
diff --git a/test/integration/dockerized_job_conf.xml b/test/integration/dockerized_job_conf.xml
index 44097003630..d4cdce9f651 100644
--- a/test/integration/dockerized_job_conf.xml
+++ b/test/integration/dockerized_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="local_docker">
         <destination id="local_docker" runner="local">
             <param id="docker_enabled">true</param>
diff --git a/test/integration/embedded_pulsar_job_conf.xml b/test/integration/embedded_pulsar_job_conf.xml
index cabf0c79cd5..f7d08cb3347 100644
--- a/test/integration/embedded_pulsar_job_conf.xml
+++ b/test/integration/embedded_pulsar_job_conf.xml
@@ -2,13 +2,10 @@
 <!-- A job config for testing the Pulsar embedded runner -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="pulsar_embed" type="runner" load="galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner">
         </plugin>
     </plugins>
-    <handlers>
-        <handler id="main"/>
-    </handlers>
     <destinations default="pulsar_embed">
         <destination id="local" runner="local">
         </destination>
diff --git a/test/integration/embedded_pulsar_metadata_job_conf.yml b/test/integration/embedded_pulsar_metadata_job_conf.yml
new file mode 100644
index 00000000000..76520bf4ed5
--- /dev/null
+++ b/test/integration/embedded_pulsar_metadata_job_conf.yml
@@ -0,0 +1,19 @@
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+  pulsar_embed:
+    load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
+
+execution:
+  default: pulsar_embed
+  environments:
+    local:
+      runner: local
+    pulsar_embed:
+      runner: pulsar_embed
+      remote_metadata: true
+      default_file_action: copy
+
+tools:
+- id: upload1
+  environment: local
diff --git a/test/integration/io_injection_job_conf.xml b/test/integration/io_injection_job_conf.xml
deleted file mode 100644
index ebecf1652f9..00000000000
--- a/test/integration/io_injection_job_conf.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
-    </plugins>
-
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
-    <destinations>
-        <destination id="local_dest" runner="local">
-            <env exec="echo 'moo std cow'" />
-            <env exec="(>&amp;2 echo 'moo err cow')" />
-        </destination>
-    </destinations>
-
-</job_conf>
diff --git a/test/integration/io_injection_job_conf.yml b/test/integration/io_injection_job_conf.yml
new file mode 100644
index 00000000000..5dc05647c89
--- /dev/null
+++ b/test/integration/io_injection_job_conf.yml
@@ -0,0 +1,11 @@
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+
+execution:
+  environments:
+    local_dest:
+      runner: local
+      env:
+        - execute: "echo 'moo std cow'"
+        - execute: "(>&2 echo 'moo err cow')"
diff --git a/test/integration/objectstore/__init__.py b/test/integration/objectstore/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/integration/objectstore_selection_job_conf.xml b/test/integration/objectstore/selection_job_conf.xml
similarity index 93%
rename from test/integration/objectstore_selection_job_conf.xml
rename to test/integration/objectstore/selection_job_conf.xml
index 9973e095dea..78628a2319f 100644
--- a/test/integration/objectstore_selection_job_conf.xml
+++ b/test/integration/objectstore/selection_job_conf.xml
@@ -5,16 +5,12 @@
 -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="dynamic" type="runner">
             <param id="rules_module">integration.objectstore_selection_rules</param>
         </plugin>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="local">
         <!-- Upload destination. -->
         <destination id="local" runner="local">
diff --git a/test/integration/objectstore_selection_job_resource_parameters_conf.xml b/test/integration/objectstore/selection_job_resource_parameters_conf.xml
similarity index 100%
rename from test/integration/objectstore_selection_job_resource_parameters_conf.xml
rename to test/integration/objectstore/selection_job_resource_parameters_conf.xml
diff --git a/test/integration/test_objectstore_jobs.py b/test/integration/objectstore/test_jobs.py
similarity index 64%
rename from test/integration/test_objectstore_jobs.py
rename to test/integration/objectstore/test_jobs.py
index 3aed7e2944c..e81960a12bc 100644
--- a/test/integration/test_objectstore_jobs.py
+++ b/test/integration/objectstore/test_jobs.py
@@ -1,4 +1,4 @@
-"""Integration tests for object stores."""
+"""Integration tests for job and object store interactions."""
 
 import os
 import string
@@ -8,10 +8,6 @@ from base.populators import (
     DatasetPopulator,
 )
 
-SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.xml")
-
-
 DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="hierarchical">
     <backends>
@@ -38,6 +34,8 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0
 </object_store>
 """)
 
+TEST_INPUT_FILES_CONTENT = "1 2 3"
+
 
 class ObjectStoreJobsIntegrationTestCase(integration_util.IntegrationTestCase):
 
@@ -59,10 +57,8 @@ class ObjectStoreJobsIntegrationTestCase(integration_util.IntegrationTestCase):
     def setUp(self):
         super(ObjectStoreJobsIntegrationTestCase, self).setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
-
-    def test_tool_simple_constructs(self):
         with self.dataset_populator.test_history() as history_id:
-            hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
+            hda1 = self.dataset_populator.new_dataset(history_id, content=TEST_INPUT_FILES_CONTENT)
             create_10_inputs = {
                 "input1": {"src": "hda", "id": hda1["id"]},
                 "input2": {"src": "hda", "id": hda1["id"]},
@@ -75,6 +71,25 @@ class ObjectStoreJobsIntegrationTestCase(integration_util.IntegrationTestCase):
             )
             self.dataset_populator.wait_for_history(history_id)
 
+    def test_files_count_and_content_in_each_objectstore_backend(self):
+        """
+        According to the ObjectStore configuration given in the
+        `DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE` variable, datasets
+        can be stored on three backends, named:
+            -   primary/files1;
+            -   primary/files2;
+            -   secondary/files3.
+
+        Objectstore _randomly_ distributes tools outputs on
+        `primary/files1` and `primary/files2`, and will use
+        `secondary/files3` if both `primary` backends fail.
+
+        This test runs a tools that creates ten dummy datasets,
+        and asserts if ObjectStore correctly creates ten files
+        in `primary/files1` and `primary/files2`, and none in
+        `secondary/files3`, assuming it will not fail persisting
+        data in `primary` backend.
+        """
         files_1_count = _files_count(self.files1_path)
         files_2_count = _files_count(self.files2_path)
         files_3_count = _files_count(self.files3_path)
@@ -83,17 +98,39 @@ class ObjectStoreJobsIntegrationTestCase(integration_util.IntegrationTestCase):
         assert files_3_count == 0
 
         # Ensure the 10 inputs were written to one of the distributed object store's disk
-        # stores (it will have either 10 or 11 depeending on whether the input was also
+        # stores (it will have either 10 or 11 depending on whether the input was also
         # written there. The other disk store may or may not have the input file so should
         # have at most one file.
-        assert (files_1_count >= 10) or (files_2_count >= 10)
-        assert (files_1_count <= 1) or (files_2_count <= 1)
+        assert (files_1_count + files_2_count == 10) or (files_1_count + files_2_count == 11)
 
         # Other sanity checks on the test - just make sure the test was setup as intended
         # and not actually testing object store behavior.
         assert (files_1_count <= 11) and (files_2_count <= 11)
         assert (files_1_count >= 0) and (files_2_count >= 0)
 
+        # TODO: ideally the following assertion should be separated in a different test method.
+        contents = []
+        path1_files = _get_datasets_files_in_path(self.files1_path)
+        path2_files = _get_datasets_files_in_path(self.files2_path)
+        path3_files = _get_datasets_files_in_path(self.files3_path)
+        for filename in path1_files + path2_files + path3_files:
+            with open(filename) as f:
+                content = f.read().strip()
+                if content != TEST_INPUT_FILES_CONTENT:
+                    contents.append(content)
+
+        for expected_content in range(1, 10):
+            assert str(expected_content) in contents
+
 
 def _files_count(directory):
     return sum(len(files) for _, _, files in os.walk(directory))
+
+
+def _get_datasets_files_in_path(directory):
+    files = []
+    for path, _, filename in os.walk(directory):
+        for f in filename:
+            if f.endswith(".dat"):
+                files.append(os.path.join(path, f))
+    return files
diff --git a/test/integration/test_objectstore_selection.py b/test/integration/objectstore/test_selection.py
similarity index 97%
rename from test/integration/test_objectstore_selection.py
rename to test/integration/objectstore/test_selection.py
index a6f25eb8cf6..da2576ecf97 100644
--- a/test/integration/test_objectstore_selection.py
+++ b/test/integration/objectstore/test_selection.py
@@ -9,8 +9,8 @@ from base.populators import (
 )
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "objectstore_selection_job_conf.xml")
-JOB_RESOURCE_PARAMETERS_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "objectstore_selection_job_resource_parameters_conf.xml")
+JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "selection_job_conf.xml")
+JOB_RESOURCE_PARAMETERS_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "selection_job_resource_parameters_conf.xml")
 
 DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="distributed" id="primary" order="0">
@@ -80,7 +80,6 @@ class ObjectStoreJobsIntegrationTestCase(integration_util.IntegrationTestCase):
         assert dynamic_s3 == files_dynamic_s3_count
 
     def test_tool_simple_constructs(self):
-
         with self.dataset_populator.test_history() as history_id:
 
             def _run_tool(tool_id, inputs):
diff --git a/test/integration/resubmission_default_job_conf.xml b/test/integration/resubmission_default_job_conf.xml
deleted file mode 100644
index a09e58e11af..00000000000
--- a/test/integration/resubmission_default_job_conf.xml
+++ /dev/null
@@ -1,43 +0,0 @@
-<?xml version="1.0"?>
-<!-- 
-    Slimmed down resubmission_job_conf.xml for testing default resubmission rules.
--->
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
-        <plugin id="first_failure_runner" type="runner" load="integration.resubmission_runners:FailOnlyFirstJobRunner" workers="2">
-        </plugin>
-        <plugin id="dynamic" type="runner">
-            <param id="rules_module">integration.resubmission_rules</param>
-        </plugin>
-    </plugins>
-
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
-    <destinations default="initial_destination">
-        <destination id="initial_destination" runner="dynamic">
-            <param id="type">python</param>
-            <param id="function">initial_destination</param>
-        </destination>
-
-        <destination id="fail_first_try" runner="first_failure_runner">
-        </destination>
-
-        <!-- Upload destination. -->
-        <destination id="local" runner="local">
-        </destination>
-
-    </destinations>
-
-    <resources default="test">
-      <group id="upload"></group>
-      <group id="test">test_name,failure_state,initial_destination,run_for</group>
-    </resources>
-
-    <tools>
-        <tool id="upload1" destination="local" resources="upload" />
-    </tools>
-
-</job_conf>
diff --git a/test/integration/resubmission_default_job_conf.yml b/test/integration/resubmission_default_job_conf.yml
new file mode 100644
index 00000000000..accb17eabd3
--- /dev/null
+++ b/test/integration/resubmission_default_job_conf.yml
@@ -0,0 +1,34 @@
+# Slimmed down resubmission_job_conf.xml for testing default resubmission rules.
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+  first_failure_runner:
+    load: integration.resubmission_runners:FailOnlyFirstJobRunner
+    workers: 1
+  dynamic:
+    rules_module: integration.resubmission_rules
+
+execution:
+  default: initial_destination
+  environments:
+    initial_destination:
+      runner: dynamic
+      type: python
+      function: initial_destination
+
+    fail_first_try:
+      runner: first_failure_runner
+    local:
+      runner: local
+
+resources:
+  default: test
+  groups:
+    upload: []
+    test: [test_name,failure_state,initial_target_environment,run_for]
+
+tools:
+  - id: upload1
+    environment: local
+    resources: upload
diff --git a/test/integration/resubmission_dynamic_job_conf.xml b/test/integration/resubmission_dynamic_job_conf.xml
index 8a25d200fca..6221974fdc4 100644
--- a/test/integration/resubmission_dynamic_job_conf.xml
+++ b/test/integration/resubmission_dynamic_job_conf.xml
@@ -1,21 +1,18 @@
 <?xml version="1.0"?>
 <!-- 
-    Slimmed down resubmission_job_conf.xml for testing dynamic resubmission rules.
+    Slimmed down resubmission_job_conf.xml for testing resubmission created from
+    dynamic destination.
 -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
-        <plugin id="failure_runner" type="runner" load="integration.resubmission_runners:FailsJobRunner" workers="2">
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
+        <plugin id="failure_runner" type="runner" load="integration.resubmission_runners:FailsJobRunner" workers="1">
         </plugin>
         <plugin id="dynamic" type="runner">
             <param id="rules_module">integration.resubmission_rules</param>
         </plugin>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="initial_destination">
         <destination id="initial_destination" runner="dynamic">
             <param id="type">python</param>
@@ -29,7 +26,7 @@
     </destinations>
 
     <tools>
-        <tool id="upload1" destination="local" resources="upload" />
+        <tool id="upload1" destination="local" />
     </tools>
 
 </job_conf>
diff --git a/test/integration/resubmission_job_conf.xml b/test/integration/resubmission_job_conf.xml
deleted file mode 100644
index 0c43cc1935c..00000000000
--- a/test/integration/resubmission_job_conf.xml
+++ /dev/null
@@ -1,105 +0,0 @@
-<?xml version="1.0"?>
-<!-- 
-    - Add ready_for_resubmission to job_wrapper.
-    - Use in the handler.
--->
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
-        <plugin id="failure_runner" type="runner" load="integration.resubmission_runners:FailsJobRunner" workers="2">
-        </plugin>
-        <plugin id="assertion_runner" type="runner" load="integration.resubmission_runners:AssertionJobRunner" workers="2">
-        </plugin>
-        <plugin id="dynamic" type="runner">
-            <param id="rules_module">integration.resubmission_rules</param>
-        </plugin>
-    </plugins>
-
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
-    <destinations default="initial_destination">
-        <destination id="initial_destination" runner="dynamic">
-            <param id="type">python</param>
-            <param id="function">initial_destination</param>
-        </destination>
-
-        <destination id="fail_first_try" runner="failure_runner">
-            <resubmit condition="walltime_reached" destination="retry_test_more_walltime" />
-            <resubmit condition="memory_limit_reached" destination="retry_test_more_mem" />
-            <resubmit condition="unknown_error" destination="retry_unknown_error" />
-        </destination>
-
-        <destination id="fail_first_if_memory_or_walltime" runner="failure_runner">
-            <resubmit condition="walltime_reached or memory_limit_reached" destination="retry_test_generic" />
-        </destination>
-
-        <destination id="fail_first_any_failure" runner="failure_runner">
-            <resubmit condition="any_failure" destination="retry_test_generic" />
-        </destination>
-
-        <!-- This will fail twice and succeed on walltime reached and will fail twice and fail hard else. -->
-        <destination id="fail_two_attempts" runner="failure_runner">
-            <resubmit condition="attempt &lt; 3" />
-            <resubmit condition="attempt == 3 and walltime_reached" destination="retry_test_generic" />
-        </destination>
-
-        <!-- Resubmit only jobs shorter than 5 seconds. -->
-        <destination id="resubmit_if_short" runner="failure_runner">
-            <resubmit condition="seconds_running &lt; 5" destination="retry_test_generic" />
-            <resubmit condition="any_failure" destination="fails_without_resubmission" />
-        </destination>
-
-        <!-- Resubmit after a delay. -->
-        <destination id="resubmit_after_delay" runner="failure_runner">
-            <resubmit condition="any_failure" delay="5" destination="retry_after_delay" />
-        </destination>
-
-        <!-- Resubmit after a couple delays. -->
-        <destination id="resubmit_after_two_delays" runner="failure_runner">
-            <!-- Delay 1.5 seconds and then 3 seconds, then finally send off too another runner. -->
-            <resubmit condition="attempt &lt; 3" delay="attempt * 1.5" />
-            <resubmit condition="any_failure" destination="retry_after_delay" />
-        </destination>
-
-        <destination id="fails_without_resubmission" runner="failure_runner">
-        </destination>
-
-        <destination id="retry_test_more_mem" runner="assertion_runner">
-            <param id="dest_name">retry_test_more_mem</param>
-        </destination>
-
-        <destination id="retry_test_more_walltime" runner="assertion_runner">
-            <param id="dest_name">retry_test_more_walltime</param>
-        </destination>
-
-        <destination id="retry_unknown_error" runner="assertion_runner">
-            <param id="dest_name">retry_unknown_error</param>
-        </destination>
-
-        <destination id="retry_after_delay" runner="assertion_runner">
-            <param id="dest_name">retry_after_delay</param>
-        </destination>
-
-        <destination id="retry_test_generic" runner="assertion_runner">
-            <param id="dest_name">retry_test_generic</param>
-        </destination>
-
-
-        <!-- Upload destination. -->
-        <destination id="local" runner="local">
-        </destination>
-
-    </destinations>
-
-    <resources default="test">
-      <group id="upload"></group>
-      <group id="test">test_name,failure_state,initial_destination,run_for</group>
-    </resources>
-
-    <tools>
-        <tool id="upload1" destination="local" resources="upload" />
-    </tools>
-
-</job_conf>
diff --git a/test/integration/resubmission_job_conf.yml b/test/integration/resubmission_job_conf.yml
new file mode 100644
index 00000000000..e55c236c718
--- /dev/null
+++ b/test/integration/resubmission_job_conf.yml
@@ -0,0 +1,114 @@
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+  failure_runner:
+    load: integration.resubmission_runners:FailsJobRunner
+    workers: 1
+  assertion_runner:
+    load: integration.resubmission_runners:AssertionJobRunner
+    workers: 1
+  dynamic:
+    rules_module: integration.resubmission_rules
+
+execution:
+  default: initial_target_environment
+  environments:
+    initial_target_environment:
+      runner: dynamic
+      type: python
+      function: initial_target_environment
+
+    fail_first_try:
+      runner: failure_runner
+      resubmit:
+      - condition: walltime_reached
+        environment: retry_test_more_walltime
+      - condition: memory_limit_reached
+        environment: retry_test_more_mem
+      - condition: unknown_error
+        environment: retry_unknown_error
+
+    fail_first_if_memory_or_walltime:
+      runner: failure_runner
+      resubmit:
+      - condition: 'walltime_reached or memory_limit_reached'
+        environment: retry_test_generic
+
+    fail_first_any_failure:
+      runner: failure_runner
+      resubmit:
+      - condition: any_failure
+        environment: retry_test_generic
+
+    # This will fail twice and succeed on walltime reached and will fail twice and fail hard else.
+    fail_two_attempts:
+      runner: failure_runner
+      resubmit:
+      - condition: 'attempt < 3'
+      - condition: 'attempt == 3 and walltime_reached'
+        environment: retry_test_generic
+
+    # Resubmit only jobs shorter than 5 seconds.
+    resubmit_if_short:
+      runner: failure_runner
+      resubmit:
+      - condition: 'seconds_running < 5'
+        environment: retry_test_generic
+      - condition: any_failure
+        environment: fails_without_resubmission
+
+    # Resubmit after a delay.
+    resubmit_after_delay:
+      runner: failure_runner
+      resubmit:
+      - condition: any_failure
+        delay: 5
+        environment: retry_after_delay
+
+    # Resubmit after a couple delays.
+    resubmit_after_two_delays:
+      runner: failure_runner
+      resubmit:
+      # Delay 1.5 seconds and then 3 seconds, then finally send off too another runner.
+      - condition: 'attempt < 3'
+        delay: 'attempt * 1.5'
+      - condition: any_failure
+        environment: retry_after_delay
+
+    fails_without_resubmission:
+      runner: failure_runner
+
+    retry_test_more_mem:
+      runner: assertion_runner
+      dest_name: retry_test_more_mem
+
+    retry_test_more_walltime:
+      runner: assertion_runner
+      dest_name: retry_test_more_walltime
+
+    retry_unknown_error:
+      runner: assertion_runner
+      dest_name: retry_unknown_error
+
+    retry_after_delay:
+      runner: assertion_runner
+      dest_name: retry_after_delay
+
+    retry_test_generic:
+      runner: assertion_runner
+      dest_name: retry_test_generic
+
+    local:
+      runner: local
+
+resources:
+  default: test
+  groups:
+    upload: []
+    test: [test_name,failure_state,initial_target_environment,run_for]
+
+tools:
+  - id: upload1
+    environment: local
+    resources: upload
diff --git a/test/integration/resubmission_job_resource_parameters_conf.xml b/test/integration/resubmission_job_resource_parameters_conf.xml
index 35f98778133..724c450d39e 100644
--- a/test/integration/resubmission_job_resource_parameters_conf.xml
+++ b/test/integration/resubmission_job_resource_parameters_conf.xml
@@ -1,6 +1,6 @@
 <parameters>
   <param label="Test Name" name="test_name" type="text" value="" help="Test name to connect client with simulated backend failures." />
   <param label="Failure Type" name="failure_state" type="text" value="" help="If set, FailsJobRunner fails with this runner state." />
-  <param label="Initial Destination" name="initial_destination" type="text" value="" help="If set, initial destination to route job to." />
+  <param label="Initial Target Environment" name="initial_target_environment" type="text" value="" help="If set, initial job environment to route job to." />
   <param label="Run For" name="run_for" type="integer" value="0" help="If greater than 0, wait this long before triggering runtime failure state (memory or walltime)." />
 </parameters>
diff --git a/test/integration/resubmission_pulsar_job_conf.xml b/test/integration/resubmission_pulsar_job_conf.xml
index e7b6a1eabc7..9ee1c867ae2 100644
--- a/test/integration/resubmission_pulsar_job_conf.xml
+++ b/test/integration/resubmission_pulsar_job_conf.xml
@@ -1,17 +1,13 @@
 <?xml version="1.0"?>
 <!-- 
-    Slimmed down resubmission_job_conf.xml for testing default resubmission rules.
+    Variant of resubmission_job_conf for testing Pulsar resubmission.
 -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="initial_pulsar">
         <destination id="initial_pulsar" runner="pulsar_rest">
             <!-- Use a reserved, unused ip to force a resubmission -->
diff --git a/test/integration/resubmission_rules/rules.py b/test/integration/resubmission_rules/rules.py
index 4d82e1d2d08..ec98b0e56d5 100644
--- a/test/integration/resubmission_rules/rules.py
+++ b/test/integration/resubmission_rules/rules.py
@@ -1,20 +1,20 @@
 from galaxy.jobs import JobDestination
 
-DEFAULT_INITIAL_DESTINATION = "fail_first_try"
+DEFAULT_INITIAL_ENVIRONMENT = "fail_first_try"
 
 
-def initial_destination(resource_params):
-    return resource_params.get("initial_destination", None) or DEFAULT_INITIAL_DESTINATION
+def initial_target_environment(resource_params):
+    return resource_params.get("initial_target_environment", None) or DEFAULT_INITIAL_ENVIRONMENT
 
 
 def dynamic_resubmit_once(resource_params):
-    """Build destination that always fails first time and always re-routes to passing destination."""
+    """Build environment that always fails first time and always re-routes to passing environment."""
     job_destination = JobDestination()
     # Always fail on the first attempt.
     job_destination['runner'] = "failure_runner"
-    # Resubmit to a valid destination.
+    # Resubmit to a valid environment.
     job_destination['resubmit'] = [dict(
         condition="any_failure",
-        destination="local",
+        environment="local",
     )]
     return job_destination
diff --git a/test/integration/resubmission_small_memory_job_conf.xml b/test/integration/resubmission_small_memory_job_conf.xml
index a919ca58628..0c068bbef76 100644
--- a/test/integration/resubmission_small_memory_job_conf.xml
+++ b/test/integration/resubmission_small_memory_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="local_too_small">
         <destination id="local_too_small" runner="local">
             <env id="GALAXY_MEMORY_MB">4</env>
diff --git a/test/integration/sets_tmp_dir_expression_job_conf.xml b/test/integration/sets_tmp_dir_expression_job_conf.xml
index ac7e5b1b233..b4be01bda77 100644
--- a/test/integration/sets_tmp_dir_expression_job_conf.xml
+++ b/test/integration/sets_tmp_dir_expression_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations>
         <destination id="local_dest" runner="local">
             <param id="tmp_dir">$(mktemp cooltmpXXXXXXXXXXXX)</param>
diff --git a/test/integration/sets_tmp_dir_to_true_job_conf.xml b/test/integration/sets_tmp_dir_to_true_job_conf.xml
index e976483f389..e5ac91ef453 100644
--- a/test/integration/sets_tmp_dir_to_true_job_conf.xml
+++ b/test/integration/sets_tmp_dir_to_true_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations>
         <destination id="local_dest" runner="local">
             <param id="tmp_dir">True</param>
diff --git a/test/integration/simple_job_conf.xml b/test/integration/simple_job_conf.xml
index abcb0768234..032c2b0fec1 100644
--- a/test/integration/simple_job_conf.xml
+++ b/test/integration/simple_job_conf.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
     <handlers>
diff --git a/test/integration/singularity_job_conf.xml b/test/integration/singularity_job_conf.xml
index 8743b71ef7e..ccdc921727e 100644
--- a/test/integration/singularity_job_conf.xml
+++ b/test/integration/singularity_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="local_singularity">
         <destination id="local_singularity" runner="local">
             <param id="singularity_enabled">true</param>
diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index 64605642e7a..370c37da79f 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -67,7 +67,7 @@ def cli_job_config(remote_connection, shell_plugin='ParamikoShell', job_plugin='
     job_conf_str = job_conf_template.substitute(shell_plugin=shell_plugin,
                                                 job_plugin=job_plugin,
                                                 **remote_connection._asdict())
-    with tempfile.NamedTemporaryFile(suffix="_slurm_integration_job_conf", mode="w", delete=False) as job_conf:
+    with tempfile.NamedTemporaryFile(suffix="_slurm_integration_job_conf.xml", mode="w", delete=False) as job_conf:
         job_conf.write(job_conf_str)
     return job_conf.name
 
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index ccff74a7b7f..24f6ede524d 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -8,7 +8,7 @@ from base.populators import (
     DatasetPopulator,
 )
 
-from galaxy.tools.deps.commands import which
+from galaxy.tool_util.deps.commands import which
 from .test_job_environments import RunsEnvironmentJobs
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
diff --git a/test/integration/test_datatype_upload.py b/test/integration/test_datatype_upload.py
index b743cea5075..58e45b0bb55 100644
--- a/test/integration/test_datatype_upload.py
+++ b/test/integration/test_datatype_upload.py
@@ -6,12 +6,17 @@ import pytest
 
 from base import integration_util  # noqa: I100,I202
 from galaxy.datatypes.registry import Registry  # noqa: I201
+from galaxy.util.checkers import (
+    is_bz2,
+    is_gzip,
+    is_zip
+)
 from galaxy.util.hash_util import md5_hash_file
 from .test_upload_configuration_options import BaseUploadContentConfigurationInstance
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 TEST_FILE_DIR = '%s/../../lib/galaxy/datatypes/test' % SCRIPT_DIRECTORY
-TEST_DATA = collections.namedtuple('UploadDatatypesData', 'path datatype uploadable')
+TestData = collections.namedtuple('UploadDatatypesData', 'path datatype uploadable')
 GALAXY_ROOT = os.path.abspath('%s/../../' % SCRIPT_DIRECTORY)
 DATATYPES_CONFIG = os.path.join(GALAXY_ROOT, 'config/datatypes_conf.xml.sample')
 PARENT_SNIFFER_MAP = {'fastqsolexa': 'fastq'}
@@ -26,14 +31,12 @@ def find_datatype(registry, filename):
     raise Exception("Couldn't guess datatype for file '%s'" % filename)
 
 
-def collect_test_data():
-    registry = Registry()
-    registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
-    test_files = os.listdir(TEST_FILE_DIR)
+def collect_test_data(registry):
+    test_files = [f for f in os.listdir(TEST_FILE_DIR) if "." in f]
     files = [os.path.join(TEST_FILE_DIR, f) for f in test_files]
     datatypes = [find_datatype(registry, f) for f in test_files]
     uploadable = [datatype.file_ext in registry.upload_file_formats for datatype in datatypes]
-    test_data_description = [TEST_DATA(*items) for items in zip(files, datatypes, uploadable)]
+    test_data_description = [TestData(*items) for items in zip(files, datatypes, uploadable)]
     return {os.path.basename(data.path): data for data in test_data_description}
 
 
@@ -51,11 +54,18 @@ def temp_file():
         yield fh
 
 
-TEST_CASES = collect_test_data()
+registry = Registry()
+registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG)
+TEST_CASES = collect_test_data(registry)
 
 
 @pytest.mark.parametrize('test_data', TEST_CASES.values(), ids=list(TEST_CASES.keys()))
 def test_upload_datatype_auto(instance, test_data, temp_file):
+    is_compressed = False
+    for is_method in (is_bz2, is_gzip, is_zip):
+        is_compressed = is_method(test_data.path)
+        if is_compressed:
+            break
     with open(test_data.path, 'rb') as content:
         if hasattr(test_data.datatype, 'sniff') or 'false' in test_data.path:
             file_type = 'auto'
@@ -75,16 +85,20 @@ def test_upload_datatype_auto(instance, test_data, temp_file):
         # state should be OK
         assert dataset['state'] == 'ok'
     # Check that correct datatype has been detected
+    file_ext = dataset['file_ext']
     if 'false' in test_data.path:
         # datasets with false in their name are not of a specific datatype
-        assert dataset['file_ext'] != PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
+        assert file_ext != PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
     else:
-        assert dataset['file_ext'] == PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
-    # download file and verify it hasn't been manipulated
-    temp_file.write(instance.dataset_populator.get_history_dataset_content(history_id=instance.history_id,
-                                                                           dataset=dataset,
-                                                                           type='bytes',
-                                                                           assert_ok=False,
-                                                                           raw=True))
-    temp_file.flush()
-    assert md5_hash_file(test_data.path) == md5_hash_file(temp_file.name)
+        assert file_ext == PARENT_SNIFFER_MAP.get(expected_file_ext, expected_file_ext)
+    datatype = registry.datatypes_by_extension[file_ext]
+    datatype_compressed = getattr(datatype, "compressed", False)
+    if not is_compressed or datatype_compressed:
+        # download file and verify it hasn't been manipulated
+        temp_file.write(instance.dataset_populator.get_history_dataset_content(history_id=instance.history_id,
+                                                                               dataset=dataset,
+                                                                               type='bytes',
+                                                                               assert_ok=False,
+                                                                               raw=True))
+        temp_file.flush()
+        assert md5_hash_file(test_data.path) == md5_hash_file(temp_file.name)
diff --git a/test/integration/test_fail_job_tool_unavailable.py b/test/integration/test_fail_job_tool_unavailable.py
new file mode 100644
index 00000000000..f317dd8fe83
--- /dev/null
+++ b/test/integration/test_fail_job_tool_unavailable.py
@@ -0,0 +1,56 @@
+import time
+
+from base import integration_util
+from base.populators import (
+    DatasetPopulator,
+    WorkflowPopulator,
+)
+
+
+class FailJobWhenToolUnavailableTestCase(integration_util.IntegrationTestCase):
+
+    require_admin_user = True
+
+    def setUp(self):
+        super(FailJobWhenToolUnavailableTestCase, self).setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+        self.history_id = self.dataset_populator.new_history()
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config, ):
+        # config["jobs_directory"] = cls.jobs_directory
+        # Disable tool dependency resolution.
+        config["tool_dependency_dir"] = "none"
+
+    def test_fail_job_when_tool_unavailable(self):
+        self.workflow_populator.run_workflow("""
+class: GalaxyWorkflow
+steps:
+  - label: sleep
+    run:
+      class: GalaxyTool
+      command: sleep 20s && echo 'hello world 2' > '$output1'
+      outputs:
+        output1:
+          format: txt
+  - tool_id: cat1
+    state:
+      input1:
+        $link: sleep#output1
+      queries:
+        input2:
+          $link: sleep#output1
+""", history_id=self.history_id, assert_ok=False, wait=False)
+        # Wait until workflow is fully scheduled, otherwise can't test effect of removing tool from queued job
+        time.sleep(10)
+        self._app.toolbox.remove_tool_by_id('cat1')
+        self.dataset_populator.wait_for_history(self.history_id, assert_ok=False)
+        state_details = self.galaxy_interactor.get('histories/%s' % self.history_id).json()['state_details']
+        assert state_details['running'] == 0
+        assert state_details['ok'] == 1
+        assert state_details['error'] == 1
+        failed_hda = self.dataset_populator.get_history_dataset_details(history_id=self.history_id, assert_ok=False, details=True)
+        assert failed_hda['state'] == 'error'
+        job = self.galaxy_interactor.get("jobs/%s" % failed_hda['creating_job']).json()
+        assert job['state'] == 'error'
diff --git a/test/integration/test_job_environments.py b/test/integration/test_job_environments.py
index 6622ada24a2..b950627600b 100644
--- a/test/integration/test_job_environments.py
+++ b/test/integration/test_job_environments.py
@@ -12,7 +12,7 @@ from base.populators import (
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 SIMPLE_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "simple_job_conf.xml")
-IO_INJECTION_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "io_injection_job_conf.xml")
+IO_INJECTION_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "io_injection_job_conf.yml")
 SETS_TMP_DIR_TO_TRUE_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "sets_tmp_dir_to_true_job_conf.xml")
 SETS_TMP_DIR_AS_EXPRESSION_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "sets_tmp_dir_expression_job_conf.xml")
 
diff --git a/test/integration/test_job_recovery.py b/test/integration/test_job_recovery.py
index 3bb54a54055..6d0d0db1641 100644
--- a/test/integration/test_job_recovery.py
+++ b/test/integration/test_job_recovery.py
@@ -8,7 +8,7 @@ from base.populators import (
 )
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-DELAY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "delay_job_conf.xml")
+DELAY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "delay_job_conf.yml")
 SIMPLE_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "simple_job_conf.xml")
 
 
diff --git a/test/integration/test_job_resubmission.py b/test/integration/test_job_resubmission.py
index 39b4bfe8c70..0ec1ab7975f 100644
--- a/test/integration/test_job_resubmission.py
+++ b/test/integration/test_job_resubmission.py
@@ -5,7 +5,7 @@ import os
 from base import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-JOB_RESUBMISSION_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_job_conf.xml")
+JOB_RESUBMISSION_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_job_conf.yml")
 JOB_RESUBMISSION_DEFAULT_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_default_job_conf.xml")
 JOB_RESUBMISSION_DYNAMIC_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_dynamic_job_conf.xml")
 JOB_RESUBMISSION_SMALL_MEMORY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_small_memory_job_conf.xml")
@@ -48,12 +48,12 @@ class JobResubmissionIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
         assert "__job_resource" in input_names
 
     def test_job_resources(self):
-        """Test initial destination dynamic rule used by remaining re-submission test case works."""
-        self._assert_job_passes(resource_parameters={"test_name": "test_job_resources", "initial_destination": "local"})
+        """Test initial environment dynamic rule used by remaining re-submission test case works."""
+        self._assert_job_passes(resource_parameters={"test_name": "test_job_resources", "initial_target_environment": "local"})
 
     def test_failure_runner(self):
         """Test FailsJobRunner used by remaining re-submission test cases."""
-        self._assert_job_fails(resource_parameters={"test_name": "test_failure_runner", "initial_destination": "fails_without_resubmission"})
+        self._assert_job_fails(resource_parameters={"test_name": "test_failure_runner", "initial_target_environment": "fails_without_resubmission"})
 
     def test_walltime_resubmission(self):
         self._assert_job_passes(resource_parameters={"test_name": "test_walltime_resubmission", "failure_state": "walltime_reached"})
@@ -66,46 +66,46 @@ class JobResubmissionIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
 
     def test_condition_expressions(self):
         self._assert_job_passes(resource_parameters={"test_name": "test_condition_expressions_0",
-                                                     "initial_destination": "fail_first_if_memory_or_walltime",
+                                                     "initial_target_environment": "fail_first_if_memory_or_walltime",
                                                      "failure_state": "memory_limit_reached"})
         self._assert_job_passes(resource_parameters={"test_name": "test_condition_expressions_1",
-                                                     "initial_destination": "fail_first_if_memory_or_walltime",
+                                                     "initial_target_environment": "fail_first_if_memory_or_walltime",
                                                      "failure_state": "walltime_reached"})
         self._assert_job_fails(resource_parameters={"test_name": "test_condition_expressions_2",
-                                                    "initial_destination": "fail_first_if_memory_or_walltime",
+                                                    "initial_target_environment": "fail_first_if_memory_or_walltime",
                                                     "failure_state": "unknown_error"})
 
     def test_condition_any_failure(self):
         self._assert_job_passes(resource_parameters={"test_name": "test_condition_any_failure",
-                                                     "initial_destination": "fail_first_any_failure",
+                                                     "initial_target_environment": "fail_first_any_failure",
                                                      "failure_state": "unknown_error"})
 
     def test_condition_attempt(self):
         self._assert_job_fails(resource_parameters={"test_name": "test_condition_attempt",
-                                                    "initial_destination": "fail_two_attempts",
+                                                    "initial_target_environment": "fail_two_attempts",
                                                     "failure_state": "unknown_error"})
         self._assert_job_passes(resource_parameters={"test_name": "test_condition_attempt",
-                                                     "initial_destination": "fail_two_attempts",
+                                                     "initial_target_environment": "fail_two_attempts",
                                                      "failure_state": "walltime_reached"})
 
     def test_condition_seconds_running(self):
         self._assert_job_passes(resource_parameters={"test_name": "test_condition_seconds_running",
-                                                     "initial_destination": "resubmit_if_short",
+                                                     "initial_target_environment": "resubmit_if_short",
                                                      "failure_state": "walltime_reached",
                                                      "run_for": "1"})
         self._assert_job_fails(resource_parameters={"test_name": "test_condition_seconds_running",
-                                                    "initial_destination": "resubmit_if_short",
+                                                    "initial_target_environment": "resubmit_if_short",
                                                     "failure_state": "walltime_reached",
                                                     "run_for": "15"})
 
     def test_resubmission_after_delay(self):
         self._assert_job_passes(resource_parameters={"test_name": "test_resubmission_after_delay",
-                                                     "initial_destination": "resubmit_after_delay",
+                                                     "initial_target_environment": "resubmit_after_delay",
                                                      "failure_state": "unknown_error"})
 
     def test_resubmission_after_delay_expression(self):
         self._assert_job_passes(resource_parameters={"test_name": "test_resubmission_after_delay_expression",
-                                                     "initial_destination": "resubmit_after_two_delays",
+                                                     "initial_target_environment": "resubmit_after_two_delays",
                                                      "failure_state": "unknown_error"})
 
 
diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py
index 743757952ad..6546ac3a20a 100644
--- a/test/integration/test_kubernetes_runner.py
+++ b/test/integration/test_kubernetes_runner.py
@@ -1,4 +1,4 @@
-"""Integration tests for the CLI shell plugins and runners."""
+"""Integration tests for the Kubernetes runner."""
 # Tested on docker for mac 18.06.1-ce-mac73 using the default kubernetes setup
 import collections
 import json
@@ -109,9 +109,9 @@ def job_config(jobs_directory):
 """)
     job_conf_str = job_conf_template.substitute(jobs_directory=jobs_directory,
                                                 tool_directory=TOOL_DIR,
-                                                k8s_config_path=os.environ.get('GALAXY_TEST_KUBE_CONFIG_PATH', '~/.kube/config'),
+                                                k8s_config_path=integration_util.k8s_config_path(),
                                                 )
-    with tempfile.NamedTemporaryFile(suffix="_kubernetes_integration_job_conf", mode="w", delete=False) as job_conf:
+    with tempfile.NamedTemporaryFile(suffix="_kubernetes_integration_job_conf.xml", mode="w", delete=False) as job_conf:
         job_conf.write(job_conf_str)
     return Config(job_conf.name)
 
@@ -226,8 +226,9 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
         details = self.dataset_populator.get_job_details(result['jobs'][0]['id'], full=True).json()
 
         assert details['state'] == 'error', details
-        assert details['stdout'] == 'The bool is not true\n', details
-        assert details['stderr'] == 'Fatal error: Exit code 127 (Failing exit code.)\nThe bool is very not true\n'
+        assert details['stdout'].strip() == 'The bool is not true', details
+        assert details['stderr'].strip() == 'The bool is very not true', details
+        assert details['exit_code'] == 127, details
 
     @skip_without_tool('Count1')
     def test_python_dep(self):
diff --git a/test/integration/test_kubernetes_staging.py b/test/integration/test_kubernetes_staging.py
new file mode 100644
index 00000000000..a8081074c76
--- /dev/null
+++ b/test/integration/test_kubernetes_staging.py
@@ -0,0 +1,117 @@
+"""Integration tests for Kubernetes pod staging.
+
+This case is way more brittle than the other integration tests distributed with Galaxy.
+This is because it requires Kubernetes, RabbitMQ, and the test itself needs to know what
+the test host IP address will be relative to a container inside Kubernetes in order to
+communicate job status updates back.
+
+For this reason, this test will only work out of the box currently with Docker for Mac,
+rabbitmq installed via Homebrew, and if a fixed port is set for the test.
+
+   GALAXY_TEST_PORT=9234 pytest test/integration/test_kubernetes_staging.py
+
+"""
+import os
+import string
+import tempfile
+
+from base import integration_util  # noqa: I100,I202
+from base.populators import skip_without_tool
+from .test_containerized_jobs import MulledJobTestCases  # noqa: I201
+from .test_job_environments import BaseJobEnvironmentIntegrationTestCase  # noqa: I201
+
+TOOL_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'tools'))
+AMQP_URL = os.environ.get("GALAXY_TEST_AMQP_URL", "amqp://guest:guest@localhost:5672//")
+GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST = os.environ.get("GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST", "host.docker.internal")
+
+
+def job_config(jobs_directory):
+    job_conf_template = string.Template("""
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+  pulsar_k8s:
+    load: galaxy.jobs.runners.pulsar:PulsarKubernetesCoexecutionJobRunner
+    galaxy_url: ${infrastructure_url}
+    amqp_url: ${amqp_url}
+
+execution:
+  default: pulsar_k8s_environment
+  environments:
+    pulsar_k8s_environment:
+      k8s_config_path: ${k8s_config_path}
+      runner: pulsar_k8s
+      docker_enabled: true
+      docker_default_container_id: busybox:ubuntu-14.04
+      pulsar_app_config:
+        message_queue_url: '${container_amqp_url}'
+      env:
+        - name: SOME_ENV_VAR
+          value: '42'
+    local_environment:
+      runner: local
+tools:
+  - id: upload1
+    environment: local_environment
+""")
+    port = os.environ.get('GALAXY_TEST_PORT')
+    assert port
+    infrastructure_url = "http://%s:%s" % (GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST, port)
+    container_amqp_url = to_infrastructure_uri(AMQP_URL)
+    job_conf_str = job_conf_template.substitute(jobs_directory=jobs_directory,
+                                                tool_directory=TOOL_DIR,
+                                                k8s_config_path=integration_util.k8s_config_path(),
+                                                amqp_url=AMQP_URL,
+                                                container_amqp_url=container_amqp_url,
+                                                infrastructure_url=infrastructure_url,
+                                                )
+    with tempfile.NamedTemporaryFile(suffix="_kubernetes_integration_job_conf.yml", mode="w", delete=False) as job_conf:
+        job_conf.write(job_conf_str)
+    return job_conf.name
+
+
+@integration_util.skip_unless_kubernetes()
+@integration_util.skip_unless_fixed_port()
+class BaseKubernetesStagingIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, MulledJobTestCases):
+
+    def setUp(self):
+        super(BaseKubernetesStagingIntegrationTestCase, self).setUp()
+        self.history_id = self.dataset_populator.new_history()
+
+    @classmethod
+    def setUpClass(cls):
+        # realpath for docker deployed in a VM on Mac, also done in driver_util.
+        cls.jobs_directory = os.path.realpath(tempfile.mkdtemp())
+        super(BaseKubernetesStagingIntegrationTestCase, cls).setUpClass()
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["jobs_directory"] = cls.jobs_directory
+        config["file_path"] = cls.jobs_directory
+        config["job_config_file"] = job_config(cls.jobs_directory)
+
+        config["default_job_shell"] = '/bin/sh'
+        # Disable tool dependency resolution.
+        config["tool_dependency_dir"] = "none"
+        config["enable_beta_mulled_containers"] = "true"
+
+    @skip_without_tool("job_environment_default")
+    def test_job_environment(self):
+        job_env = self._run_and_get_environment_properties()
+        assert job_env.some_env == '42'
+
+
+def to_infrastructure_uri(uri):
+    # remap MQ or file server URI hostnames for in-container versions, this is sloppy
+    # should actually parse the URI and rebuild with correct host
+    # similar code found in Pulsar integration_tests.py.
+    infrastructure_uri = uri
+    if GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST:
+        if "0.0.0.0" in infrastructure_uri:
+            infrastructure_uri = infrastructure_uri.replace("0.0.0.0", GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST)
+        elif "localhost" in infrastructure_uri:
+            infrastructure_uri = infrastructure_uri.replace("localhost", GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST)
+        elif "127.0.0.1" in infrastructure_uri:
+            infrastructure_uri = infrastructure_uri.replace("127.0.0.1", GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST)
+    return infrastructure_uri
diff --git a/test/integration/test_page_revision_json_encoding.py b/test/integration/test_page_revision_json_encoding.py
new file mode 100644
index 00000000000..f509c9b8c10
--- /dev/null
+++ b/test/integration/test_page_revision_json_encoding.py
@@ -0,0 +1,40 @@
+"""Test pages save JSON with unencoded IDs.
+
+Verifies the database doesn't get saved with encoded IDs (that would be bad because
+the security parameter to encode IDs may be changed by admins). Test case also verifies
+exported API values are encoded though.
+"""
+
+from base import api_asserts
+from base import integration_util
+from base.populators import (
+    DatasetPopulator,
+)
+from galaxy import model  # noqa: I101,I201
+
+
+class PageJsonEncodingIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    def setUp(self):
+        super(PageJsonEncodingIntegrationTestCase, self).setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+
+    def test_page_encoding(self):
+        history_id = self.dataset_populator.new_history()
+        request = dict(
+            slug="mypage",
+            title="MY PAGE",
+            content='''<p>Page!<div class="embedded-item" id="History-%s"></div></p>''' % history_id,
+        )
+        page_response = self._post("pages", request)
+        api_asserts.assert_status_code_is_ok(page_response)
+        sa_session = self._app.model.context
+        page_revision = sa_session.query(model.PageRevision).all()[0]
+        assert '''id="History-1"''' in page_revision.content, page_revision.content
+        assert '''id="History-%s"''' % history_id not in page_revision.content, page_revision.content
+
+        show_page_response = self._get("pages/%s" % page_response.json()["id"])
+        api_asserts.assert_status_code_is_ok(show_page_response)
+        content = show_page_response.json()["content"]
+        assert '''id="History-1"''' not in content, content
+        assert '''id="History-%s"''' % history_id in content, content
diff --git a/test/integration/test_pulsar_embedded_metadata.py b/test/integration/test_pulsar_embedded_metadata.py
index d5b5582dbcb..5fcafe73dd9 100644
--- a/test/integration/test_pulsar_embedded_metadata.py
+++ b/test/integration/test_pulsar_embedded_metadata.py
@@ -5,7 +5,7 @@ import os
 from base import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_metadata_job_conf.xml")
+EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_metadata_job_conf.yml")
 
 
 class EmbeddedPulsarIntegrationInstance(integration_util.IntegrationInstance):
diff --git a/test/integration/test_work_queue_put_failure.py b/test/integration/test_work_queue_put_failure.py
new file mode 100644
index 00000000000..b155d01abb3
--- /dev/null
+++ b/test/integration/test_work_queue_put_failure.py
@@ -0,0 +1,41 @@
+import tempfile
+
+from base import integration_util
+from base.populators import DatasetPopulator
+
+job_conf_yaml = """
+runners:
+  local:
+    load: galaxy.jobs.runners.pulsar:PulsarRESTJobRunner
+    workers: 1
+execution:
+  default: local
+  environments:
+    local:
+      runner: local
+"""
+
+
+class WorkQueuePutFailureTestCase(integration_util.IntegrationTestCase):
+
+    def setUp(self):
+        super(WorkQueuePutFailureTestCase, self).setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.history_id = self.dataset_populator.new_history()
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config, ):
+        # config["jobs_directory"] = cls.jobs_directory
+        fd, path = tempfile.mkstemp(suffix='job_conf.yml')
+        with open(path, 'w') as job_conf:
+            job_conf.write(job_conf_yaml)
+        config["job_config_file"] = path
+        # Disable tool dependency resolution.
+        config["tool_dependency_dir"] = "none"
+
+    def test_job_fails(self):
+        self.dataset_populator.new_dataset(self.history_id, content="1 2 3")
+        self.dataset_populator.wait_for_history(self.history_id, assert_ok=False)
+        state_details = self.galaxy_interactor.get('histories/%s' % self.history_id).json()['state_details']
+        assert state_details['running'] == 0
+        assert state_details['error'] == 1
diff --git a/test/integration/test_workflow_sync.py b/test/integration/test_workflow_sync.py
index 9fdbdc8061d..8e496043d69 100644
--- a/test/integration/test_workflow_sync.py
+++ b/test/integration/test_workflow_sync.py
@@ -33,7 +33,7 @@ class WorkflowSyncTestCase(integration_util.IntegrationTestCase):
         with self.workflow_populator.export_for_update(workflow_id) as workflow_object:
             workflow_object["annotation"] = "new annotation"
         with open(workflow_path, "r") as f:
-            data = yaml.load(f)
+            data = yaml.safe_load(f)
             assert data["doc"] == "new annotation"
 
     def test_sync_ga(self):
diff --git a/test/selenium_tests/framework.py b/test/selenium_tests/framework.py
index 480b9e801d8..853c2a04ad1 100644
--- a/test/selenium_tests/framework.py
+++ b/test/selenium_tests/framework.py
@@ -92,10 +92,12 @@ def managed_history(f):
             f(self, *args, **kwds)
         finally:
             if "GALAXY_TEST_NO_CLEANUP" not in os.environ:
-                current_history_id = self.current_history_id()
-                self.dataset_populator.cancel_history_jobs(current_history_id)
-                self.api_delete("histories/%s" % current_history_id)
-
+                try:
+                    current_history_id = self.current_history_id()
+                    self.dataset_populator.cancel_history_jobs(current_history_id)
+                    self.api_delete("histories/%s" % current_history_id)
+                except Exception:
+                    print("Faild to cleanup managed history, selenium connection corrupted somehow?")
     return func_wrapper
 
 
@@ -532,9 +534,17 @@ class SeleniumSessionGetPostMixin(object):
         response = requests.get(full_url, data=data, cookies=self.selenium_test_case.selenium_to_requests_cookies())
         return response
 
-    def _post(self, route, data={}):
+    def _post(self, route, data=None, files=None):
         full_url = self.selenium_test_case.build_url("api/" + route, for_selenium=False)
-        response = requests.post(full_url, data=data, cookies=self.selenium_test_case.selenium_to_requests_cookies())
+        if data is None:
+            data = {}
+
+        if files is None:
+            files = data.get("__files", None)
+            if files is not None:
+                del data["__files"]
+
+        response = requests.post(full_url, data=data, cookies=self.selenium_test_case.selenium_to_requests_cookies(), files=files)
         return response
 
     def _delete(self, route, data={}):
diff --git a/test/selenium_tests/test_admin_app.py b/test/selenium_tests/test_admin_app.py
index a2db96290cc..205458a9ca9 100644
--- a/test/selenium_tests/test_admin_app.py
+++ b/test/selenium_tests/test_admin_app.py
@@ -27,13 +27,12 @@ class AdminAppTestCase(SeleniumTestCase):
         self.screenshot("admin_display_applications")
 
         admin_component.index.jobs.wait_for_and_click()
-        with self.main_panel():
-            admin_component.update_jobs.wait_for_visible()
+        admin_component.update_jobs.wait_for_visible()
         self.screenshot("admin_manage_jobs")
 
         admin_component.index.local_data.wait_for_and_click()
         title_element = admin_component.dm_title.wait_for_visible()
-        assert title_element.text == "Data Manager"
+        assert title_element.text == "Local Data"
         self.screenshot("admin_local_data")
 
     @selenium_test
@@ -70,7 +69,7 @@ class AdminAppTestCase(SeleniumTestCase):
         self.admin_open()
         admin_component.index.local_data.wait_for_and_click()
         title_element = admin_component.dm_title.wait_for_visible()
-        assert title_element.text == "Data Manager"
+        assert title_element.text == "Local Data"
         admin_component.dm_data_managers_card.wait_for_visible()
         admin_component.dm_jobs_button(data_manager="test-data-manager").wait_for_visible()
         self.screenshot("admin_data_manager")
diff --git a/test/selenium_tests/test_saved_histories.py b/test/selenium_tests/test_histories_list.py
similarity index 82%
rename from test/selenium_tests/test_saved_histories.py
rename to test/selenium_tests/test_histories_list.py
index a0821224d34..8f200f2640b 100644
--- a/test/selenium_tests/test_saved_histories.py
+++ b/test/selenium_tests/test_histories_list.py
@@ -9,17 +9,17 @@ from .framework import (
 class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
 
     @selenium_test
-    def test_saved_histories_list(self):
+    def test_histories_list(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
         self.assert_histories_in_grid([self.history2_name, self.history3_name])
 
     @selenium_test
     def test_history_switch(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
         self.screenshot("histories_saved_grid")
-        self.click_popup_option(self.history2_name, 'Switch')
+        self.click_grid_popup_option(self.history2_name, 'Switch')
         self.sleep_for(self.wait_types.UX_RENDER)
 
         @retry_assertion_during_transitions
@@ -31,21 +31,21 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
     @selenium_test
     def test_history_view(self):
         self._login()
-        self.navigate_to_saved_histories_page()
-        self.click_popup_option(self.history2_name, 'View')
+        self.navigate_to_histories_page()
+        self.click_grid_popup_option(self.history2_name, 'View')
         history_name = self.wait_for_selector('.name.editable-text')
         self.assertEqual(history_name.text, self.history2_name)
 
     @selenium_test
     def test_history_publish(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
         # Publish the history
-        self.click_popup_option(self.history2_name, 'Share or Publish')
+        self.click_grid_popup_option(self.history2_name, 'Share or Publish')
         self.components.histories.sharing.make_accessible_and_publish.wait_for_and_click()
 
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
         self.histories_click_advanced_search()
         self.select_filter('sharing', 'published')
@@ -56,9 +56,9 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
     @selenium_test
     def test_rename_history(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
-        self.click_popup_option('Unnamed history', 'Rename')
+        self.click_grid_popup_option('Unnamed history', 'Rename')
 
         # Rename the history
         history_name_input = self.wait_for_selector('.ui-form-element input.ui-input')
@@ -67,17 +67,17 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
 
         self.wait_for_and_click_selector("button#submit")
 
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
         self.assert_histories_in_grid([self.history1_name, self.history2_name, self.history3_name])
 
     @selenium_test
     def test_delete_and_undelete_history(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
         # Delete the history
-        self.click_popup_option(self.history2_name, 'Delete')
+        self.click_grid_popup_option(self.history2_name, 'Delete')
 
         self.assert_histories_in_grid([self.history2_name], False)
 
@@ -86,7 +86,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.sleep_for(self.wait_types.UX_RENDER)
 
         # Restore the history
-        self.click_popup_option(self.history2_name, 'Undelete')
+        self.click_grid_popup_option(self.history2_name, 'Undelete')
 
         self.assert_grid_histories_are([])
         self.select_filter('deleted', 'False')
@@ -98,10 +98,10 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self._login()
         self.create_history(self.history4_name)
 
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
         self.assert_histories_in_grid([self.history4_name])
 
-        self.click_popup_option(self.history4_name, 'Delete Permanently')
+        self.click_grid_popup_option(self.history4_name, 'Delete Permanently')
         alert = self.driver.switch_to.alert
         alert.accept()
 
@@ -115,7 +115,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
     @selenium_test
     def test_delete_and_undelete_multiple_histories(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
         delete_button_selector = 'input[type="button"][value="Delete"]'
         undelete_button_selector = 'input[type="button"][value="Undelete"]'
@@ -144,7 +144,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
     @selenium_test
     def test_sort_by_name(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
         self.wait_for_and_click_selector('.sort-link[sort_key="name"]')
         actual_histories = self.get_histories()
@@ -162,17 +162,16 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
     @selenium_test
     def test_standard_search(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
-        input_selector = '#input-free-text-search-filter'
-        search_input = self.wait_for_selector(input_selector)
+        search_input = self.components.grids.free_text_search.wait_for_visible()
         search_input.send_keys(self.history2_name)
         self.send_enter(search_input)
 
         self.assert_grid_histories_are([self.history2_name])
 
         self.unset_filter('free-text-search', self.history2_name)
-        search_input = self.wait_for_selector(input_selector)
+        search_input = self.components.grids.free_text_search.wait_for_visible()
         search_input.send_keys(self.history4_name)
         self.send_enter(search_input)
 
@@ -181,7 +180,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
     @selenium_test
     def test_advanced_search(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
         self.histories_click_advanced_search()
 
@@ -209,7 +208,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
     @selenium_test
     def test_tags(self):
         self._login()
-        self.navigate_to_saved_histories_page()
+        self.navigate_to_histories_page()
 
         # Insert a tag
         tags_cell = self.get_history_tags_cell(self.history2_name)
@@ -269,10 +268,10 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.wait_for_and_click_selector(close_button_selector)
         self.sleep_for(self.wait_types.UX_RENDER)
 
-    def navigate_to_saved_histories_page(self):
+    def navigate_to_histories_page(self):
         self.home()
         self.click_masthead_user()  # Open masthead menu
-        self.components.masthead.saved_histories.wait_for_and_click()
+        self.components.masthead.histories.wait_for_and_click()
 
     def setup_shared_state(self):
         SavedHistoriesTestCase.user_email = self._get_random_email()
@@ -299,23 +298,6 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
             (filter_key, filter_value)
         self.wait_for_and_click_selector(filter_selector)
 
-    def click_popup_option(self, history_name, option_label):
-        history_menu_button = None
-        grid = self.wait_for_selector('#grid-table-body')
-        for row in grid.find_elements_by_tag_name('tr'):
-            name_cell = row.find_elements_by_tag_name('td')[1]
-            if name_cell.text == history_name:
-                history_menu_button = name_cell
-                break
-
-        if history_menu_button is None:
-            raise AssertionError('Failed to find history with name [%s]' % history_name)
-
-        popup_menu_button = history_menu_button.find_element_by_css_selector('.dropdown-toggle')
-        popup_menu_button.click()
-        popup_option = self.driver.find_element_by_link_text(option_label)
-        popup_option.click()
-
     def get_history_tags_cell(self, history_name):
         tags_cell = None
         grid = self.wait_for_selector('#grid-table-body')
diff --git a/test/selenium_tests/test_library_landing.py b/test/selenium_tests/test_library_landing.py
index 06343e8af1c..001e227030e 100644
--- a/test/selenium_tests/test_library_landing.py
+++ b/test/selenium_tests/test_library_landing.py
@@ -17,9 +17,9 @@ class LibraryLandingTestCase(SeleniumTestCase):
     def test_create_new_close(self):
         num_displayed_libraries = self._num_displayed_libraries()
         self.libraries_index_click_create_new()
-        self.wait_for_selector_visible(".ui-modal")
+        self.wait_for_selector_visible(".new-row")
         self.screenshot("libraries_new")
-        close_button = self.wait_for_selector_clickable("#button-1")
+        close_button = self.wait_for_selector_clickable(".cancel_library_btn")
         close_button.click()
         self.wait_for_overlays_cleared()
         assert self._num_displayed_libraries() == num_displayed_libraries
@@ -53,11 +53,6 @@ class LibraryLandingTestCase(SeleniumTestCase):
 
         self._search_for_only_with_name(new_name)
 
-    @selenium_test
-    def test_help(self):
-        help_link = self.wait_for_selector_clickable(".library-help-button")
-        self.assertEqual(help_link.get_attribute("href"), "https://galaxyproject.org/data-libraries/screen/list-of-libraries/")
-
     @selenium_test
     def test_sorting(self):
         # Throw in another library to ensure filtering is working...
diff --git a/test/selenium_tests/test_pages.py b/test/selenium_tests/test_pages.py
new file mode 100644
index 00000000000..922ed4ce351
--- /dev/null
+++ b/test/selenium_tests/test_pages.py
@@ -0,0 +1,63 @@
+from .framework import (
+    managed_history,
+    selenium_test,
+    SeleniumTestCase,
+)
+
+
+class PagesTestCase(SeleniumTestCase):
+
+    ensure_registered = True
+
+    @selenium_test
+    @managed_history
+    def test_simple_page_creation_edit_and_view(self):
+        # Upload a file to test embedded object stuff
+        test_path = self.get_filename("1.fasta")
+        self.perform_upload(test_path)
+        self.history_panel_wait_for_hid_ok(1)
+        self.navigate_to_pages()
+        self.screenshot("pages_grid")
+
+        self.components.pages.create.wait_for_and_click()
+        name = self._get_random_name(prefix="page")
+        slug = self._get_random_name(prefix="pageslug")
+        self.tool_set_value("title", name)
+        self.tool_set_value("slug", slug)
+        self.screenshot("pages_create_form")
+
+        # Sometimes 'submit' button not yet hooked up?
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        self.components.pages.submit.wait_for_and_click()
+
+        self.click_grid_popup_option(name, "Edit content")
+        self.components.pages.editor.wym_iframe.wait_for_visible()
+        self.screenshot("pages_editor_new")
+        self.driver.switch_to.frame(0)
+        try:
+            self.components.pages.editor.wym_iframe_content.wait_for_and_send_keys("moo\n\n\ncow\n\n")
+        finally:
+            self.driver.switch_to.default_content()
+
+        self.components.pages.editor.embed_button.wait_for_and_click()
+        self.screenshot("pages_editor_embed_menu")
+        self.components.pages.editor.embed_dataset.wait_for_and_click()
+        saved_datasets_element = self.components.pages.editor.dataset_selector.wait_for_and_click()
+        self.screenshot("pages_editor_embed_dataset_dialog")
+        checkboxes = saved_datasets_element.find_elements_by_css_selector("input[type='checkbox']")
+        assert len(checkboxes) > 0
+        checkboxes[0].click()
+        self.components.pages.editor.embed_dialog_add_button.wait_for_and_click()
+
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.components.pages.editor.save.wait_for_and_click()
+        self.screenshot("pages_editor_saved")
+        self.home()
+        self.navigate_to_pages()
+        self.click_grid_popup_option(name, "View")
+        self.screenshot("pages_view_simple")
+
+    def navigate_to_pages(self):
+        self.click_masthead_user()  # Open masthead menu
+        self.components.masthead.pages.wait_for_and_click()
diff --git a/test/selenium_tests/test_workflow_editor.py b/test/selenium_tests/test_workflow_editor.py
index 0b124e696e5..4cf21ce11c0 100644
--- a/test/selenium_tests/test_workflow_editor.py
+++ b/test/selenium_tests/test_workflow_editor.py
@@ -63,7 +63,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         editor.label_input.wait_for_and_click()  # Seems to help force the save of whole annotation.
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("workflow_editor_data_input_filled_in")
-        self.workflow_editor_save_and_close()
+        self.workflow_editor_click_save()
         self.workflow_index_open_with_name(name)
         data_input_node = editor.node._(label="input1")
         data_input_node.title.wait_for_and_click()
@@ -89,7 +89,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         editor.label_input.wait_for_and_click()  # Seems to help force the save of whole annotation.
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("workflow_editor_data_collection_input_filled_in")
-        self.workflow_editor_save_and_close()
+        self.workflow_editor_click_save()
         self.workflow_index_open_with_name(name)
         data_input_node = editor.node._(label="input1")
         data_input_node.title.wait_for_and_click()
@@ -116,7 +116,7 @@ class WorkflowEditorTestCase(SeleniumTestCase):
         editor.label_input.wait_for_and_click()  # Seems to help force the save of whole annotation.
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("workflow_editor_parameter_input_filled_in")
-        self.workflow_editor_save_and_close()
+        self.workflow_editor_click_save()
         self.workflow_index_open_with_name(name)
         data_input_node = editor.node._(label="input1")
         data_input_node.title.wait_for_and_click()
@@ -334,10 +334,6 @@ steps:
         self.assert_modal_has_text("Tool is not installed")
         self.screenshot("workflow_editor_missing_tool")
 
-    def workflow_editor_save_and_close(self):
-        self.workflow_editor_click_option("Save")
-        self.workflow_editor_click_option("Close")
-
     def workflow_editor_maximize_center_pane(self, collapse_left=True, collapse_right=True):
         if collapse_left:
             self.components._.left_panel_collapse.wait_for_and_click()
diff --git a/test/unit/config/test_config_manage.py b/test/unit/config/test_config_manage.py
index 28b299757dd..0bb17d83208 100644
--- a/test/unit/config/test_config_manage.py
+++ b/test/unit/config/test_config_manage.py
@@ -17,7 +17,7 @@ def test_reports_conversion_1607_sample():
         config_dir.assert_is_yaml("config/reports.yml")
         config_dir.assert_moved("config/reports.ini", "config/reports.ini.backup")
         with config_dir.open("config/reports.yml") as f:
-            config = yaml.load(f)
+            config = yaml.safe_load(f)
         assert "reports" in config
         reports_config = config["reports"] or {}
         assert "use_beaker_session" not in reports_config
@@ -56,7 +56,7 @@ def test_shed_conversion_1607_prefix():
         config_dir.assert_is_yaml("config/tool_shed.yml")
         config_dir.assert_moved("config/tool_shed.ini", "config/tool_shed.ini.backup")
         with config_dir.open("config/tool_shed.yml") as f:
-            config = yaml.load(f)
+            config = yaml.safe_load(f)
         assert "uwsgi" in config
         uwsgi_config = config["uwsgi"]
         assert "module" not in uwsgi_config
@@ -70,7 +70,7 @@ def test_allow_library_path_paste_conversion():
         config_dir.assert_is_yaml("config/galaxy.yml")
         config_dir.assert_moved("config/galaxy.ini", "config/galaxy.ini.backup")
         with config_dir.open("config/galaxy.yml") as f:
-            config = yaml.load(f)
+            config = yaml.safe_load(f)
         assert "galaxy" in config
         galaxy_config = config["galaxy"]
         assert galaxy_config["allow_path_paste"] is True
@@ -106,7 +106,7 @@ class _TestConfigDirectory(object):
     def assert_is_yaml(self, path):
         self.assert_exists(path)
         with self.open(path, "r") as f:
-            return yaml.load(f)
+            return yaml.safe_load(f)
 
     def open(self, path, *args):
         return open(os.path.join(self.temp_directory, path), *args)
diff --git a/test/unit/datatypes/test_data.py b/test/unit/datatypes/test_data.py
index 969916d57b9..d1f85571714 100644
--- a/test/unit/datatypes/test_data.py
+++ b/test/unit/datatypes/test_data.py
@@ -10,4 +10,4 @@ from galaxy.util import galaxy_directory
 
 def test_get_file_peek():
     # should get the first 5 lines of the file without a trailing newline character
-    assert get_file_peek(os.path.join(galaxy_directory(), 'test-data/1.tabular'), line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11'
+    assert get_file_peek(os.path.join(galaxy_directory(), 'test-data/1.tabular'), line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11\n'
diff --git a/test/unit/datatypes/test_sniff.py b/test/unit/datatypes/test_sniff.py
new file mode 100644
index 00000000000..faf75443281
--- /dev/null
+++ b/test/unit/datatypes/test_sniff.py
@@ -0,0 +1,79 @@
+import tempfile
+
+import pytest
+
+from galaxy.datatypes.sniff import (
+    convert_newlines,
+    convert_newlines_sep2tabs,
+    get_test_fname,
+)
+
+
+def assert_converts_to_1234_convert_sep2tabs(content, expected='1\t2\n3\t4\n'):
+    with tempfile.NamedTemporaryFile(delete=False, mode='w') as tf:
+        tf.write(content)
+    rval = convert_newlines_sep2tabs(tf.name, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
+    assert expected == open(tf.name).read()
+    assert rval == (2, None), rval
+
+
+def assert_converts_to_1234_convert(content, block_size=1024):
+    fname = get_test_fname('temp2.txt')
+    with open(fname, 'w') as fh:
+        fh.write(content)
+    rval = convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir(), block_size=block_size)
+    actual_contents = open(fname).read()
+    assert '1 2\n3 4\n' == actual_contents, actual_contents
+    assert rval == (2, None), "rval != %s for %s" % (rval, content)
+
+
+@pytest.mark.parametrize('source,block_size', [
+    ("1 2\r3 4", None),
+    ("1 2\n3 4", None),
+    ("1 2\r\n3 4", None),
+    ("1 2\r3 4\r", None),
+    ("1 2\n3 4\n", None),
+    ("1 2\r\n3 4\r\n", None),
+    ("1 2\r3 4", 2),
+    ("1 2\n3 4", 2),
+    ("1 2\r\n3 4", 2),
+    ("1 2\r3 4\r", 2),
+    ("1 2\n3 4\n", 2),
+    ("1 2\r\n3 4\r\n", 2),
+    ("1 2\r3 4", 3),
+    ("1 2\n3 4", 3),
+    ("1 2\r\n3 4", 3),
+    ("1 2\r3 4\r", 3),
+    ("1 2\n3 4\n", 3),
+    ("1 2\r\n3 4\r\n", 3),
+])
+def test_convert_newlines(source, block_size):
+    # Verify ends with newline - with or without that on inputs - for any of
+    # \r \\n or \\r\\n newlines.
+    if block_size:
+        assert_converts_to_1234_convert(source, block_size)
+    else:
+        assert_converts_to_1234_convert(source)
+
+
+def test_convert_newlines_non_utf():
+    fname = get_test_fname("dosimzml")
+    rval = convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir(), in_place=False)
+    new_file = rval[1]
+    assert open(new_file, "rb").read() == open(get_test_fname("1imzml"), "rb").read()
+
+
+@pytest.mark.parametrize('source,expected', [
+    ("1 2\n3 4\n", None),
+    ("1    2\n3    4\n", None),
+    ("1\t2\n3\t4\n", None),
+    ("1\t2\r3\t4\r", None),
+    ("1\t2\r\n3\t4\r\n", None),
+    ("1    2\r\n3       4\r\n", None),
+    ("1 2     \n3 4 \n", '1\t2\t\n3\t4\t\n'),
+])
+def test_convert_sep2tabs(source, expected):
+    if expected:
+        assert_converts_to_1234_convert_sep2tabs(source, expected=expected)
+    else:
+        assert_converts_to_1234_convert_sep2tabs(source)
diff --git a/test/unit/datatypes/test_vcf.py b/test/unit/datatypes/test_vcf.py
index 66537272baf..f068591f229 100644
--- a/test/unit/datatypes/test_vcf.py
+++ b/test/unit/datatypes/test_vcf.py
@@ -11,19 +11,22 @@ from .util import (
 
 
 def test_vcf_sniff():
-    vcf = Vcf()
-    vcf_gz = VcfGz()
-    with get_input_files('1.vcf_bgzip', '1.vcf') as input_files:
-        compressed, uncompressed = input_files
-        assert vcf_gz.sniff(compressed) is True
-        assert vcf_gz.sniff(uncompressed) is False
-        assert vcf.sniff(compressed) is False
-        assert vcf.sniff(uncompressed) is True
+    vcf_datatype = Vcf()
+    vcf_bgzip_datatype = VcfGz()
+    with get_input_files('1.vcf_bgzip', '1.vcf', 'vcf_gzipped.vcf.gz') as input_files:
+        vcf_bgzip, uncompressed, compressed = input_files
+        assert vcf_bgzip_datatype.sniff(vcf_bgzip) is True
+        assert vcf_bgzip_datatype.sniff(uncompressed) is False
+        assert vcf_bgzip_datatype.sniff(compressed) is False
+        assert vcf_datatype.sniff(vcf_bgzip) is False
+        assert vcf_datatype.sniff(uncompressed) is True
+        # Cannot sniff the vcf.gz file as vcf directly, works only when
+        # auto_decompress is enabled
 
 
-def test_vcf_gz_set_meta():
-    vcf_gz = VcfGz()
+def test_vcf_bgzip_set_meta():
+    vcf_bgzip_datatype = VcfGz()
     with get_input_files('1.vcf_bgzip') as input_files, get_dataset(input_files[0], index_attr='tabix_index') as dataset:
-        vcf_gz.set_meta(dataset)
+        vcf_bgzip_datatype.set_meta(dataset)
         f = pysam.VariantFile(dataset.file_name, index_filename=dataset.metadata.tabix_index.file_name)
         assert isinstance(f.index, pysam.libcbcf.TabixIndex) is True
diff --git a/test/unit/jobs/job_conf.sample_advanced.yml b/test/unit/jobs/job_conf.sample_advanced.yml
new file mode 100644
index 00000000000..a56605c71a0
--- /dev/null
+++ b/test/unit/jobs/job_conf.sample_advanced.yml
@@ -0,0 +1,592 @@
+# TODO: translocate docs for all pulsar embedded
+# TODO: translocate docs for all kubernetes
+# TODO: implement and demo embedded job_metrics.
+# TODO: translocate docker option docs into docker_local environment description
+# TODO: translocate singluarity option docs into singularity_local environment description
+# TODO: all destinations from condor on
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 4
+  drmaa:
+    load: galaxy.jobs.runners.drmaa:DRMAAJobRunner
+
+    # Different DRMs handle successfully completed jobs differently,
+    # these options can be changed to handle such differences and
+    # are explained in detail on the Galaxy wiki. Defaults are shown
+    invalidjobexception_state: ok
+    invalidjobexception_retries: 0
+    internalexception_state: ok
+    internalexception_retries: 0
+  sge:
+    load: galaxy.jobs.runners.drmaa:DRMAAJobRunner
+    # Override the $DRMAA_LIBRARY_PATH environment variable
+    drmaa_library_path: /sge/lib/libdrmaa.so
+  cli: 
+    load: galaxy.jobs.runners.cli:ShellJobRunner
+  condor: 
+    load: galaxy.jobs.runners.condor:CondorJobRunner
+  slurm: 
+    load: galaxy.jobs.runners.slurm:SlurmJobRunner
+  dynamic:
+    # The dynamic runner is not a real job running plugin and is
+    # always loaded, so it does not need to be explicitly stated in
+    # runners. However, if you wish to change the base module
+    # containing your dynamic rules, you can do so.
+    # The `load` attribute is not required (and ignored if
+    # included).
+    rules_module: galaxy.jobs.rules
+
+  godocker:
+    # Go-Docker is a batch computing/cluster management tool using Docker
+    # See https://bitbucket.org/osallou/go-docker for more details.
+    load: galaxy.jobs.runners.godocker:GodockerJobRunner
+    # Specify the instance of GoDocker
+    godocker_master: GODOCKER_URL
+    # GoDocker username
+    user: USERNAME
+    # GoDocker API key
+    key: APIKEY
+    # Specify the project present in the GoDocker setup
+    godocker_project: galaxy
+
+  chronos:
+    # Chronos is a framework for the Apache Mesos software; a software which manages
+    # computer clusters. Specifically, Chronos runs of top of Mesos and it's used
+    # for job orchestration.
+    # 
+    # This runner requires a shared file system where the directories of
+    # `job_working_directory`, `file_path` and `new_file_path` settings defined on
+    # the `galaxy.ini` file are shared amongst the Mesos agents (i.e. nodes which
+    # actually run the jobs).
+    load: galaxy.jobs.runners.chronos:ChronosJobRunner
+    # Hostname which runs Chronos instance.
+    chronos: '`chronos_host`'
+    # The email address of the person responsible for the job.
+    owner: foo@bar.com
+    # Username to access Mesos cluster.
+    username: username
+    # Password to access Mesos cluster.
+    password: password
+    # True to communicate with Chronos over HTTPS; false otherwise
+    insecure: true
+
+  # Pulsar runners (see more at https://pulsar.readthedocs.io/)
+  pulsar_rest:
+    load: galaxy.jobs.runners.pulsar:PulsarRESTJobRunner
+    # Allow optimized HTTP calls with libcurl (defaults to urllib)
+    transport: curl
+    # Experimental Caching*: Undocumented, don't use.
+    #cache: false
+
+  pulsar_mq:
+    load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
+    # AMQP URL to connect to.
+    amqp_url: amqp://guest:guest@localhost:5672//
+    # URL remote Pulsar apps should transfer files to this Galaxy
+    # instance to/from. This can be unspecified/empty if
+    # `galaxy_infrastructure_url1 is set in galaxy.yml.
+    galaxy_url: http://localhost:8080
+
+    # AMQP does not guarantee that a published message is received by
+    # the AMQP server, so Galaxy/Pulsar can request that the consumer
+    # acknowledge messages and will resend them if acknowledgement is
+    # not received after a configurable timeout. 
+    #amqp_acknowledge: false
+
+    # Galaxy reuses Pulsar's persistence_directory parameter (via the
+    # Pulsar client lib) to store a record of received
+    # acknowledgements, and to keep track of messages which have not
+    # been acknowledged.
+    #persistence_directory: /path/to/dir
+
+    # Number of seconds to wait for an acknowledgement before
+    # republishing a message.
+    #amqp_republish_time: 30
+
+    # Pulsar job manager to communicate with (see Pulsar
+    # docs for information on job managers).
+    #manager: _default_
+
+    # The AMQP client can provide an SSL client certificate (e.g. for
+    # validation), the following options configure that certificate
+    # (see for reference:
+    # https://kombu.readthedocs.io/en/latest/reference/kombu.connection.html
+    # ). If you simply want to use SSL but not use/validate a client
+    # cert, just use the ?ssl=1 query on the amqp URL instead.
+    #amqp_connect_ssl_ca_certs: /path/to/cacert.pem
+    #amqp_connect_ssl_keyfile: /path/to/key.pem
+    #amqp_connect_ssl_certfile: /path/to/cert.pem
+    #amqp_connect_ssl_cert_reqs: cert_required
+    # By default, the AMQP consumer uses a nonblocking connection with
+    # a 0.2 second timeout. In testing, this works fine for
+    # unencrypted AMQP connections, but with SSL it will cause the
+    # client to reconnect to the server after each timeout. Set to a
+    # higher value (in seconds) (or `None` to use blocking connections).
+    #amqp_consumer_timeout: None
+
+  pulsar_k8s:
+    # Use a two-container Kubernetes to run jobs - one for staging and one
+    # for tool execution.
+    load: galaxy.jobs.runners.pulsar:PulsarKubernetesCoexecutionJobRunner
+    galaxy_url: http://docker.for.mac.localhost:8080
+    amqp_url: amqp://guest:guest@localhost:5672//
+
+  pulsar_legacy:
+    # Pulsar job runner with default parameters matching those
+    # of old LWR job runner. If your Pulsar server is running on a
+    # Windows machine for instance this runner should still be used.
+
+    # These destinations still needs to target a Pulsar server,
+    # older LWR plugins and destinations still work in Galaxy can
+    # target LWR servers, but this support should be considered
+    # deprecated and will disappear with a future release of Galaxy.
+    load: galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner
+
+handling:
+  processes:
+    handler0:
+    handler1:
+    sge_handler:
+      # Restrict a handler to load specific runners, by default they will load all.
+      plugins: ['sge']
+    special_handler0:
+      tags: [special_handlers]
+    special_handler1:
+      tags: [special_handlers]
+
+
+execution:
+  default: local
+  environments:
+    local:
+      runner: local
+
+    multicore_local:
+      runner: local
+      # Warning: Local slot count doesn't tie up additional worker threads, to prevent over
+      # allocating machine define a second local runner with different name and fewer workers
+      # to run this destination.
+      local_slots: 4
+      # Embed metadata collection in local job script (defaults to true for most runners).
+      embed_metadata_in_job: true
+
+    docker_local:
+      runner: local
+      docker_enabled: true
+
+    singularity_local:
+      runner: local
+      singularity_enabled: true
+
+    # The above Docker and Singularity examples describe how to specify
+    # default and override containers but fuller descriptions can be used
+    # also to tweak extra options. Like in the above examples, "container_override"
+    # will override the tool centric container resolution specified by the container
+    # resolvers configuration and "containers" will provide a default if no such
+    # container is found during resolution.
+
+    # resolve_dependencies defaults to false, but can be set to true to use
+    # dependency resolution inside the container (you'll likely want to ensure
+    # Galaxy's tool dependency directory and/or Conda prefix is mounted in the
+    # container if this is set. shell (defaults to /bin/sh) can be used to tell
+    # Galaxy to use bash for instance in the target contanier.
+
+    # If using these options, docker_enabled and/or singularity_enabled should
+    # also be set to true to enable the desired container technology. If multiple
+    # such containers are defined (as in the example below), the first one matching
+    # the enabled container types for this destination will be used.
+    customized_container:
+      runner: local
+      container:
+        - type: docker
+          shell: '/bin/sh'
+          resolve_dependencies: false
+          identifier: 'busybox:ubuntu-14.04'
+        - type: singularity
+          shell: '/bin/sh'
+          resolve_dependencies: false
+          identifier: '/path/to/default/container'
+      container_override:
+        - type: docker
+          shell: '/bin/sh'
+          resolve_dependencies: false
+          identifier: 'busybox:ubuntu-14.04'
+        - type: singularity
+          shell: '/bin/sh'
+          resolve_dependencies: false
+          identifier: '/path/to/default/container'
+    pbs:
+      runner: pbs
+      tags: [mycluster]
+    pbs_longjobs:
+      runner: pbs
+      tags: [mycluster, longjobs]
+      Resource_List: 'walltime=72:00:00'
+    remote_cluster:
+      runner: drmaa
+      tags: [longjobs]
+      # Set to False if cluster nodes don't shared Galaxy library,
+      # it will perform metadata calculation locally after the job finishes.
+      embed_metadata_in_job: true
+      # If jobs are configured to run as the real user, this option allows
+      # users that are not mapped to any real users to run jobs
+      # as a Galaxy (fallback). Default is false.
+      allow_guests: true
+    java_cluster:
+      runner: drmaa
+      env:
+        # set arbitrary environment variables at runtime. General
+        # dependencies for tools should be configured via
+        # tool_dependency_dir and package options and these
+        # options should be reserved for defining cluster
+        # specific options.
+        - name: '_JAVA_OPTIONS'
+          value: '-Xmx6G'
+        - name: ANOTHER_OPTION
+          raw: true  # disable auto-quoting.
+          value: "'5'"
+        - file: /mnt/java_cluster/environment_setup.sh  # script will be sourced
+        - execute: 'module load javastuff/2.10'
+        # files to source and exec statements will be handled on remote
+        # clusters. These don't need to be available on the Galaxy server
+        # itself.
+
+    # Following three environments demonstrate setting up per-job temp directory handling.
+    # In these cases TEMP, TMP, and TMPDIR will be set for each job dispatched to these
+    # environments.
+
+    # The first simply tells Galaxy to create a temp directory in the job directory, the
+    # other forms can be used to issue shell commands before the job runs on the worker node to
+    # allocate a temp directory. In these other cases, Galaxy will not clean up these
+    # directories so either use directories managed by the job resource manager or setup
+    # tooling to clean old temp directories up outside of Galaxy.
+    clean_tmp_by_job:
+      runner: drmma
+      tmp_dir: true
+    clean_tmp_drm:
+      runner: drmma
+      tmp_dir: $DRM_SET_VARIABLES_FOR_THIS_JOB
+    clean_tmp_fast_scratch:
+      runner: drmma
+      tmp_dir: '$(mktemp -d /mnt/scratch/fastest/gxyjobXXXXXXXXXXX)'
+
+    real_user_cluster:
+      # The drmaa runner can be used to run jobs as the submitting user,
+      # make sure to setup 3 real user parameters in galaxy.yml.
+      runner: drmaa
+
+    dynamic:
+      runner: dynamic
+      # A destination that represents a method in the dynamic runner.
+      # foo should be a Python function defined in any file in
+      # lib/galaxy/jobs/rules.
+      function: foo
+    dtd_destination:
+      runner: dynamic
+      # DTD is a special dynamic job destination type that builds up
+      # rules given a YAML-based DSL (see config/tool_destinations.yml.sample
+      # for the syntax).
+      type: dtd
+    load_balance:
+      runner: dynamic
+       # Randomly assign jobs to various static destination ids
+      type: choose_one
+      destination_ids: cluster1,cluster2,cluster3
+    load_balance_with_data_locality:
+      runner: dynamic
+      # Randomly assign jobs to various static destination ids,
+      # but keep jobs in the same workflow invocation together and
+      # for those jobs ran outside of workflows keep jobs in same
+      # history together.
+
+      type: choose_one
+      destination_ids: cluster1,cluster2,cluster3
+      hash_by: workflow_invocation,history
+    burst_out:
+      runner: dynamic
+      # Burst out from static destination local_cluster_8_core to
+      # static destination shared_cluster_8_core when there are about
+      # 50 Galaxy jobs assigned to any of the local_cluster_XXX
+      # destinations (either running or queued). If there are fewer
+      # than 50 jobs, just use local_cluster_8_core destination.
+
+      # Uncomment job_state parameter to make this bursting happen when
+      # roughly 50 jobs are queued instead.
+      type: burst
+      from_destination_ids: [local_cluster_8_core, local_cluster_1_core, local_cluster_16_core]
+      to_destination_id: shared_cluster_8_core
+      num_jobs: 50
+      # job_states: queued
+    burst_if_queued:
+      runner: dynamic
+      # Dynamic destinations can be chained together to create more
+      # complex rules. In this example, the built-in burst stock rule
+      # determines whether to burst, and if so, directs to burst_if_size,
+      # a user-defined dynamic destination. This destination in turn will
+      # conditionally route it to a remote pulsar node if the input size
+      # is below a certain threshold, or route to local if not.
+      type: burst
+      from_destination_ids: local
+      to_destination_id: burst_if_size
+      num_jobs: 2
+      job_states: queued
+    burst_if_size:
+      runner: dynamic
+      type: python
+      function: to_destination_if_size
+      # Also demonstrates a destination level override of the
+      # rules_module. This rules_module will take precedence over the
+      # plugin level rules module when resolving the dynamic function
+      rules_module: galaxycloudrunner.rules
+      max_size: 1g
+      to_destination_id: galaxycloudrunner
+      fallback_destination_id: local
+    galaxycloudrunner:
+      runner: dynamic
+      # Demonstrates how to use the galaxycloudrunner, which enables dynamic bursting
+      # to cloud destinations. For detailed information on how to use the galaxycloudrunner,
+      # consult the documentation at: https://galaxycloudrunner.readthedocs.io/
+      type: python
+      function: cloudlaunch_pulsar_burst
+      rules_module: galaxycloudrunner.rules
+      cloudlaunch_api_endpoint: https://launch.usegalaxy.org/cloudlaunch/api/v1
+      # Obtain your CloudLaunch token by visiting: https://launch.usegalaxy.org/profile
+      cloudlaunch_api_token: 37c46c89bcbea797bc7cd76fee10932d2c6a2389
+      # id of the PulsarRESTJobRunner plugin. Defaults to "pulsar"
+      pulsar_runner_id: pulsar
+      # Destination to fallback to if no nodes are available
+      fallback_destination: local
+      # Pick next available server and resubmit if an unknown error occurs
+      # resubmit: {condition: 'unknown_error and attempt <= 3', environment: galaxycloudrunner}
+
+    docker_dispatch:
+      runner: dynamic
+      # Follow dynamic destination type will send all tool's that
+      # support docker to static destination defined by
+      # docker_destination_id (docker_cluster in this example) and all
+      # other tools to default_destination_id (normal_cluster in this
+      # example).
+      type: docker_dispatch
+      docker_destination_id: docker_cluster
+      default_destination_id: normal_cluster
+
+    # Pulsar enviornment examples
+    secure_pulsar_rest_dest:
+       runner: pulsar_rest
+       # URL of Pulsar server.
+       url: https://examle.com:8913/
+       
+       # If set, private_token must match token in remote Pulsar's
+       # configuration.
+       private_token: 123456789changeme
+       
+       # Uncomment the following statement to disable file staging (e.g.
+       # if there is a shared file system between Galaxy and the Pulsar
+       # server). Alternatively action can be set to 'copy' - to replace
+       # http transfers with file system copies, 'remote_transfer' to cause
+       # the Pulsar to initiate HTTP transfers instead of Galaxy, or
+       # 'remote_copy' to cause Pulsar to initiate file system copies.
+       # If setting this to 'remote_transfer' be sure to specify a
+       # 'galaxy_url' attribute on the runner plugin above. -->
+       default_file_action: none
+
+       # The above option is just the default, the transfer behavior
+       # none|copy|http|remote_transfer|remote_copy can be configured on a per
+       # path basis via the following file or dictionary. See Pulsar documentation
+       # for more details and examples.
+       #file_action_config: file_actions.yaml
+       #file_actions: {}
+       
+       # The non-legacy Pulsar runners will attempt to resolve Galaxy
+       # dependencies remotely - to enable this set a tool_dependency_dir
+       # in Pulsar's configuration (can work with all the same dependency
+       # resolutions mechanisms as Galaxy - tool Shed installs, Galaxy
+       # packages, etc...). To disable this behavior, set the follow parameter
+       # to none. To generate the dependency resolution command locally
+       # set the following parameter local.
+       #dependency_resolution: none
+
+       # Uncomment following option to enable setting metadata on remote
+       # Pulsar server. The 'use_remote_datatypes' option is available for
+       # determining whether to use remotely configured datatypes or local
+       # ones (both alternatives are a little brittle). 
+       #remote_metadata: true
+       #use_remote_datatypes: false
+       #remote_property_galaxy_home: /path/to/remote/galaxy-central
+       
+       # If remote Pulsar server is configured to run jobs as the real user,
+       # uncomment the following line to pass the current Galaxy user
+       # along. 
+       #submit_user: $__user_name__
+       
+       # Various other submission parameters can be passed along to the Pulsar
+       # whose use will depend on the remote Pulsar's configured job manager.
+       # For instance:
+       #submit_native_specification: -P bignodes -R y -pe threads 8
+       
+       # Disable parameter rewriting and rewrite generated commands
+       # instead. This may be required if remote host is Windows machine
+       # but probably not otherwise.
+       #rewrite_parameters: false
+
+    pulsar_mq_dest:
+       runner: pulsar_mq
+       # The RESTful Pulsar client sends a request to Pulsar
+       # to populate various system properties. This
+       # extra step can be disabled and these calculated here
+       # on client by uncommenting jobs_directory and
+       # specifying any additional remote_property_ of
+       # interest, this is not optional when using message
+       # queues.
+       jobs_directory: /path/to/remote/pulsar/files/staging/
+       # Otherwise MQ and Legacy pulsar destinations can be supplied
+       # all the same destination parameters as the RESTful client documented
+       # above (though url and private_token are ignored when using a MQ).
+
+    pulsar_k8s_environment:
+      runner: pulsar_k8s
+      docker_enabled: true  # probably shouldn't be needed but is still
+      docker_default_container_id: 'conda/miniconda2'
+      # Specify a non-default Pulsar staging container.
+      #pulsar_container_image: 'galaxy/pulsar-pod-staging:0.12.0'
+
+    # Example CLI runners.
+    ssh_torque:
+      runner: cli
+      shell_plugin: SecureShell
+      job_plugin: Torque
+      shell_username: foo
+      shell_hostname: foo.example.org
+      job_Resource_List: walltime=24:00:00,ncpus=4
+
+    ssh_slurm:
+      runner: cli
+      shell_plugin: SecureShell
+      job_plugin: Slurm
+      shell_username: foo
+      shell_hostname: my_host
+      job_time: 2:00:00
+      job_ncpus: 4
+      job_partition: my_partition
+
+    local_lsf_8cpu_16GbRam:
+      runner: cli
+      shell_plugin: LocalShell
+      job_plugin: LSF
+      job_memory: 16000
+      job_cores: 8
+      job_project: BigMem
+
+# Tools can be configured to use specific destinations or handlers,
+# identified by either the "id" or "tags" attribute.  If assigned to
+# a tag, a handler or destination that matches that tag will be
+# chosen at random. 
+tools:
+- id: bwa
+  handler: handler0
+- id: bowtie
+  handler: handler1
+- id: bar
+  enviroment: dynamic
+- 
+  # Next example defines resource group to insert into tool interface
+  # and pass to dynamic destination (as resource_params argument).
+  id: longbar
+  environment: dynamic
+  resources: all
+- 
+  # Pick a handler randomly from those declaring this tag.
+  id: baz
+  handler: special_handlers
+  environment: bigmem
+- 
+  # legacy trackerster parameter for tool mapping
+  id: foo
+  handler: handler0
+  source: trackster
+
+resources:
+  default: default
+  groups:
+    # Group different parameters defined in job_resource_params_conf.xml
+    # together and assign these groups ids. Tool section below can map
+    # tools to different groups.
+    default: []
+    memoryonly: [memory]
+    all: [processors, memory, time, project]
+
+# Certain limits can be defined. The 'concurrent_jobs' limits all
+# control the number of jobs that can be "active" at a time, that
+# is, dispatched to a runner and in the 'queued' or 'running'
+# states.
+
+# A race condition exists that will allow environment_* concurrency
+# limits to be surpassed when multiple handlers are allowed to
+# handle jobs for the same environment. To prevent this, assign all
+# jobs for a specific environment to a single handler.
+limits:
+- 
+  # Limit on the number of jobs a user with a registered Galaxy
+  # account can have active across all environments.
+  type: registered_user_concurrent_jobs
+  value: 2
+
+- 
+  # Likewise, but for unregistered/anonymous users.
+  type: anonymous_user_concurrent_jobs
+  value: 1
+
+- 
+  # The number of jobs a user can have active in the specified
+  # environment, or across all environments identified by the
+  # specified tag. (formerly: concurrent_jobs)
+  type: environment_user_concurrent_jobs
+  id: local
+  value: 1
+
+-
+  type: environment_user_concurrent_jobs
+  tag: mycluster
+  value: 2
+
+-
+  type: environment_user_concurrent_jobs
+  tag: longjobs
+  value: 1
+
+-
+  # The number of jobs that can be active in the specified
+  # environment (or across all environments identified by the
+  # specified tag) by any/all users.
+  type: environment_total_concurrent_jobs
+  id: local
+  value: 16
+
+-
+  type: environment_total_concurrent_jobs
+  tag: longjobs
+  value: 100
+
+-
+  # Amount of time a job can run (in any environment) before it
+  # will be terminated by Galaxy.
+  type: walltime
+  value: '24:00:00'
+
+- 
+  # Total walltime that jobs may not exceed during a set period.
+  # If total walltime of finished jobs exceeds this value, any
+  # new jobs are paused.  `window` is a number in days,
+  # representing the period.
+  type: total_walltime
+  window: 30
+  value: '24:00:00'
+
+- 
+  # Size that any defined tool output can grow to before the job
+  # will be terminated. This does not include temporary files
+  # created by the job. Format is flexible, e.g.:
+  # '10GB' = '10g' = '10240 Mb' = '10737418240'
+  type: output_size
+  value: '10GB'
diff --git a/test/unit/jobs/test_command_factory.py b/test/unit/jobs/test_command_factory.py
index b5493c3698a..f997190badf 100644
--- a/test/unit/jobs/test_command_factory.py
+++ b/test/unit/jobs/test_command_factory.py
@@ -45,7 +45,11 @@ class TestCommandFactory(TestCase):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command("%s/tool_script.sh > ../tool_stdout 2> ../tool_stderr; return_code=$?" % self.job_wrapper.working_directory))
+        self.__assert_command_is(_surround_command(
+            "%s %s/tool_script.sh > ../tool_stdout 2> ../tool_stderr; return_code=$?" % (
+                self.job_wrapper.shell,
+                self.job_wrapper.working_directory,
+            )))
         self.__assert_tool_script_is("#!/bin/sh\n%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE))
 
     def test_remote_dependency_resolution(self):
@@ -174,6 +178,7 @@ class MockJobWrapper(object):
             )
         )
         self.shell = "/bin/sh"
+        self.use_metadata_binary = False
 
     def get_command_line(self):
         return self.command_line
diff --git a/test/unit/jobs/test_datasets.py b/test/unit/jobs/test_datasets.py
index a12dd7ce603..1a920d83bfa 100644
--- a/test/unit/jobs/test_datasets.py
+++ b/test/unit/jobs/test_datasets.py
@@ -1,4 +1,4 @@
-from galaxy.jobs.datasets import DatasetPath
+from galaxy.job_execution.datasets import DatasetPath
 
 
 def test_dataset_path():
diff --git a/test/unit/jobs/test_job_configuration.py b/test/unit/jobs/test_job_configuration.py
index 226276c68be..9aec01cb6d4 100644
--- a/test/unit/jobs/test_job_configuration.py
+++ b/test/unit/jobs/test_job_configuration.py
@@ -5,25 +5,28 @@ import tempfile
 import unittest
 
 import mock
+from pykwalify.core import Core
 
 from galaxy.jobs import JobConfiguration
 from galaxy.util import bunch
-from galaxy.web.stack import ApplicationStack, UWSGIApplicationStack
+from galaxy.web_stack import ApplicationStack, UWSGIApplicationStack
 
 # File would be slightly more readable if contents were embedded directly, but
 # there are advantages to testing the documentation/examples.
 SIMPLE_JOB_CONF = os.path.join(os.path.dirname(__file__), "..", "..", "..", "config", "job_conf.xml.sample_basic")
 ADVANCED_JOB_CONF = os.path.join(os.path.dirname(__file__), "..", "..", "..", "config", "job_conf.xml.sample_advanced")
+ADVANCED_JOB_CONF_YAML = os.path.join(os.path.dirname(__file__), "job_conf.sample_advanced.yml")
 CONDITIONAL_RUNNER_JOB_CONF = os.path.join(os.path.dirname(__file__), "conditional_runners_job_conf.xml")
 HANDLER_TEMPLATE_JOB_CONF = os.path.join(os.path.dirname(__file__), "handler_template_job_conf.xml")
 
 
-class JobConfXmlParserTestCase(unittest.TestCase):
+class BaseJobConfXmlParserTestCase(unittest.TestCase):
+    extension = "xml"
 
     def setUp(self):
         self.temp_directory = tempfile.mkdtemp()
         self.config = bunch.Bunch(
-            job_config_file=os.path.join(self.temp_directory, "job_conf.xml"),
+            job_config_file=os.path.join(self.temp_directory, "job_conf.%s" % self.extension),
             use_tasked_jobs=False,
             job_resource_params_file="/tmp/fake_absent_path",
             config_dict={},
@@ -31,16 +34,85 @@ class JobConfXmlParserTestCase(unittest.TestCase):
             track_jobs_in_database=True,
             server_name="main",
         )
-        self.__write_config_from(SIMPLE_JOB_CONF)
-        self.__app = None
-        self.__application_stack = None
-        self.__job_configuration = None
-        self.__job_configuration_base_pools = None
-        self.__uwsgi_opt = None
+        self._write_config_from(SIMPLE_JOB_CONF)
+        self._app = None
+        self._application_stack = None
+        self._job_configuration = None
+        self._job_configuration_base_pools = None
+        self._uwsgi_opt = None
 
     def tearDown(self):
         shutil.rmtree(self.temp_directory)
 
+    # TODO: Add job metrics parsing test.
+
+    @property
+    def app(self):
+        if not self._app:
+            self._app = bunch.Bunch(
+                config=self.config,
+                job_metrics=MockJobMetrics(),
+                application_stack=self.application_stack
+            )
+        return self._app
+
+    @property
+    def application_stack(self):
+        if not self._application_stack:
+            self._application_stack = ApplicationStack()
+        return self._application_stack
+
+    @property
+    def job_config(self):
+        if not self._job_configuration:
+            base_handler_pools = self._job_configuration_base_pools or JobConfiguration.DEFAULT_BASE_HANDLER_POOLS
+            mock_uwsgi = mock.Mock()
+            mock_uwsgi.mule_id = lambda: 1
+            with mock.patch('galaxy.web_stack.uwsgi', mock_uwsgi), \
+                    mock.patch('galaxy.web_stack.uwsgi.opt', self._uwsgi_opt), \
+                    mock.patch('galaxy.jobs.JobConfiguration.DEFAULT_BASE_HANDLER_POOLS', base_handler_pools):
+                self._job_configuration = JobConfiguration(self.app)
+        return self._job_configuration
+
+    def _with_uwsgi_application_stack(self, **uwsgi_opt):
+        self._uwsgi_opt = uwsgi_opt
+        self._application_stack = UWSGIApplicationStack()
+
+    def _with_handlers_config(self, assign_with=None, default=None, handlers=None, base_pools=None):
+        handlers = handlers or []
+        template = {
+            'assign_with': ' assign_with="%s"' % assign_with if assign_with is not None else '',
+            'default': ' default="%s"' % default if default is not None else '',
+            'handlers': '\n'.join([
+                '<handler id="{id}"{tags}/>'.format(
+                    id=x['id'],
+                    tags=' tags="%s"' % x['tags'] if 'tags' in x else ''
+                ) for x in handlers]),
+        }
+        self._job_configuration_base_pools = base_pools
+        self._write_config_from(HANDLER_TEMPLATE_JOB_CONF, template=template)
+
+    def _write_config_from(self, path, template=None):
+        template = template or {}
+        contents = open(path, "r").read()
+        if template:
+            contents = contents.format(**template)
+        self._write_config(contents)
+
+    def _write_config(self, contents):
+        with open(os.path.join(self.temp_directory, "job_conf.%s" % self.extension), "w") as f:
+            f.write(contents)
+
+    def _with_advanced_config(self):
+        if self.extension == "xml":
+            self._write_config_from(ADVANCED_JOB_CONF)
+        else:
+            self._write_config_from(ADVANCED_JOB_CONF_YAML)
+
+
+class SimpleJobConfXmlParserTestCase(BaseJobConfXmlParserTestCase):
+    extension = "xml"
+
     def test_load_simple_runner(self):
         runner_plugin = self.job_config.runner_plugins[0]
         assert runner_plugin["id"] == "local"
@@ -58,14 +130,14 @@ class JobConfXmlParserTestCase(unittest.TestCase):
         assert task_runners[0]["workers"] == 5
 
     def test_explicit_handler_default(self):
-        self.__with_handlers_config(
+        self._with_handlers_config(
             handlers=[{'id': 'handler0', 'tags': 'handlers'}, {'id': 'handler1', 'tags': 'handlers'}],
             default='handlers'
         )
         assert self.job_config.default_handler_id == "handlers"
 
     def test_handler_tag_parsing(self):
-        self.__with_handlers_config(
+        self._with_handlers_config(
             handlers=[{'id': 'handler0', 'tags': 'handlers'}, {'id': 'handler1', 'tags': 'handlers'}],
             default='handlers'
         )
@@ -78,72 +150,72 @@ class JobConfXmlParserTestCase(unittest.TestCase):
         assert self.job_config.handlers == {}
 
     def test_implicit_db_assign_handler_assign_with_explicit_handlers(self):
-        self.__with_handlers_config(handlers=[{'id': 'handler0'}, {'id': 'handler1'}])
+        self._with_handlers_config(handlers=[{'id': 'handler0'}, {'id': 'handler1'}])
         assert self.job_config.handler_assignment_methods == ['db-preassign']
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['handler0', 'handler1']
+        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'handler1']
 
     def test_implict_uwsgi_mule_message_handler_assign(self):
-        self.__with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
+        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
         assert self.job_config.handler_assignment_methods == ['uwsgi-mule-message']
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers['_default_'] == ['main.job-handlers.1']
 
     def test_implict_uwsgi_mule_message_handler_assign_with_explicit_handlers(self):
-        self.__with_handlers_config(handlers=[{'id': 'handler0'}, {'id': 'handler1'}])
-        self.__with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
-        assert self.job_config.handler_assignment_methods == ['uwsgi-mule-message', 'db-preassign']
+        self._with_handlers_config(handlers=[{'id': 'handler0'}, {'id': 'handler1'}])
+        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
+        assert self.job_config.handler_assignment_methods == ['uwsgi-mule-message', 'db-preassign'], self.job_config.handler_assignment_methods
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['handler0', 'handler1', 'main.job-handlers.1']
+        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'handler1', 'main.job-handlers.1']
 
     def test_explicit_mem_self_handler_assign(self):
-        self.__with_handlers_config(assign_with='mem-self')
+        self._with_handlers_config(assign_with='mem-self')
         assert self.job_config.handler_assignment_methods == ['mem-self']
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers == {}
         assert not self.config.track_jobs_in_database
 
     def test_explicit_mem_self_handler_assign_with_handlers(self):
-        self.__with_handlers_config(assign_with='mem-self', handlers=[{'id': 'handler0'}])
+        self._with_handlers_config(assign_with='mem-self', handlers=[{'id': 'handler0'}])
         assert self.job_config.handler_assignment_methods == ['mem-self']
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers['_default_'] == ['handler0']
 
     def test_explicit_db_preassign_handler_assign_with_uwsgi(self):
-        self.__with_handlers_config(assign_with='db-preassign', handlers=[{'id': 'handler0'}])
-        self.__with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
+        self._with_handlers_config(assign_with='db-preassign', handlers=[{'id': 'handler0'}])
+        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
         assert self.job_config.handler_assignment_methods == ['db-preassign']
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['handler0', 'main.job-handlers.1']
+        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'main.job-handlers.1']
 
     def test_explicit_db_transaction_isolation_handler_assign(self):
-        self.__with_handlers_config(assign_with='db-transaction-isolation')
+        self._with_handlers_config(assign_with='db-transaction-isolation')
         assert self.job_config.handler_assignment_methods == ['db-transaction-isolation']
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers == {}
 
     def test_explicit_db_transaction_isolation_handler_assign_with_uwsgi(self):
-        self.__with_handlers_config(assign_with='db-transaction-isolation', handlers=[{'id': 'handler0'}])
-        self.__with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
+        self._with_handlers_config(assign_with='db-transaction-isolation', handlers=[{'id': 'handler0'}])
+        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
         assert self.job_config.handler_assignment_methods == ['db-transaction-isolation']
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['handler0', 'main.job-handlers.1']
+        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'main.job-handlers.1']
 
     def test_explicit_db_skip_locked_handler_assign(self):
-        self.__with_handlers_config(assign_with='db-skip-locked')
+        self._with_handlers_config(assign_with='db-skip-locked')
         assert self.job_config.handler_assignment_methods == ['db-skip-locked']
         assert self.job_config.default_handler_id is None
         assert self.job_config.handlers == {}
 
     def test_explicit_db_skip_locked_handler_assign_with_uwsgi(self):
-        self.__with_handlers_config(assign_with='db-skip-locked', handlers=[{'id': 'handler0'}])
-        self.__with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
+        self._with_handlers_config(assign_with='db-skip-locked', handlers=[{'id': 'handler0'}])
+        self._with_uwsgi_application_stack(mule='lib/galaxy/main.py', farm='job-handlers:1')
         assert self.job_config.handler_assignment_methods == ['db-skip-locked']
         assert self.job_config.default_handler_id is None
-        assert self.job_config.handlers['_default_'] == ['handler0', 'main.job-handlers.1']
+        assert sorted(self.job_config.handlers['_default_']) == ['handler0', 'main.job-handlers.1']
 
     def test_uwsgi_farms_as_handler_tags(self):
-        self.__with_uwsgi_application_stack(
+        self._with_uwsgi_application_stack(
             mule=['lib/galaxy/main.py'] * 2,
             farm=['job-handlers:1', 'job-handlers.foo:2']
         )
@@ -152,8 +224,8 @@ class JobConfXmlParserTestCase(unittest.TestCase):
         assert self.job_config.handlers['foo'] == ['main.job-handlers.foo.1']
 
     def test_uwsgi_overlapping_pools(self):
-        self.__with_handlers_config(base_pools=('workflow-schedulers', 'job-handlers'))
-        self.__with_uwsgi_application_stack(
+        self._with_handlers_config(base_pools=('workflow-schedulers', 'job-handlers'))
+        self._with_uwsgi_application_stack(
             mule=['lib/galaxy/main.py'] * 3,
             farm=['job-handlers:1', 'workflow-schedulers:2', 'job-handlers.foo:3']
         )
@@ -166,33 +238,6 @@ class JobConfXmlParserTestCase(unittest.TestCase):
         assert local_dest.id == "local"
         assert local_dest.runner == "local"
 
-    def test_load_destination_params(self):
-        self.__with_advanced_config()
-        pbs_dest = self.job_config.destinations["pbs_longjobs"][0]
-        assert pbs_dest.id == "pbs_longjobs"
-        assert pbs_dest.runner == "pbs"
-        dest_params = pbs_dest.params
-        assert dest_params["Resource_List"] == "walltime=72:00:00"
-
-    def test_destination_tags(self):
-        self.__with_advanced_config()
-        longjob_dests = self.job_config.destinations["longjobs"]
-        assert len(longjob_dests) == 2
-        assert longjob_dests[0].id == "pbs_longjobs"
-        assert longjob_dests[1].id == "remote_cluster"
-
-    def test_load_tool(self):
-        self.__with_advanced_config()
-        baz_tool = self.job_config.tools["baz"][0]
-        assert baz_tool.id == "baz"
-        assert baz_tool.handler == "special_handlers"
-        assert baz_tool.destination == "bigmem"
-
-    def test_load_tool_params(self):
-        self.__with_advanced_config()
-        foo_tool = self.job_config.tools["foo"][0]
-        assert foo_tool.params["source"] == "trackster"
-
     def test_default_limits(self):
         limits = self.job_config.limits
         assert limits.registered_user_concurrent_jobs is None
@@ -204,39 +249,8 @@ class JobConfXmlParserTestCase(unittest.TestCase):
         assert limits.destination_user_concurrent_jobs == {}
         assert limits.destination_total_concurrent_jobs == {}
 
-    def test_limit_overrides(self):
-        self.__with_advanced_config()
-        limits = self.job_config.limits
-        assert limits.registered_user_concurrent_jobs == 2
-        assert limits.anonymous_user_concurrent_jobs == 1
-        assert limits.destination_user_concurrent_jobs["local"] == 1
-        assert limits.destination_user_concurrent_jobs["mycluster"] == 2
-        assert limits.destination_user_concurrent_jobs["longjobs"] == 1
-        assert limits.walltime_delta == datetime.timedelta(0, 0, 0, 0, 0, 24)
-        assert limits.total_walltime["delta"] == datetime.timedelta(0, 0, 0, 0, 0, 24)
-        assert limits.total_walltime["window"] == 30
-
-    def test_env_parsing(self):
-        self.__with_advanced_config()
-        env_dest = self.job_config.destinations["java_cluster"][0]
-        assert len(env_dest.env) == 4, len(env_dest.env)
-        assert env_dest.env[0]["name"] == "_JAVA_OPTIONS"
-        assert env_dest.env[0]["value"] == '-Xmx6G'
-
-        assert env_dest.env[1]["name"] == "ANOTHER_OPTION"
-        assert env_dest.env[1]["raw"] is True
-
-        assert env_dest.env[2]["file"] == "/mnt/java_cluster/environment_setup.sh"
-
-        assert env_dest.env[3]["execute"] == "module load javastuff/2.10"
-
-    def test_macro_expansion(self):
-        self.__with_advanced_config()
-        for name in ["foo_small", "foo_medium", "foo_large", "foo_longrunning"]:
-            assert self.job_config.destinations[name]
-
     def test_conditional_runners(self):
-        self.__write_config_from(CONDITIONAL_RUNNER_JOB_CONF)
+        self._write_config_from(CONDITIONAL_RUNNER_JOB_CONF)
         runner_ids = [r["id"] for r in self.job_config.runner_plugins]
         assert "local2" in runner_ids
         assert "local3" not in runner_ids
@@ -245,7 +259,7 @@ class JobConfXmlParserTestCase(unittest.TestCase):
         assert "local3_dest" not in self.job_config.destinations
 
     def test_conditional_runners_from_environ(self):
-        self.__write_config_from(CONDITIONAL_RUNNER_JOB_CONF)
+        self._write_config_from(CONDITIONAL_RUNNER_JOB_CONF)
         os.environ["LOCAL2_ENABLED"] = "False"
         os.environ["LOCAL3_ENABLED"] = "True"
         try:
@@ -259,64 +273,134 @@ class JobConfXmlParserTestCase(unittest.TestCase):
             del os.environ["LOCAL2_ENABLED"]
             del os.environ["LOCAL3_ENABLED"]
 
-    # TODO: Add job metrics parsing test.
+    def test_macro_expansion(self):
+        self._with_advanced_config()
+        for name in ["foo_small", "foo_medium", "foo_large", "foo_longrunning"]:
+            assert self.job_config.destinations[name]
 
-    @property
-    def app(self):
-        if not self.__app:
-            self.__app = bunch.Bunch(
-                config=self.config,
-                job_metrics=MockJobMetrics(),
-                application_stack=self.application_stack
-            )
-        return self.__app
 
-    @property
-    def application_stack(self):
-        if not self.__application_stack:
-            self.__application_stack = ApplicationStack()
-        return self.__application_stack
+class AdvancedJobConfXmlParserTestCase(BaseJobConfXmlParserTestCase):
 
-    @property
-    def job_config(self):
-        if not self.__job_configuration:
-            base_handler_pools = self.__job_configuration_base_pools or JobConfiguration.DEFAULT_BASE_HANDLER_POOLS
-            mock_uwsgi = mock.Mock()
-            mock_uwsgi.mule_id = lambda: 1
-            with mock.patch('galaxy.web.stack.uwsgi', mock_uwsgi), \
-                    mock.patch('galaxy.web.stack.uwsgi.opt', self.__uwsgi_opt), \
-                    mock.patch('galaxy.jobs.JobConfiguration.DEFAULT_BASE_HANDLER_POOLS', base_handler_pools):
-                self.__job_configuration = JobConfiguration(self.app)
-        return self.__job_configuration
+    def test_load_destination_params(self):
+        self._with_advanced_config()
+        pbs_dest = self.job_config.destinations["pbs_longjobs"][0]
+        assert pbs_dest.id == "pbs_longjobs", pbs_dest
+        assert pbs_dest.runner == "pbs"
+        dest_params = pbs_dest.params
+        assert dest_params["Resource_List"] == "walltime=72:00:00"
 
-    def __with_uwsgi_application_stack(self, **uwsgi_opt):
-        self.__uwsgi_opt = uwsgi_opt
-        self.__application_stack = UWSGIApplicationStack()
+    def test_destination_tags(self):
+        self._with_advanced_config()
+        longjob_dests_ids = sorted([j.id for j in self.job_config.destinations["longjobs"]])
+        assert len(longjob_dests_ids) == 2
+        assert longjob_dests_ids[0] == "pbs_longjobs"
+        assert longjob_dests_ids[1] == "remote_cluster"
 
-    def __with_advanced_config(self):
-        self.__write_config_from(ADVANCED_JOB_CONF)
+    def test_load_tool(self):
+        self._with_advanced_config()
+        baz_tool = self.job_config.tools["baz"][0]
+        assert baz_tool.id == "baz"
+        assert baz_tool.handler == "special_handlers"
+        assert baz_tool.destination == "bigmem"
 
-    def __with_handlers_config(self, assign_with=None, default=None, handlers=None, base_pools=None):
-        handlers = handlers or []
-        template = {
-            'assign_with': ' assign_with="%s"' % assign_with if assign_with is not None else '',
-            'default': ' default="%s"' % default if default is not None else '',
-            'handlers': '\n'.join([
-                '<handler id="{id}"{tags}/>'.format(
-                    id=x['id'],
-                    tags=' tags="%s"' % x['tags'] if 'tags' in x else ''
-                ) for x in handlers]),
-        }
-        self.__job_configuration_base_pools = base_pools
-        self.__write_config_from(HANDLER_TEMPLATE_JOB_CONF, template=template)
+    def test_load_tool_params(self):
+        self._with_advanced_config()
+        foo_tool = self.job_config.tools["foo"][0]
+        assert foo_tool.params["source"] == "trackster"
 
-    def __write_config_from(self, path, template=None):
-        template = template or {}
-        self.__write_config(open(path, "r").read().format(**template))
+    def test_limit_overrides(self):
+        self._with_advanced_config()
+        limits = self.job_config.limits
+        assert limits.registered_user_concurrent_jobs == 2
+        assert limits.anonymous_user_concurrent_jobs == 1
+        assert limits.destination_user_concurrent_jobs["local"] == 1
+        assert limits.destination_user_concurrent_jobs["mycluster"] == 2
+        assert limits.destination_user_concurrent_jobs["longjobs"] == 1
+        assert limits.walltime_delta == datetime.timedelta(0, 0, 0, 0, 0, 24)
+        assert limits.total_walltime["delta"] == datetime.timedelta(0, 0, 0, 0, 0, 24)
+        assert limits.total_walltime["window"] == 30
 
-    def __write_config(self, contents):
-        with open(os.path.join(self.temp_directory, "job_conf.xml"), "w") as f:
-            f.write(contents)
+    def test_env_parsing(self):
+        self._with_advanced_config()
+        env_dest = self.job_config.destinations["java_cluster"][0]
+        assert len(env_dest.env) == 4, len(env_dest.env)
+        assert env_dest.env[0]["name"] == "_JAVA_OPTIONS"
+        assert env_dest.env[0]["value"] == '-Xmx6G'
+
+        assert env_dest.env[1]["name"] == "ANOTHER_OPTION"
+        assert env_dest.env[1]["raw"] is True
+
+        assert env_dest.env[2]["file"] == "/mnt/java_cluster/environment_setup.sh"
+
+        assert env_dest.env[3]["execute"] == "module load javastuff/2.10"
+
+    def test_runners_kwds(self):
+        self._with_advanced_config()
+        sge_runner = [r for r in self.job_config.runner_plugins if r["id"] == "sge"][0]
+        assert sge_runner["kwds"]["drmaa_library_path"] == "/sge/lib/libdrmaa.so"
+
+        drmaa_runner = [r for r in self.job_config.runner_plugins if r["id"] == "drmaa"][0]
+        assert drmaa_runner["kwds"]["invalidjobexception_state"] == "ok"
+
+        assert self.job_config.dynamic_params["rules_module"] == "galaxy.jobs.rules"
+
+    def test_container_tag_in_destination(self):
+        self._with_advanced_config()
+        container_dest = self.job_config.destinations["customized_container"][0]
+        assert "container" in container_dest.params
+        assert "container_override" in container_dest.params
+        container = container_dest.params["container"]
+        assert len(container) == 2
+        container0 = container[0]
+        assert container0["type"] == "docker"
+        assert container0["identifier"] == "busybox:ubuntu-14.04"
+
+        container_override = container_dest.params["container_override"]
+        assert len(container_override) == 2
+
+        container_override1 = container_override[1]
+        assert container_override1["type"] == "singularity"
+        assert container_override1["identifier"] == "/path/to/default/container"
+        assert not container_override1["resolve_dependencies"]
+
+    def test_tool_mapping_parameters(self):
+        self._with_advanced_config()
+        assert self.job_config.tools["foo"][-1].params["source"] == "trackster"
+        assert self.job_config.tools["longbar"][-1].destination == "dynamic"
+        assert self.job_config.tools["longbar"][-1].resources == "all"
+
+    def test_handler_runner_plugins(self):
+        self._with_advanced_config()
+        assert self.job_config.handler_runner_plugins["sge_handler"] == ["sge"]
+        assert "special_handler1" not in self.job_config.handler_runner_plugins
+
+    def test_resource_groups(self):
+        self._with_advanced_config()
+        assert self.job_config.default_resource_group == "default"
+        assert self.job_config.resource_groups["memoryonly"] == ["memory"]
+
+
+class AdvancedJobConfYamlParserTestCase(AdvancedJobConfXmlParserTestCase):
+    extension = "yml"
+
+
+def test_yaml_advanced_validation():
+    schema = os.path.join(os.path.dirname(__file__), "..", "..", "..", "lib", "galaxy", "webapps", "galaxy", "job_config_schema.yml")
+    integration_tests_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "test", "integration")
+    valid_files = [
+        ADVANCED_JOB_CONF_YAML,
+        os.path.join(integration_tests_dir, "delay_job_conf.yml"),
+        os.path.join(integration_tests_dir, "embedded_pulsar_metadata_job_conf.yml"),
+        os.path.join(integration_tests_dir, "io_injection_job_conf.yml"),
+        os.path.join(integration_tests_dir, "resubmission_job_conf.yml"),
+        os.path.join(integration_tests_dir, "resubmission_default_job_conf.yml"),
+    ]
+    for valid_file in valid_files:
+        c = Core(
+            source_file=valid_file,
+            schema_files=[schema],
+        )
+        c.validate()
 
 
 class MockJobMetrics(object):
diff --git a/test/unit/jobs/test_job_metrics.py b/test/unit/jobs/test_job_metrics.py
new file mode 100644
index 00000000000..1450cb1a68c
--- /dev/null
+++ b/test/unit/jobs/test_job_metrics.py
@@ -0,0 +1,7 @@
+from galaxy.job_metrics import JobMetrics
+
+
+def test_job_metrics_load():
+    # Just construct the manager to make sure all the plugin classes load fine
+    # and package is configured properly.
+    JobMetrics()
diff --git a/test/unit/jobs/test_job_wrapper.py b/test/unit/jobs/test_job_wrapper.py
index 5e370587116..50389f204ef 100644
--- a/test/unit/jobs/test_job_wrapper.py
+++ b/test/unit/jobs/test_job_wrapper.py
@@ -191,6 +191,9 @@ class MockObjectStore(object):
     def create(self, *args, **kwds):
         pass
 
+    def exists(self, *args, **kwargs):
+        return True
+
     def get_filename(self, *args, **kwds):
         if kwds.get("base_dir", "") == "job_work":
             return self.working_directory
diff --git a/test/unit/jobs/test_runner_local.py b/test/unit/jobs/test_runner_local.py
index acaafbc5557..7675b96a577 100644
--- a/test/unit/jobs/test_runner_local.py
+++ b/test/unit/jobs/test_runner_local.py
@@ -5,8 +5,8 @@ from unittest import TestCase
 
 import psutil
 
+from galaxy import job_metrics
 from galaxy import model
-from galaxy.jobs import metrics
 from galaxy.jobs.runners import local
 from galaxy.util import bunch
 from ..tools_support import (
@@ -20,7 +20,7 @@ class TestLocalJobRunner(TestCase, UsesApp, UsesTools):
     def setUp(self):
         self.setup_app()
         self._init_tool()
-        self.app.job_metrics = metrics.JobMetrics()
+        self.app.job_metrics = job_metrics.JobMetrics()
         self.job_wrapper = MockJobWrapper(self.app, self.test_directory, self.tool)
 
     def tearDown(self):
@@ -144,6 +144,7 @@ class MockJobWrapper(object):
         self.shell = "/bin/bash"
         self.cleanup_job = "never"
         self.tmp_dir_creation_statement = ""
+        self.use_metadata_binary = False
 
         # Cruft for setting metadata externally, axe at some point.
         self.external_output_metadata = bunch.Bunch(
diff --git a/test/unit/managers/base.py b/test/unit/managers/base.py
index d87544a546c..8377d48d6b1 100644
--- a/test/unit/managers/base.py
+++ b/test/unit/managers/base.py
@@ -100,14 +100,18 @@ class BaseTestCase(unittest.TestCase):
         self.assertTrue(True, 'is uuid: ' + item)
 
     def assertORMFilter(self, item, msg=None):
-        if not isinstance(item, sqlalchemy.sql.elements.BinaryExpression):
-            self.fail('Not an orm filter: ' + str(type(item)))
-        self.assertTrue(True, msg or ('is an orm filter: ' + str(item)))
+        if not isinstance(item.filter, (sqlalchemy.sql.elements.BinaryExpression, sqlalchemy.sql.elements.BooleanClauseList)):
+            self.fail('Not an orm filter: ' + str(type(item.filter)))
+        self.assertTrue(True, msg or ('is an orm filter: ' + str(item.filter)))
+
+    def assertORMFunctionFilter(self, item, msg=None):
+        assert item.filter_type == 'orm_function'
+        assert callable(item.filter)
 
     def assertFnFilter(self, item, msg=None):
-        if not item or not callable(item):
-            self.fail('Not a fn filter: ' + str(type(item)))
-        self.assertTrue(True, msg or ('is a fn filter: ' + str(item)))
+        if not item.filter or not callable(item.filter):
+            self.fail('Not a fn filter: ' + str(type(item.filter)))
+        self.assertTrue(True, msg or ('is a fn filter: ' + str(item.filter)))
 
     def assertIsJsonifyable(self, item):
         # TODO: use galaxy's override
diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py
index 25ab7ec0d22..7d4e80c0d8c 100644
--- a/test/unit/managers/test_HDAManager.py
+++ b/test/unit/managers/test_HDAManager.py
@@ -654,13 +654,15 @@ class HDAFilterParserTestCase(HDATestCase):
         self.assertORMFilter(self.filter_parser.parse_filter('state', 'eq', 'ok'))
         self.assertORMFilter(self.filter_parser.parse_filter('state', 'in', ['queued', 'running']))
         self.assertORMFilter(self.filter_parser.parse_filter('visible', 'eq', True))
+        # taggable
+        self.assertORMFunctionFilter(self.filter_parser.parse_filter('tag', 'eq', 'wot'))
+        self.assertORMFunctionFilter(self.filter_parser.parse_filter('tag', 'has', 'wot'))
+        # genomebuild
         self.assertFnFilter(self.filter_parser.parse_filter('genome_build', 'eq', 'wot'))
         self.assertFnFilter(self.filter_parser.parse_filter('genome_build', 'contains', 'wot'))
+        # data_type
         self.assertFnFilter(self.filter_parser.parse_filter('data_type', 'eq', 'wot'))
         self.assertFnFilter(self.filter_parser.parse_filter('data_type', 'isinstance', 'wot'))
-        # taggable
-        self.assertFnFilter(self.filter_parser.parse_filter('tag', 'eq', 'wot'))
-        self.assertFnFilter(self.filter_parser.parse_filter('tag', 'has', 'wot'))
         # annotatable
         self.assertFnFilter(self.filter_parser.parse_filter('annotation', 'has', 'wot'))
 
diff --git a/test/unit/managers/test_HistoryContentsManager.py b/test/unit/managers/test_HistoryContentsManager.py
index 255c4d17e88..17ee7ec3c19 100644
--- a/test/unit/managers/test_HistoryContentsManager.py
+++ b/test/unit/managers/test_HistoryContentsManager.py
@@ -8,7 +8,7 @@ import unittest
 from sqlalchemy import column, desc, false, true
 from sqlalchemy.sql import text
 
-from galaxy.managers import collections, hdas, history_contents
+from galaxy.managers import base, collections, hdas, history_contents
 from galaxy.managers.histories import HistoryManager
 from .base import BaseTestCase
 from .base import CreatesCollectionsMixin
@@ -17,6 +17,7 @@ default_password = '123456'
 user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
 user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
 user4_data = dict(email='user4@user4.user4', username='user4', password=default_password)
+parsed_filter = base.ModelFilterParser.parsed_filter
 
 
 # =============================================================================
@@ -135,15 +136,15 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
         self.app.model.context.flush()
 
         # TODO: cross db compat?
-        filters = [text('deleted = 1')]
+        filters = [parsed_filter(filter_type="orm", filter=text('deleted = 1'))]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), deleted)
 
         # even stranger that sqlalx can use the first model in the union (HDA) for columns across the union
         HDA = self.hda_manager.model_class
         self.assertEqual(self.contents_manager.contents(history,
-            filters=[HDA.deleted == true()]), deleted)
+            filters=[parsed_filter("orm", HDA.deleted == true())]), deleted)
         filter_limited_contents = self.contents_manager.contents(history,
-            filters=[HDA.deleted == true()], limit=2, offset=1)
+            filters=[parsed_filter("orm", HDA.deleted == true())], limit=2, offset=1)
         self.assertEqual(filter_limited_contents, deleted[1:])
 
         self.log("should allow filter on visible")
@@ -153,43 +154,43 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
         invisible = [contents[2], contents[5], contents[6]]
         self.app.model.context.flush()
 
-        filters = [text('visible = 0')]
+        filters = [parsed_filter("orm", text('visible = 0'))]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), invisible)
         self.assertEqual(self.contents_manager.contents(history,
-            filters=[HDA.visible == false()]), invisible)
+            filters=[parsed_filter("orm", HDA.visible == false())]), invisible)
         filter_limited_contents = self.contents_manager.contents(history,
-            filters=[HDA.visible == false()], limit=2, offset=1)
+            filters=[parsed_filter("orm", HDA.visible == false())], limit=2, offset=1)
         self.assertEqual(filter_limited_contents, invisible[1:])
 
         self.log("should allow filtering more than one attribute")
         deleted_and_invisible = [contents[6]]
 
-        filters = [text('deleted = 1'), text('visible = 0')]
+        filters = [parsed_filter("orm", text('deleted = 1')), parsed_filter("orm", text('visible = 0'))]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), deleted_and_invisible)
         self.assertEqual(self.contents_manager.contents(history,
-            filters=[HDA.deleted == true(), HDA.visible == false()]), deleted_and_invisible)
+            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())]), deleted_and_invisible)
         offset_too_far = self.contents_manager.contents(history,
-            filters=[HDA.deleted == true(), HDA.visible == false()], limit=2, offset=1)
+            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())], limit=2, offset=1)
         self.assertEqual(offset_too_far, [])
 
         self.log("should allow filtering more than one attribute")
         deleted_and_invisible = [contents[6]]
         # note the two syntaxes both work
         self.assertEqual(self.contents_manager.contents(history,
-            filters=[text('deleted = 1'), text('visible = 0')]), deleted_and_invisible)
+            filters=[parsed_filter("orm", text('deleted = 1')), parsed_filter("orm", text('visible = 0'))]), deleted_and_invisible)
         self.assertEqual(self.contents_manager.contents(history,
-            filters=[HDA.deleted == true(), HDA.visible == false()]), deleted_and_invisible)
+            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())]), deleted_and_invisible)
         offset_too_far = self.contents_manager.contents(history,
-            filters=[HDA.deleted == true(), HDA.visible == false()], limit=2, offset=1)
+            filters=[parsed_filter("orm", HDA.deleted == true()), parsed_filter("orm", HDA.visible == false())], limit=2, offset=1)
         self.assertEqual(offset_too_far, [])
 
         self.log("should allow filtering using like")
         # find 'hda-4'
         self.assertEqual([contents[4]],
-            self.contents_manager.contents(history, filters=[HDA.name.like('%-4')]))
+            self.contents_manager.contents(history, filters=[parsed_filter("orm", HDA.name.like('%-4'))]))
         # the collections added above have the default name 'test collection'
         self.assertEqual(self.contents_manager.subcontainers(history),
-            self.contents_manager.contents(history, filters=[HDA.name.like('%collect%')]))
+            self.contents_manager.contents(history, filters=[parsed_filter("orm", HDA.name.like('%collect%'))]))
 
     def test_order_by(self):
         user2 = self.user_manager.create(**user2_data)
@@ -245,7 +246,7 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
                 update_time = item.collection.update_time
             return update_time
 
-        results = self.contents_manager.contents(history, filters=[column('update_time') >= update_time])
+        results = self.contents_manager.contents(history, filters=[parsed_filter("orm", column('update_time') >= update_time)])
         self.assertEqual(results, [contents[3]])
 
     def test_filtered_counting(self):
@@ -269,11 +270,11 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
         self.app.model.context.flush()
 
         HDA = self.hda_manager.model_class
-        self.assertEqual(self.contents_manager.contents_count(history, filters=[HDA.deleted == true()]), 3)
-        filters = [text('visible = 0')]
+        self.assertEqual(self.contents_manager.contents_count(history, filters=[parsed_filter("orm", HDA.deleted == true())]), 3)
+        filters = [parsed_filter("orm", text('visible = 0'))]
         self.assertEqual(self.contents_manager.contents_count(history, filters=filters), 3)
 
-        filters = [text('deleted = 1'), text('visible = 0')]
+        filters = [parsed_filter("orm", text('deleted = 1')), parsed_filter("orm", text('visible = 0'))]
         self.assertEqual(self.contents_manager.contents_count(history, filters=filters), 1)
 
     def test_type_id(self):
@@ -286,13 +287,13 @@ class HistoryAsContainerTestCase(HistoryAsContainerBaseTestCase):
         contents.append(self.add_list_collection_to_history(history, contents[4:6]))
 
         self.log("should be able to use eq and in with hybrid type_id")
-        filters = [column('type_id') == u'dataset-2']
+        filters = [parsed_filter("orm", column('type_id') == u'dataset-2')]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), [contents[1]])
-        filters = [column('type_id').in_([u'dataset-1', u'dataset-3'])]
+        filters = [parsed_filter("orm", column('type_id').in_([u'dataset-1', u'dataset-3']))]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), [contents[0], contents[2]])
-        filters = [column('type_id') == u'dataset_collection-1']
+        filters = [parsed_filter("orm", column('type_id') == u'dataset_collection-1')]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), [contents[3]])
-        filters = [column('type_id').in_([u'dataset-2', u'dataset_collection-2'])]
+        filters = [parsed_filter("orm", column('type_id').in_([u'dataset-2', u'dataset_collection-2']))]
         self.assertEqual(self.contents_manager.contents(history, filters=filters), [contents[1], contents[6]])
 
 
diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
index 21e363d6b76..eb5f05658c3 100644
--- a/test/unit/managers/test_HistoryManager.py
+++ b/test/unit/managers/test_HistoryManager.py
@@ -29,6 +29,7 @@ default_password = '123456'
 user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
 user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
 user4_data = dict(email='user4@user4.user4', username='user4', password=default_password)
+parsed_filter = base.ModelFilterParser.parsed_filter
 
 
 class HistoryManagerTestCase(BaseTestCase):
@@ -697,7 +698,7 @@ class HistoryFiltersTestCase(BaseTestCase):
         self.assertEqual(len(filters), 3)
 
         self.log('values should be parsed')
-        self.assertIsInstance(filters[1].right, sqlalchemy.sql.elements.True_)
+        self.assertIsInstance(filters[1].filter.right, sqlalchemy.sql.elements.True_)
 
     def test_parse_filters_invalid_filters(self):
         self.log('should error on non-column attr')
@@ -763,7 +764,7 @@ class HistoryFiltersTestCase(BaseTestCase):
         history3 = self.history_manager.create(name='history3', user=user2)
 
         filters = self.filter_parser.parse_filters([('annotation', 'has', 'no play'), ])
-        anno_filter = filters[0]
+        anno_filter = filters[0].filter
 
         history3.add_item_annotation(self.trans.sa_session, user2, history3, "All work and no play")
         self.trans.sa_session.flush()
@@ -797,7 +798,7 @@ class HistoryFiltersTestCase(BaseTestCase):
         self.log('should have parsed out a single filter')
         self.assertEqual(len(filters), 1)
 
-        filter_ = filters[0]
+        filter_ = filters[0].filter
         fake = galaxy_mock.OpenObject()
         fake.name = '123'
         self.log('123 should return true through the filter')
diff --git a/test/unit/queue_worker/test_database_heartbeat.py b/test/unit/queue_worker/test_database_heartbeat.py
index 1f86ae4f849..da6f4f4ea9a 100644
--- a/test/unit/queue_worker/test_database_heartbeat.py
+++ b/test/unit/queue_worker/test_database_heartbeat.py
@@ -3,8 +3,8 @@ import time
 
 import pytest
 
-from galaxy.web.stack import application_stack_instance
-from galaxy.web.stack.database_heartbeat import DatabaseHeartbeat
+from galaxy.model.database_heartbeat import DatabaseHeartbeat
+from galaxy.web_stack import application_stack_instance
 
 
 @pytest.fixture
diff --git a/test/unit/queue_worker/test_queue_worker.py b/test/unit/queue_worker/test_queue_worker.py
index c943eb95987..651c3b9b97d 100644
--- a/test/unit/queue_worker/test_queue_worker.py
+++ b/test/unit/queue_worker/test_queue_worker.py
@@ -3,14 +3,14 @@ import time
 
 import pytest
 
+from galaxy.model.database_heartbeat import DatabaseHeartbeat
 from galaxy.queue_worker import (
     GalaxyQueueWorker,
     send_control_task,
     send_local_control_task,
 )
 from galaxy.queues import connection_from_config
-from galaxy.web.stack import application_stack_instance
-from galaxy.web.stack.database_heartbeat import DatabaseHeartbeat
+from galaxy.web_stack import application_stack_instance
 
 
 def bar(app, **kwargs):
diff --git a/test/unit/test_fix_type_error.py b/test/unit/test_fix_type_error.py
new file mode 100644
index 00000000000..a107daf9ecc
--- /dev/null
+++ b/test/unit/test_fix_type_error.py
@@ -0,0 +1,23 @@
+import six
+
+from galaxy.util.pastescript.loadwsgi import fix_type_error
+
+if six.PY2:
+    argtype = ' keyword'
+else:
+    argtype = ''
+EXP_STRING = "a_func() got multiple values for%s argument 'kwarg'; got (1, 2, kwarg=...), wanted (argone, kwarg=True)" % argtype
+
+
+def a_func(argone, kwarg=True):
+    pass
+
+
+def test_fix_type_error():
+    args = [1, 2]
+    kwargs = {'kwarg': False}
+    try:
+        a_func(*args, **kwargs)
+    except TypeError:
+        exc_info = fix_type_error(None, a_func, args, kwargs)
+    assert exc_info[1].args[0] == EXP_STRING
diff --git a/test/unit/test_model_store.py b/test/unit/test_model_store.py
index 8614658bfe7..4f26f5b2574 100644
--- a/test/unit/test_model_store.py
+++ b/test/unit/test_model_store.py
@@ -283,6 +283,7 @@ def test_import_export_composite_datasets():
     h = model.History(name="Test History", user=u)
 
     d1 = _create_datasets(sa_session, h, 1, extension="html")[0]
+    d1.dataset.create_extra_files_path()
     sa_session.add_all((h, d1))
     sa_session.flush()
 
diff --git a/test/unit/test_verify.py b/test/unit/test_verify.py
new file mode 100644
index 00000000000..8de580cec5b
--- /dev/null
+++ b/test/unit/test_verify.py
@@ -0,0 +1,76 @@
+import collections
+import os
+import tempfile
+
+import pytest
+
+from galaxy.tools.verify import (
+    files_contains,
+    files_diff,
+    files_re_match,
+    files_re_match_multiline,
+)
+
+
+F1 = b"A\nB\nC"
+F2 = b"A\nB\nD\nE" * 61
+F3 = b"A\nB\n\xfc"
+F4 = b"A\r\nB\nC"
+MULTILINE_MATCH = b".*"
+TestFile = collections.namedtuple('TestFile', 'value path')
+
+
+def generate_tests(multiline=False):
+    files = []
+    for b, ext in [(F1, '.txt'), (F2, '.txt'), (F3, '.pdf'), (F4, '.txt'), (MULTILINE_MATCH, '.txt')]:
+        fd, path = tempfile.mkstemp(suffix=ext)
+        with os.fdopen(fd, 'wb') as out:
+            out.write(b)
+        files.append(TestFile(b, path))
+    f1, f2, f3, f4, multiline_match = files
+    if multiline:
+        tests = [(multiline_match, f1, {'lines_diff': 0, 'sort': True}, None)]
+    else:
+        tests = [(f1, f1, {'lines_diff': 0, 'sort': True}, None)]
+    tests.extend([
+        (f1, f2, {'lines_diff': 0, 'sort': True}, AssertionError),
+        (f1, f3, None, AssertionError),
+        (f1, f4, None, None),
+    ])
+    return tests
+
+
+@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests())
+def test_files_contains(file1, file2, attributes, expect):
+    if expect is not None:
+        with pytest.raises(expect):
+            files_contains(file1.path, file2.path, attributes)
+    else:
+        files_contains(file2.path, file2.path, attributes)
+
+
+@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests())
+def test_files_diff(file1, file2, attributes, expect):
+    if expect is not None:
+        with pytest.raises(expect):
+            files_diff(file1.path, file2.path, attributes)
+    else:
+        files_diff(file1.path, file2.path, attributes)
+
+
+@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests())
+def test_files_re_match(file1, file2, attributes, expect):
+    if expect is not None:
+        with pytest.raises(expect):
+            files_re_match(file1.path, file2.path, attributes)
+    else:
+        files_re_match(file1.path, file2.path, attributes)
+
+
+@pytest.mark.parametrize('file1,file2,attributes,expect', generate_tests(multiline=True))
+def test_files_re_match_multiline(file1, file2, attributes, expect):
+    if expect is not None:
+        with pytest.raises(expect):
+            files_re_match_multiline(file1.path, file2.path, attributes)
+    else:
+        files_re_match_multiline(file1.path, file2.path, attributes)
diff --git a/test/unit/tools/test_actions.py b/test/unit/tools/test_actions.py
index 3c23507ab6b..b870e516d2e 100644
--- a/test/unit/tools/test_actions.py
+++ b/test/unit/tools/test_actions.py
@@ -4,12 +4,12 @@ from xml.etree.ElementTree import XML
 
 from galaxy import model
 from galaxy.exceptions import UserActivationRequiredException
+from galaxy.tool_util.parser.output_objects import ToolOutput
 from galaxy.tools.actions import (
     DefaultToolAction,
     determine_output_format,
     on_text_for_names
 )
-from galaxy.tools.parser.output_objects import ToolOutput
 from .. import tools_support
 
 
@@ -274,6 +274,9 @@ class MockObjectStore(object):
         self.first_create = True
         self.object_store_id = "mycoolid"
 
+    def exists(self, *args, **kwargs):
+        return True
+
     def create(self, dataset):
         self.created_datasets.append(dataset)
         if self.first_create:
diff --git a/test/unit/tools/test_citations.py b/test/unit/tools/test_citations.py
index 0a8a8cce197..8e5371b4cd9 100644
--- a/test/unit/tools/test_citations.py
+++ b/test/unit/tools/test_citations.py
@@ -1,7 +1,3 @@
-import tempfile
-from contextlib import contextmanager
-from shutil import rmtree
-
 from galaxy.managers.citations import (
     BibtexCitation,
     CitationCollection,
@@ -23,8 +19,7 @@ EXAMPLE_BIBTEX_CITATION = """<citation type="bibtex">@article{goecks2010galaxy,
 def test_parse_citation():
     xml_text = EXAMPLE_BIBTEX_CITATION
     citation_elem = parse_xml_string(xml_text)
-    with temp_directory() as test_directory:
-        citation = parse_citation(citation_elem, test_directory, None)
+    citation = parse_citation(citation_elem, None)
     bibtex = citation.to_bibtex()
     assert "title={Galaxy" in bibtex
 
@@ -41,16 +36,7 @@ def test_citation_collection():
     assert len(citation_collection) == 2
 
 
-@contextmanager
-def temp_directory():
-    base_path = tempfile.mkdtemp()
-    try:
-        yield base_path
-    finally:
-        rmtree(base_path)
-
-
 class QuickBibtexCitation(BibtexCitation):
 
     def __init__(self, raw_bibtex):
-        self._set_raw_bibtex(raw_bibtex)
+        self.raw_bibtex = raw_bibtex
diff --git a/test/unit/tools/test_collect_primary_datasets.py b/test/unit/tools/test_collect_primary_datasets.py
index 0f1814680b3..d33d5e4bb84 100644
--- a/test/unit/tools/test_collect_primary_datasets.py
+++ b/test/unit/tools/test_collect_primary_datasets.py
@@ -6,8 +6,8 @@ from galaxy import (
     model,
     util
 )
-from galaxy.tools.parser import output_collection_def
-from galaxy.tools.provided_metadata import LegacyToolProvidedMetadata, NullToolProvidedMetadata
+from galaxy.tool_util.parser import output_collection_def
+from galaxy.tool_util.provided_metadata import LegacyToolProvidedMetadata, NullToolProvidedMetadata
 from .. import tools_support
 
 DEFAULT_TOOL_OUTPUT = "out1"
@@ -408,6 +408,9 @@ class MockObjectStore(object):
         path = self.created_datasets[dataset]
         return os.stat(path).st_size
 
+    def exists(self, *args, **kwargs):
+        return True
+
     def get_filename(self, dataset):
         return self.created_datasets[dataset]
 
diff --git a/test/unit/tools/test_conda_resolution.py b/test/unit/tools/test_conda_resolution.py
index 7db7d9093a4..f86bd527c95 100644
--- a/test/unit/tools/test_conda_resolution.py
+++ b/test/unit/tools/test_conda_resolution.py
@@ -3,12 +3,12 @@ import shutil
 import unittest
 from tempfile import mkdtemp
 
-from galaxy.tools.deps import (
+from galaxy.tool_util.deps import (
     conda_util,
     DependencyManager
 )
-from galaxy.tools.deps.requirements import ToolRequirement
-from galaxy.tools.deps.resolvers.conda import CondaDependencyResolver
+from galaxy.tool_util.deps.requirements import ToolRequirement
+from galaxy.tool_util.deps.resolvers.conda import CondaDependencyResolver
 
 
 def skip_unless_environ(var):
diff --git a/test/unit/tools/test_cwl_util.py b/test/unit/tools/test_cwl_util.py
new file mode 100644
index 00000000000..24c2ac95cf7
--- /dev/null
+++ b/test/unit/tools/test_cwl_util.py
@@ -0,0 +1,25 @@
+import tempfile
+
+from galaxy.tool_util.cwl.util import output_properties
+
+
+def test_output_properties_in_memory():
+    props = output_properties(content=b"hello world", basename="hello.txt")
+    assert props["basename"] == "hello.txt"
+    assert props["nameroot"] == "hello"
+    assert props["nameext"] == ".txt"
+    assert props["size"] == 11
+    assert props["checksum"] == "sha1$2aae6c35c94fcfb415dbe95f408b9ce91ee846ed"
+
+
+def test_output_properties_path():
+    f = tempfile.NamedTemporaryFile(mode="w")
+    f.write("hello world")
+    f.flush()
+
+    props = output_properties(path=f.name, basename="hello.txt")
+    assert props["basename"] == "hello.txt"
+    assert props["nameroot"] == "hello"
+    assert props["nameext"] == ".txt"
+    assert props["size"] == 11
+    assert props["checksum"] == "sha1$2aae6c35c94fcfb415dbe95f408b9ce91ee846ed"
diff --git a/test/unit/tools/test_evaluation.py b/test/unit/tools/test_evaluation.py
index e79eb235ef8..37243fbfdbf 100644
--- a/test/unit/tools/test_evaluation.py
+++ b/test/unit/tools/test_evaluation.py
@@ -2,8 +2,8 @@ import os
 from unittest import TestCase
 from xml.etree.ElementTree import XML
 
+from galaxy.job_execution.datasets import DatasetPath
 from galaxy.jobs import SimpleComputeEnvironment
-from galaxy.jobs.datasets import DatasetPath
 from galaxy.model import (
     Dataset,
     History,
@@ -12,6 +12,7 @@ from galaxy.model import (
     JobParameter,
     JobToInputDatasetAssociation
 )
+from galaxy.tool_util.parser.output_objects import ToolOutput
 from galaxy.tools.evaluation import ToolEvaluator
 # For MockTool
 from galaxy.tools.parameters import params_from_strings
@@ -25,7 +26,6 @@ from galaxy.tools.parameters.grouping import (
     ConditionalWhen,
     Repeat
 )
-from galaxy.tools.parser.output_objects import ToolOutput
 from galaxy.util.bunch import Bunch
 # Test fixtures for Galaxy infrastructure.
 from ..tools_support import UsesApp
@@ -266,6 +266,7 @@ class MockTool(object):
 
     def __init__(self, app):
         self.profile = 16.01
+        self.python_template_version = '2.7'
         self.app = app
         self.hooks_called = []
         self.environment_variables = []
diff --git a/test/unit/tools/test_fill_template.py b/test/unit/tools/test_fill_template.py
new file mode 100644
index 00000000000..48d280e27dc
--- /dev/null
+++ b/test/unit/tools/test_fill_template.py
@@ -0,0 +1,77 @@
+import sys
+
+import pytest
+from Cheetah.NameMapper import NotFound
+
+from galaxy.util.template import fill_template
+
+SIMPLE_TEMPLATE = """#for item in $a_list:
+    echo $item
+    #end for
+"""
+FILLED_SIMPLE_TEMPLATE = """    echo 1
+    echo 2
+"""
+LIST_COMPREHENSION_TEMPLATE = """#for $i in [1]:
+#set $v = "".join([str(_) for _ in [1] if _ == $i])
+echo $v
+#end for
+"""
+DICT_COMPREHENSION_TEMPLATE = """#for $i in [1]:
+#set $v = {_:_ for _ in [1] if _ == $i}
+echo $v[$i]
+#end for
+"""
+SET_COMPR_TEMPLATE = """#for $i in [1]:
+#set $v = {_ for _ in [1] if _ == $i}
+echo $v.pop()
+#end for
+"""
+GEN_EXPR_TEMPLATE = """#for $i in [1]:
+#set $v = list((_ for _ in [1] if _ == $i))
+echo $v[0]
+#end for
+"""
+TWO_TO_THREE_TEMPLATE = """#set $a = [x for x in {'a': '1'}.iterkeys()][0]
+#set $b = [x for x in {'a': '1'}.iteritems()][0][0]
+#set $c = [x for x in {'a': '1'}.itervalues()][0]
+$a $b $c"""
+
+
+def test_fill_simple_template():
+    template_str = str(fill_template(SIMPLE_TEMPLATE, {'a_list': [1, 2]}))
+    assert template_str == FILLED_SIMPLE_TEMPLATE
+
+
+def test_fill_list_comprehension_template():
+    if sys.version_info.major > 2:
+        with pytest.raises(NotFound):
+            fill_template(LIST_COMPREHENSION_TEMPLATE, retry=0)
+    else:
+        template_str = fill_template(LIST_COMPREHENSION_TEMPLATE, retry=0)
+        assert template_str == 'echo 1\n'
+
+
+def test_fill_list_comprehension_template_2():
+    template_str = fill_template(LIST_COMPREHENSION_TEMPLATE, python_template_version='2', retry=1)
+    assert template_str == 'echo 1\n'
+
+
+def test_fill_dict_comprehension():
+    with pytest.raises(NotFound):
+        fill_template(DICT_COMPREHENSION_TEMPLATE, retry=1)
+
+
+def test_set_comprehension():
+    with pytest.raises(NotFound):
+        fill_template(SET_COMPR_TEMPLATE, retry=1)
+
+
+def test_gen_expr():
+    with pytest.raises(NotFound):
+        fill_template(GEN_EXPR_TEMPLATE, retry=1)
+
+
+def test_fix_template_two_to_three():
+    template_str = fill_template(TWO_TO_THREE_TEMPLATE, python_template_version='2', retry=1)
+    assert template_str == 'a a 1'
diff --git a/test/unit/tools/test_metadata.py b/test/unit/tools/test_metadata.py
index 2c7e2e99fd0..7b23673da75 100644
--- a/test/unit/tools/test_metadata.py
+++ b/test/unit/tools/test_metadata.py
@@ -3,9 +3,10 @@ import subprocess
 import unittest
 
 from galaxy import model
-from galaxy.jobs.datasets import DatasetPath
+from galaxy.job_execution.datasets import DatasetPath
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.objectstore import ObjectStorePopulator
+from galaxy.util import safe_makedirs
 from .. import tools_support
 
 
@@ -143,14 +144,15 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesApp, tools_support.U
             f.write(contents)
 
     def metadata_command(self, output_datasets):
-        metadata_compute_strategy = get_metadata_compute_strategy(self.app, self.job.id)
+        metadata_compute_strategy = get_metadata_compute_strategy(self.app.config, self.job.id)
         self.metadata_compute_strategy = metadata_compute_strategy
 
         exec_dir = None
         dataset_files_path = self.app.model.Dataset.file_path
         config_root = self.app.config.root
         config_file = None
-        datatypes_config = os.path.join(self.job_working_directory, 'registry.xml')
+        datatypes_config = os.path.join(self.job_working_directory, 'metadata', 'registry.xml')
+        safe_makedirs(os.path.join(self.job_working_directory, 'metadata'))
         self.app.datatypes_registry.to_xml_file(path=datatypes_config)
         job_metadata = os.path.join(self.tool_working_directory, self.tool.provided_metadata_file)
         output_fnames = [DatasetPath(o.dataset.id, o.dataset.file_name, None) for o in output_datasets.values()]
diff --git a/test/unit/jobs/test_job_output_checker.py b/test/unit/tools/test_output_checker.py
similarity index 93%
rename from test/unit/jobs/test_job_output_checker.py
rename to test/unit/tools/test_output_checker.py
index eb6a76cdcea..b2158f5a327 100644
--- a/test/unit/jobs/test_job_output_checker.py
+++ b/test/unit/tools/test_output_checker.py
@@ -1,8 +1,8 @@
 from unittest import TestCase
 
-from galaxy.jobs.output_checker import check_output, DETECTED_JOB_STATE
-from galaxy.tools.parser.error_level import StdioErrorLevel
-from galaxy.tools.parser.interface import ToolStdioRegex
+from galaxy.tool_util.output_checker import check_output, DETECTED_JOB_STATE
+from galaxy.tool_util.parser.error_level import StdioErrorLevel
+from galaxy.tool_util.parser.interface import ToolStdioRegex
 from galaxy.util.bunch import Bunch
 
 
diff --git a/test/unit/tools/test_parsing.py b/test/unit/tools/test_parsing.py
index 772a4b98418..168bd09f0fd 100644
--- a/test/unit/tools/test_parsing.py
+++ b/test/unit/tools/test_parsing.py
@@ -5,7 +5,8 @@ import tempfile
 import unittest
 from math import isinf
 
-from galaxy.tools.parser.factory import get_tool_source
+from galaxy.tool_util.parser.factory import get_tool_source
+from galaxy.util import galaxy_directory
 
 
 TOOL_XML_1 = """
@@ -41,6 +42,42 @@ TOOL_XML_1 = """
 </tool>
 """
 
+TOOL_WITH_TOKEN = r"""
+<tool id="tool_with_token" name="Token" version="1">
+    <macros>
+        <token name="@ESCAPE_IDENTIFIER@">
+<![CDATA[
+#set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
+        ]]></token>
+        <token name="@NESTED_TOKEN@">
+<![CDATA[
+    before
+    @ESCAPE_IDENTIFIER@
+    after
+        ]]></token>
+    </macros>
+    <command>
+@NESTED_TOKEN@
+    </command>
+</tool>
+"""
+
+TOOL_WITH_RECURSIVE_TOKEN = r"""
+<tool id="tool_with_recursive_token" name="Token" version="1">
+    <macros>
+        <token name="@NESTED_TOKEN@">
+<![CDATA[
+    before
+    @NESTED_TOKEN@
+    after
+        ]]></token>
+    </macros>
+    <command>
+@NESTED_TOKEN@
+    </command>
+</tool>
+"""
+
 TOOL_YAML_1 = """
 name: "Bowtie Mapper"
 class: GalaxyTool
@@ -302,6 +339,16 @@ class XmlLoaderTestCase(BaseLoaderTestCase):
     def test_refresh_option(self):
         assert self._tool_source.parse_refresh() is False
 
+    def test_nested_token(self):
+        tool_source = self._get_tool_source(source_contents=TOOL_WITH_TOKEN)
+        command = tool_source.parse_command()
+        assert command
+        assert '@' not in command
+
+    def test_recursive_token(self):
+        with self.assertRaises(Exception):
+            self._get_tool_source(source_contents=TOOL_WITH_RECURSIVE_TOKEN)
+
 
 class YamlLoaderTestCase(BaseLoaderTestCase):
     source_file_name = "bwa.yml"
@@ -475,7 +522,7 @@ class DataSourceLoaderTestCase(BaseLoaderTestCase):
 
 
 class ApplyRulesToolLoaderTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "lib/galaxy/tools/apply_rules.xml")
+    source_file_name = os.path.join(galaxy_directory(), "lib/galaxy/tools/apply_rules.xml")
     source_contents = None
 
     def test_tool_type(self):
@@ -491,7 +538,7 @@ class ApplyRulesToolLoaderTestCase(BaseLoaderTestCase):
 
 
 class BuildListToolLoaderTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "lib/galaxy/tools/build_list.xml")
+    source_file_name = os.path.join(galaxy_directory(), "lib/galaxy/tools/build_list.xml")
     source_contents = None
 
     def test_tool_type(self):
@@ -501,7 +548,7 @@ class BuildListToolLoaderTestCase(BaseLoaderTestCase):
 
 
 class SpecialToolLoaderTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "lib/galaxy/tools/imp_exp/exp_history_to_archive.xml")
+    source_file_name = os.path.join(galaxy_directory(), "lib/galaxy/tools/imp_exp/exp_history_to_archive.xml")
     source_contents = None
 
     def test_tool_type(self):
@@ -526,7 +573,7 @@ class SpecialToolLoaderTestCase(BaseLoaderTestCase):
 
 
 class CollectionTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "test/functional/tools/collection_two_paired.xml")
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_two_paired.xml")
     source_contents = None
 
     def test_tests(self):
@@ -540,7 +587,7 @@ class CollectionTestCase(BaseLoaderTestCase):
 
 
 class CollectionOutputXmlTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "test/functional/tools/collection_creates_pair.xml")
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_creates_pair.xml")
     source_contents = None
 
     def test_tests(self):
@@ -549,7 +596,7 @@ class CollectionOutputXmlTestCase(BaseLoaderTestCase):
 
 
 class CollectionOutputYamlTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "test/functional/tools/collection_creates_pair_y.yml")
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_creates_pair_y.yml")
     source_contents = None
 
     def test_tests(self):
@@ -558,7 +605,7 @@ class CollectionOutputYamlTestCase(BaseLoaderTestCase):
 
 
 class ExpectationsTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "test/functional/tools/detect_errors.xml")
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/detect_errors.xml")
     source_contents = None
 
     def test_tests(self):
diff --git a/test/unit/tools/test_select_parameters.py b/test/unit/tools/test_select_parameters.py
index 7e778c4602f..28cfe50e33d 100644
--- a/test/unit/tools/test_select_parameters.py
+++ b/test/unit/tools/test_select_parameters.py
@@ -11,7 +11,7 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
         try:
             self.param.from_json("42", self.trans, {"input_bam": model.HistoryDatasetAssociation()})
         except ValueError as err:
-            assert str(err) == "An invalid option was selected for my_name, '42', please verify."
+            assert str(err) == "parameter 'my_name': an invalid option ('42') was selected (valid options: ?)"
             return
         assert False
 
@@ -20,7 +20,7 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
         try:
             self.param.from_json("42", self.trans)
         except ValueError as err:
-            assert str(err) == "Parameter my_name requires a value, but has no legal values defined."
+            assert str(err) == "parameter 'my_name': requires a value, but no legal values defined"
             return
         assert False
 
@@ -34,7 +34,7 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
         try:
             self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": None})
         except ValueError as err:
-            assert str(err) == "Parameter my_name requires a value, but has no legal values defined."
+            assert str(err) == "parameter 'my_name': requires a value, but no legal values defined"
             return
         assert False
 
diff --git a/test/unit/tools/test_tool_dependency_description.py b/test/unit/tools/test_tool_dependency_description.py
index 9dccd45beb4..6425a003b1c 100644
--- a/test/unit/tools/test_tool_dependency_description.py
+++ b/test/unit/tools/test_tool_dependency_description.py
@@ -1,5 +1,5 @@
 from galaxy.model import tool_shed_install
-from galaxy.tools.deps import (
+from galaxy.tool_util.deps import (
     dependencies,
     requirements
 )
diff --git a/test/unit/tools/test_tool_deps.py b/test/unit/tools/test_tool_deps.py
index 012d30f9b17..0f609201a77 100644
--- a/test/unit/tools/test_tool_deps.py
+++ b/test/unit/tools/test_tool_deps.py
@@ -12,17 +12,20 @@ from shutil import rmtree
 from stat import S_IXUSR
 from subprocess import PIPE, Popen
 
-from galaxy.tools.deps import DependencyManager
-from galaxy.tools.deps.requirements import (
+from galaxy.tool_util.deps import build_dependency_manager_from_dict, DependencyManager
+from galaxy.tool_util.deps.requirements import (
     ToolRequirement,
     ToolRequirements
 )
-from galaxy.tools.deps.resolvers import NullDependency
-from galaxy.tools.deps.resolvers.galaxy_packages import GalaxyPackageDependency
-from galaxy.tools.deps.resolvers.lmod import LmodDependency, LmodDependencyResolver
-from galaxy.tools.deps.resolvers.modules import ModuleDependency, ModuleDependencyResolver
+from galaxy.tool_util.deps.resolvers import NullDependency
+from galaxy.tool_util.deps.resolvers.galaxy_packages import GalaxyPackageDependency
+from galaxy.tool_util.deps.resolvers.lmod import LmodDependency, LmodDependencyResolver
+from galaxy.tool_util.deps.resolvers.modules import ModuleDependency, ModuleDependencyResolver
 from galaxy.util.bunch import Bunch
 
+# If true, test created DependencyManager objects by serializing out to json and re-constituting.
+ROUND_TRIP_TEST_DEPENDENCY_MANAGER_SERIALIZATION = True
+
 
 def test_tool_dependencies():
     # Setup directories
@@ -560,6 +563,13 @@ def test_config_module_defaults():
         module_resolver = dependency_resolvers[0]
         assert module_resolver.module_checker.__class__.__name__ == "AvailModuleChecker"
 
+    with __parse_resolvers('''
+-  type: modules
+   prefetch: false
+''', extension=".yml") as dependency_resolvers:
+        module_resolver = dependency_resolvers[0]
+        assert module_resolver.module_checker.__class__.__name__ == "AvailModuleChecker"
+
 
 def test_config_modulepath():
     # Test reads and splits MODULEPATH if modulepath is not specified.
@@ -623,23 +633,27 @@ def __environ(values, remove=[]):
 
 
 @contextmanager
-def __parse_resolvers(xml_content):
-    with __dependency_manager(xml_content) as dm:
+def __parse_resolvers(file_content, extension=".xml"):
+    with __dependency_manager(file_content, extension=extension) as dm:
         yield dm.dependency_resolvers
 
 
 @contextmanager
-def __dependency_manager(xml_content):
+def __dependency_manager(file_content, extension=".xml"):
     with __test_base_path() as base_path:
-        with tempfile.NamedTemporaryFile('w+') as tmp:
-            tmp.write(xml_content)
+        with tempfile.NamedTemporaryFile('w+', suffix=extension) as tmp:
+            tmp.write(file_content)
             tmp.flush()
             dm = __dependency_manager_for_base_path(default_base_path=base_path, conf_file=tmp.name)
             yield dm
 
 
 def __dependency_manager_for_base_path(default_base_path, conf_file=None):
-    return DependencyManager(default_base_path=default_base_path, conf_file=conf_file, app_config={"conda_auto_init": False})
+    dm = DependencyManager(default_base_path=default_base_path, conf_file=conf_file, app_config={"conda_auto_init": False})
+    if ROUND_TRIP_TEST_DEPENDENCY_MANAGER_SERIALIZATION:
+        as_dict = dm.to_dict()
+        dm = build_dependency_manager_from_dict(as_dict)
+    return dm
 
 
 class _SimpleDependencyManager(object):
diff --git a/test/unit/tools/test_tool_loader.py b/test/unit/tools/test_tool_loader.py
index 3f2619973ae..f07c1e8c2b5 100644
--- a/test/unit/tools/test_tool_loader.py
+++ b/test/unit/tools/test_tool_loader.py
@@ -3,7 +3,7 @@ from shutil import rmtree
 from string import Template
 from tempfile import mkdtemp
 
-from galaxy.tools.loader import load_tool, template_macro_params
+from galaxy.tool_util.loader import load_tool, template_macro_params
 from galaxy.util import parse_xml
 
 
diff --git a/test/unit/tools/test_toolbox.py b/test/unit/tools/test_toolbox.py
index d9787714246..f16b565e693 100644
--- a/test/unit/tools/test_toolbox.py
+++ b/test/unit/tools/test_toolbox.py
@@ -374,6 +374,15 @@ class ToolBoxTestCase(BaseToolBoxTestCase):
         # Assert tools merged in tool panel.
         assert len(self.toolbox._tool_panel) == 1
 
+    def test_get_section_by_label(self):
+        self._add_config(
+            """<toolbox><section id="tid" name="Completely unrelated"><label id="lab1" text="Label 1" /><label id="lab2" text="Label 2" /></section></toolbox>""")
+        assert len(self.toolbox._tool_panel) == 1
+        section = self.toolbox._tool_panel['tid']
+        tool_panel_section_key, section_by_label = self.toolbox.get_section(section_id='nope', new_label='Completely unrelated', create_if_needed=True)
+        assert section_by_label is section
+        assert tool_panel_section_key == 'tid'
+
     def test_get_tool_id(self):
         self._init_tool()
         self._setup_two_versions_in_config()
@@ -562,9 +571,6 @@ class SimplifiedToolBox(ToolBox):
         # Need to start thread now for new reload callback to take effect
         self.app.watchers.start()
 
-    def handle_panel_update(self, section_dict):
-        self.create_section(section_dict)
-
 
 def reload_callback(test_case):
     test_case.app.tool_cache.cleanup()
diff --git a/test/unit/tools/test_wrappers.py b/test/unit/tools/test_wrappers.py
index cc2c5b15183..57248754e06 100644
--- a/test/unit/tools/test_wrappers.py
+++ b/test/unit/tools/test_wrappers.py
@@ -3,7 +3,7 @@ import tempfile
 from xml.etree.ElementTree import XML
 
 from galaxy.datatypes.metadata import MetadataSpecCollection
-from galaxy.jobs.datasets import DatasetPath
+from galaxy.job_execution.datasets import DatasetPath
 from galaxy.tools.parameters.basic import (
     DrillDownSelectToolParameter,
     IntegerToolParameter,
@@ -88,6 +88,12 @@ def test_input_value_wrapper(tool):
     parameter = IntegerToolParameter(tool, XML('<param name="blah" type="integer" value="10" min="0" />'))
     wrapper = InputValueWrapper(parameter, "5")
     assert str(wrapper) == "5"
+    assert int(wrapper) == 5
+    assert wrapper == "5"
+    assert wrapper == 5
+    assert wrapper == 5.0
+    assert wrapper > 2
+    assert wrapper < 10
 
 
 def test_dataset_wrapper():
diff --git a/test/unit/tools_support.py b/test/unit/tools_support.py
index 70ec4965a78..1724558830b 100644
--- a/test/unit/tools_support.py
+++ b/test/unit/tools_support.py
@@ -11,8 +11,8 @@ from collections import defaultdict
 
 import galaxy.datatypes.registry
 import galaxy.model
+from galaxy.tool_util.parser import get_tool_source
 from galaxy.tools import create_tool_from_source
-from galaxy.tools.parser import get_tool_source
 from galaxy.util.bunch import Bunch
 from .unittest_utils import galaxy_mock
 
diff --git a/test/unit/unittest_utils/galaxy_mock.py b/test/unit/unittest_utils/galaxy_mock.py
index dcc931cb274..5e64098bbe8 100644
--- a/test/unit/unittest_utils/galaxy_mock.py
+++ b/test/unit/unittest_utils/galaxy_mock.py
@@ -15,10 +15,10 @@ from galaxy.datatypes import registry
 from galaxy.jobs.manager import NoopManager
 from galaxy.model import mapping, tags
 from galaxy.security import idencoding
-from galaxy.tools.deps.containers import NullContainerFinder
+from galaxy.tool_util.deps.containers import NullContainerFinder
 from galaxy.util.bunch import Bunch
 from galaxy.util.dbkeys import GenomeBuilds
-from galaxy.web.stack import ApplicationStack
+from galaxy.web_stack import ApplicationStack
 
 
 # =============================================================================
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 0c6ecf8325e..640aa1607b8 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -104,7 +104,7 @@ def add_file(dataset, registry, output_path):
         try:
             dataset.path = sniff.stream_url_to_file(dataset.path)
         except Exception as e:
-            raise UploadProblemException('Unable to fetch %s\n%s' % (dataset.path, str(e)))
+            raise UploadProblemException('Unable to fetch %s\n%s' % (dataset.path, unicodify(e)))
 
     # See if we have an empty file
     if not os.path.exists(dataset.path):
@@ -186,7 +186,7 @@ def add_composite_file(dataset, registry, output_path, files_path):
             try:
                 temp_name = sniff.stream_to_file(urlopen(path_or_url), prefix='url_paste')
             except Exception as e:
-                raise UploadProblemException('Unable to fetch %s\n%s' % (path_or_url, str(e)))
+                raise UploadProblemException('Unable to fetch %s\n%s' % (path_or_url, unicodify(e)))
 
             return temp_name, is_url
 
@@ -318,7 +318,7 @@ def __main__():
             else:
                 metadata.append(add_file(dataset, registry, output_path))
         except UploadProblemException as e:
-            metadata.append(file_err(str(e), dataset))
+            metadata.append(file_err(unicodify(e), dataset))
     __write_job_metadata(metadata)
 
 
diff --git a/tools/expression_tools/parse_values_from_file.xml b/tools/expression_tools/parse_values_from_file.xml
new file mode 100644
index 00000000000..8013a1fc6d9
--- /dev/null
+++ b/tools/expression_tools/parse_values_from_file.xml
@@ -0,0 +1,106 @@
+<tool name="Parse parameter value" id="param_value_from_file" version="0.1.0" tool_type="expression">
+    <description>from dataset</description>
+    <expression type="ecma5.1">{
+var output;
+if ($job.remove_newlines || $job.param_type != 'text') {
+   $job.input1.contents = $job.input1.contents.trim();
+}
+if ($job.param_type == 'integer') {
+    output = parseInt($job.input1.contents);
+} else if ($job.param_type == 'float') {
+    output = parseFloat($job.input1.contents);
+} else if ($job.param_type == 'boolean') {
+    const trueValues = ['yes', 'true', '1']
+    const falseValues = ['no', 'false', '0']
+    let lowerCaseContents = $job.input1.contents.toLowerCase();
+    if (trueValues.includes(lowerCaseContents)) {
+        output = true;
+    } else if (falseValues.includes(lowerCaseContents)) {
+        output = false;
+    }
+    else {
+        return 'NOT A BOOLEAN VALUE';
+    }
+} else {
+    output = $job.input1.contents;
+}
+return {'output': output};
+    }</expression>
+    <inputs>
+        <param type="data" label="Input file containing parameter to parse out of" load_contents="64000" name="input1" />
+        <param name="param_type" type="select" label="Select type of parameter to parse">
+            <option value="text">Text</option>
+            <option value="integer">Integer</option>
+            <option value="float">Float</option>
+            <option value="boolean">Boolean</option>
+        </param>
+        <param name="remove_newlines" checked="true" type="boolean" label="Remove newlines ?" help="Uncheck this only if newlines should be preserved in parameter"/>
+    </inputs>
+    <outputs>
+        <output type="text" name="text_param" from="output">
+            <filter>param_type == 'text'</filter>
+        </output>
+        <output type="integer" name="integer_param" from="output">
+            <filter>param_type == 'integer'</filter>
+        </output>
+        <output type="float" name="float_param" from="output">
+            <filter>param_type == 'float'</filter>
+        </output>
+        <output type="boolean" name="boolean_param" from="output">
+            <filter>param_type == 'boolean'</filter>
+        </output>
+     </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input1" value="simple_line.txt"/>
+            <param name="param_type" value="text"/>
+            <param name="remove_newlines" value="true"/>
+            <output name="text_param">
+                <assert_contents>
+                    <has_line line="&quot;This is a line of text.&quot;"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="simple_line.txt"/>
+            <param name="param_type" value="text"/>
+            <param name="remove_newlines" value="false"/>
+            <output name="text_param">
+                <assert_contents>
+                    <has_line line="&quot;This is a line of text.\n&quot;"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="1.integer.txt"/>
+            <param name="param_type" value="integer"/>
+            <param name="remove_newlines" value="false"/>
+            <output name="integer_param">
+                <assert_contents>
+                    <has_line line="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="1.integer.txt"/>
+            <param name="param_type" value="float"/>
+            <param name="remove_newlines" value="false"/>
+            <output name="float_param">
+                <assert_contents>
+                    <has_line line="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="1.bool.txt"/>
+            <param name="param_type" value="boolean"/>
+            <param name="remove_newlines" value="false"/>
+            <output name="boolean_param">
+                <assert_contents>
+                    <has_line line="false"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help></help>
+</tool>
diff --git a/tools/filters/bed2gff.xml b/tools/filters/bed2gff.xml
index 4734b747e42..9914fac8a62 100644
--- a/tools/filters/bed2gff.xml
+++ b/tools/filters/bed2gff.xml
@@ -3,7 +3,7 @@
   <edam_operations>
     <edam_operation>operation_3434</edam_operation>
   </edam_operations>
-  <command interpreter="python">bed_to_gff_converter.py $input $out_file1</command>
+  <command>python '$__tool_directory__/bed_to_gff_converter.py' '$input' '$out_file1'</command>
   <inputs>
     <param format="bed" name="input" type="data" label="Convert this dataset"/>
   </inputs>
@@ -13,7 +13,12 @@
   <tests>
     <test>
       <param name="input" value="9.bed"/>
-      <output name="out_file1" file="bed2gff_out.gff"/>
+      <output name="out_file1">
+          <assert_contents>
+              <has_line line="chr28&#009;bed2gff&#009;mRNA&#009;346188&#009;388197&#009;0&#009;+&#009;.&#009;mRNA BC114771;"/>
+              <has_line line="chr28&#009;bed2gff&#009;exon&#009;388086&#009;388197&#009;0&#009;+&#009;.&#009;exon BC114771;"/>
+          </assert_contents>
+      </output>
     </test>
   </tests>
   <help>
diff --git a/tools/filters/bed_to_gff_converter.py b/tools/filters/bed_to_gff_converter.py
index dab53f94a85..768891fdcf8 100644
--- a/tools/filters/bed_to_gff_converter.py
+++ b/tools/filters/bed_to_gff_converter.py
@@ -13,8 +13,6 @@ def __main__():
     skipped_lines = 0
     first_skipped_line = 0
     out = open(output_name, 'w')
-    out.write("##gff-version 2\n")
-    out.write("##bed_to_gff_converter.py\n\n")
     i = 0
     for i, line in enumerate(open(input_name)):
         complete_bed = False
diff --git a/tools/stats/grouping.py b/tools/stats/grouping.py
index 6dad86e9a2c..87bfcb89436 100644
--- a/tools/stats/grouping.py
+++ b/tools/stats/grouping.py
@@ -67,17 +67,12 @@ def main():
     if sys.argv[5] != "None":
         asciitodelete = sys.argv[5]
         if asciitodelete:
-            oldfile = open(inputfile, 'r')
             newinputfile = "input_cleaned.tsv"
-            newfile = open(newinputfile, 'w')
-            asciitodelete = asciitodelete.split(',')
-            for i in range(len(asciitodelete)):
-                asciitodelete[i] = chr(int(asciitodelete[i]))
-            for line in oldfile:
-                if line[0] not in asciitodelete:
-                    newfile.write(line)
-            oldfile.close()
-            newfile.close()
+            with open(inputfile, 'r') as oldfile, open(newinputfile, 'w') as newfile:
+                asciitodelete = {chr(int(_)) for _ in asciitodelete.split(',')}
+                for line in oldfile:
+                    if line[0] not in asciitodelete:
+                        newfile.write(line)
             inputfile = newinputfile
 
     # get operations and options in separate arrays
@@ -112,20 +107,18 @@ def main():
         we need to add 1 to group_col.
         if POS2 is not specified, the newer versions of sort will consider the entire line for sorting. To prevent this, we set POS2=POS1.
         """
-        case = ''
+        group_col_str = str(group_col + 1)
+        command_line = ["sort", "-t", "\t", "-k%s,%s" % (group_col_str, group_col_str), "-o", tmpfile.name, inputfile]
         if ignorecase == 1:
-            case = '-f'
-        command_line = "sort -t $'\\t' %s -k%s,%s -o %s %s" % (case, group_col + 1, group_col + 1, tmpfile.name, inputfile)
+            command_line.append('-f')
     except Exception as exc:
         stop_err('Initialization error -> %s' % str(exc))
 
     try:
-        subprocess.check_output(command_line, stderr=subprocess.STDOUT, shell=True)
+        subprocess.check_output(command_line, stderr=subprocess.STDOUT)
     except subprocess.CalledProcessError as e:
         stop_err("Sorting input dataset resulted in error: %s: %s" % (e.returncode, e.output))
 
-    fout = open(sys.argv[1], "w")
-
     def is_new_item(line):
         try:
             item = line.split("\t")[group_col]
@@ -136,52 +129,56 @@ def main():
             return item.lower()
         return item
 
-    for key, line_list in groupby(tmpfile, key=is_new_item):
-        op_vals = [[] for _ in ops]
-        out_str = key
+    with open(sys.argv[1], "w") as fout:
 
-        for line in line_list:
-            fields = line.split("\t")
-            for i, col in enumerate(cols):
-                col = int(col) - 1  # cXX from galaxy is 1-based
-                try:
-                    val = fields[col].strip()
-                    op_vals[i].append(val)
-                except IndexError:
-                    sys.stderr.write('Could not access the value for column %s on line: "%s". Make sure file is tab-delimited.\n' % (col + 1, line))
-                    sys.exit(1)
+        for key, line_list in groupby(tmpfile, key=is_new_item):
+            op_vals = [[] for _ in ops]
+            out_str = key
 
-        # Generate string for each op for this group
-        for i, op in enumerate(ops):
-            data = op_vals[i]
-            rval = ""
-            if op == "mode":
-                rval = mode(data)
-            elif op == "length":
-                rval = len(data)
-            elif op == "random":
-                rval = random.choice(data)
-            elif op in ['cat', 'cat_uniq']:
-                if op == 'cat_uniq':
-                    data = numpy.unique(data)
-                rval = ','.join(data)
-            elif op == "unique":
-                rval = len(numpy.unique(data))
-            else:
-                # some kind of numpy fn
-                try:
-                    data = float_wdefault(data, default_val[i], col + 1)
-                except ValueError:
-                    sys.stderr.write("Operation %s expected number values but got %s instead.\n" % (op, data))
-                    sys.exit(1)
-                rval = getattr(numpy, op)(data)
-                if round_val[i] == 'yes':
-                    rval = int(round(rval))
+            for line in line_list:
+                fields = line.split("\t")
+                for i, col in enumerate(cols):
+                    col = int(col) - 1  # cXX from galaxy is 1-based
+                    try:
+                        val = fields[col].strip()
+                        op_vals[i].append(val)
+                    except IndexError:
+                        sys.stderr.write('Could not access the value for column %s on line: "%s". Make sure file is tab-delimited.\n' % (col + 1, line))
+                        sys.exit(1)
+
+            # Generate string for each op for this group
+            for i, op in enumerate(ops):
+                data = op_vals[i]
+                rval = ""
+                if op == "mode":
+                    rval = mode(data)
+                elif op == "length":
+                    rval = len(data)
+                elif op == "random":
+                    rval = random.choice(data)
+                elif op in ['cat', 'cat_uniq']:
+                    if op == 'cat_uniq':
+                        data = numpy.unique(data)
+                    rval = ','.join(data)
+                elif op == "unique":
+                    rval = len(numpy.unique(data))
                 else:
-                    rval = '%g' % rval
-            out_str += "\t%s" % rval
+                    # some kind of numpy fn
+                    try:
+                        data = float_wdefault(data, default_val[i], col + 1)
+                    except ValueError:
+                        sys.stderr.write("Operation %s expected number values but got %s instead.\n" % (op, data))
+                        sys.exit(1)
+                    rval = getattr(numpy, op)(data)
+                    if round_val[i] == 'yes':
+                        rval = int(round(rval))
+                    else:
+                        rval = '%g' % rval
+                out_str += "\t%s" % rval
 
-        fout.write(out_str + "\n")
+            fout.write(out_str + "\n")
+
+    tmpfile.close()
 
     # Generate a useful info message.
     msg = "--Group by c%d: " % (group_col + 1)
@@ -200,8 +197,6 @@ def main():
         msg += op + "[c" + cols[i] + "] "
 
     print(msg)
-    fout.close()
-    tmpfile.close()
 
 
 if __name__ == "__main__":
diff --git a/tools/stats/grouping.xml b/tools/stats/grouping.xml
index 9546ce139ae..ce7b6dd826c 100644
--- a/tools/stats/grouping.xml
+++ b/tools/stats/grouping.xml
@@ -2,6 +2,7 @@
   <description>data by a column and perform aggregate operation on other columns.</description>
   <requirements>
     <requirement type="package" version="1.15.4">numpy</requirement>
+    <requirement type="package" version="8.31">coreutils</requirement>
   </requirements>
   <command detect_errors="exit_code">
   python '$__tool_directory__/grouping.py'
@@ -79,7 +80,7 @@
     </test>
     <!-- Test with an empty first field-->
     <test>
-      <param name="input1" value="1.tabular"/>
+      <param name="input1" value="groupby_in_1.tabular"/>
       <param name="groupcol" value="1"/>
       <param name="ignorecase" value="true"/>
       <repeat name="operations">
@@ -170,7 +171,7 @@
       </assert_stderr>
     </test>
     <test>
-      <param name="input1" value="1.tabular"/>
+      <param name="input1" value="groupby_in_1.tabular"/>
       <param name="groupcol" value="1"/>
       <param name="ignorecase" value="true"/>
       <repeat name="operations">
diff --git a/tools/stats/gsummary.py b/tools/stats/gsummary.py
index 5acb74458bd..13865a7b411 100755
--- a/tools/stats/gsummary.py
+++ b/tools/stats/gsummary.py
@@ -13,7 +13,7 @@ except ImportError:
 
 def stop_err(msg):
     sys.stderr.write(msg)
-    sys.exit()
+    sys.exit(1)
 
 
 def S3_METHODS(all="key"):
diff --git a/tox.ini b/tox.ini
index 9904d2a82f1..0aec466cf97 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,7 +1,7 @@
 [tox]
 # envlist is the list of environments that are tested when `tox` is run without any option
 # hyphens in an environment name are used to delimit factors
-envlist = check_py3_compatibility, py{27,35}-first_startup, py{27,35}-lint, py27-lint_docstring_include_list, py{27,35}-unit, validate_test_tools
+envlist = check_py3_compatibility, py{27,35}-first_startup, py{27,35}-lint, py27-lint_docstring_include_list, py{27,35}-unit, test_galaxy_packages, validate_test_tools
 skipsdist = True
 
 [testenv]
@@ -35,6 +35,9 @@ commands = bash .ci/flake8_wrapper_docstrings.sh --exclude
 [testenv:py27-lint_docstring_include_list]
 commands = bash .ci/flake8_wrapper_docstrings.sh --include
 
+[testenv:test_galaxy_packages]
+commands = bash packages/test.sh
+
 [testenv:validate_test_tools]
 commands = bash .ci/validate_test_tools.sh