diff --git a/client/galaxy/scripts/layout/masthead.js b/client/galaxy/scripts/layout/masthead.js
index 527ce3f8b46..d6b9aaad59e 100644
--- a/client/galaxy/scripts/layout/masthead.js
+++ b/client/galaxy/scripts/layout/masthead.js
@@ -1,7 +1,7 @@
-import Utils from "utils/utils";
 import Menu from "layout/menu";
 import Scratchbook from "layout/scratchbook";
 import QuotaMeter from "mvc/user/user-quotameter";
+
 /** Masthead **/
 var View = Backbone.View.extend({
     initialize: function(options) {
@@ -62,7 +62,9 @@ var View = Backbone.View.extend({
                 var text = "";
                 self.collection.each(model => {
                     var q = model.get("onbeforeunload") && model.get("onbeforeunload")();
-                    q && (text += `${q} `);
+                    if (q) {
+                        text += `${q} `;
+                    }
                 });
                 if (text !== "") {
                     return text;
diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index d848465994e..49edea8089f 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -105,15 +105,15 @@ var Collection = Backbone.Collection.extend({
         //
         // Webhooks
         //
-        Webhooks.add({
-            url: "api/webhooks/masthead/all",
+        Webhooks.load({
+            type: "masthead",
             callback: function(webhooks) {
                 $(document).ready(() => {
-                    $.each(webhooks.models, (index, model) => {
+                    webhooks.each(model => {
                         var webhook = model.toJSON();
                         if (webhook.activate) {
                             var obj = {
-                                id: webhook.name,
+                                id: webhook.id,
                                 icon: webhook.config.icon,
                                 url: webhook.config.url,
                                 tooltip: webhook.config.tooltip,
diff --git a/client/galaxy/scripts/layout/page.js b/client/galaxy/scripts/layout/page.js
index 8cef58f32d2..a2ce69c1655 100644
--- a/client/galaxy/scripts/layout/page.js
+++ b/client/galaxy/scripts/layout/page.js
@@ -2,6 +2,7 @@ import Masthead from "layout/masthead";
 import Panel from "layout/panel";
 import Modal from "mvc/ui/ui-modal";
 import Utils from "utils/utils";
+
 var View = Backbone.View.extend({
     el: "body",
     className: "full-content",
@@ -61,11 +62,12 @@ var View = Backbone.View.extend({
         this.render();
 
         // start the router
-        this.router &&
+        if (this.router) {
             Backbone.history.start({
                 root: Galaxy.root,
                 pushState: true
             });
+        }
     },
 
     render: function() {
diff --git a/client/galaxy/scripts/mvc/history/options-menu.js b/client/galaxy/scripts/mvc/history/options-menu.js
index e8f280ebf40..a330160c045 100644
--- a/client/galaxy/scripts/mvc/history/options-menu.js
+++ b/client/galaxy/scripts/mvc/history/options-menu.js
@@ -175,13 +175,13 @@ var menu = [
 ];
 
 // Webhooks
-Webhooks.add({
-    url: "api/webhooks/history-menu/all",
+Webhooks.load({
+    type: "history-menu",
     async: false, // (hypothetically) slows down the performance
     callback: function(webhooks) {
         var webhooks_menu = [];
 
-        $.each(webhooks.models, (index, model) => {
+        webhooks.each(model => {
             var webhook = model.toJSON();
             if (webhook.activate) {
                 webhooks_menu.push({
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js
index 65f8c197c37..87404c7da92 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-base.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js
@@ -6,6 +6,7 @@ import Utils from "utils/utils";
 import Deferred from "utils/deferred";
 import Ui from "mvc/ui/ui-misc";
 import FormBase from "mvc/form/form-view";
+import Webhooks from "mvc/webhooks";
 import Citations from "components/Citations.vue";
 import Vue from "vue";
 export default FormBase.extend({
@@ -200,19 +201,23 @@ export default FormBase.extend({
         }
 
         // add tool menu webhooks
-        $.getJSON("/api/webhooks/tool-menu/all", webhooks => {
-            _.each(webhooks, webhook => {
-                if (webhook.activate && webhook.config.function) {
-                    menu_button.addMenu({
-                        icon: webhook.config.icon,
-                        title: webhook.config.title,
-                        onclick: function() {
-                            var func = new Function("options", webhook.config.function);
-                            func(options);
-                        }
-                    });
-                }
-            });
+        Webhooks.load({
+            type: "tool-menu",
+            callback: function(webhooks) {
+                webhooks.each(model => {
+                    var webhook = model.toJSON();
+                    if (webhook.activate && webhook.config.function) {
+                        menu_button.addMenu({
+                            icon: webhook.config.icon,
+                            title: webhook.config.title,
+                            onclick: function() {
+                                var func = new Function("options", webhook.config.function);
+                                func(options);
+                            }
+                        });
+                    }
+                });
+            }
         });
 
         return {
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
index 1beea452ce9..00a5e78f845 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
@@ -598,7 +598,7 @@ var View = Backbone.View.extend({
                     if ($.isArray(response) && response.length > 0) {
                         self.$el.append($("<div/>", { id: "webhook-view" }));
                         var WebhookApp = new Webhooks.WebhookView({
-                            urlRoot: `${Galaxy.root}api/webhooks/workflow`,
+                            type: "workflow",
                             toolId: job_def.tool_id,
                             toolVersion: job_def.tool_version
                         });
diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index f946fdd325a..5dec9427bff 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -227,7 +227,7 @@ var View = Backbone.View.extend({
                 if (response.jobs && response.jobs.length > 0) {
                     self.$el.append($("<div/>", { id: "webhook-view" }));
                     var WebhookApp = new Webhooks.WebhookView({
-                        urlRoot: `${Galaxy.root}api/webhooks/tool`,
+                        type: "tool",
                         toolId: job_def.tool_id
                     });
                 }
diff --git a/client/galaxy/scripts/mvc/webhooks.js b/client/galaxy/scripts/mvc/webhooks.js
index 44c460fde3b..c1f2400fcf5 100644
--- a/client/galaxy/scripts/mvc/webhooks.js
+++ b/client/galaxy/scripts/mvc/webhooks.js
@@ -1,66 +1,86 @@
-/**
-  Webhooks
-**/
+import Utils from "utils/utils";
 
-var WebhookModel = Backbone.Model.extend({
-    defaults: {
-        activate: false
+const Webhooks = Backbone.Collection.extend({
+    url: function() {
+        return `${Galaxy.root}api/webhooks`;
     }
 });
 
-var Webhooks = Backbone.Collection.extend({
-    model: WebhookModel
-});
-
-var WebhookView = Backbone.View.extend({
+const WebhookView = Backbone.View.extend({
     el: "#webhook-view",
 
     initialize: function(options) {
-        var me = this;
-        var toolId = options.toolId || "";
-        var toolVersion = options.toolVersion || "";
+        const toolId = options.toolId || "";
+        const toolVersion = options.toolVersion || "";
 
         this.$el.attr("tool_id", toolId);
         this.$el.attr("tool_version", toolVersion);
 
-        this.model = new WebhookModel();
-        this.model.urlRoot = options.urlRoot;
-        this.model.fetch({
-            success: function() {
-                me.render();
+        const webhooks = new Webhooks();
+        webhooks.fetch({
+            success: data => {
+                if (options.type) {
+                    data.reset(filterType(data, options.type));
+                }
+                if (data.length > 0) {
+                    this.render(weightedRandomPick(data));
+                }
             }
         });
     },
 
-    render: function() {
-        var webhook = this.model.toJSON();
-
-        this.$el.html(`<div id="${webhook.name}"></div>`);
-        if (webhook.styles)
-            $("<style/>", { type: "text/css" })
-                .text(webhook.styles)
-                .appendTo("head");
-        if (webhook.script)
-            $("<script/>", { type: "text/javascript" })
-                .text(webhook.script)
-                .appendTo("head");
-
+    render: function(model) {
+        const webhook = model.toJSON();
+        this.$el.html(`<div id="${webhook.id}"></div>`);
+        Utils.appendScriptStyle(webhook);
         return this;
     }
 });
 
-var add = options => {
-    var webhooks = new Webhooks();
-
-    webhooks.url = Galaxy.root + options.url;
+const load = options => {
+    const webhooks = new Webhooks();
     webhooks.fetch({
-        async: options.async ? options.async : true,
-        success: options.callback
+        async: options.async !== undefined ? options.async : true,
+        success: data => {
+            if (options.type) {
+                data.reset(filterType(data, options.type));
+            }
+            options.callback(data);
+        }
     });
 };
 
+function filterType(data, type) {
+    return data.models.filter(item => {
+        let itype = item.get("type");
+        if (itype) {
+            return itype.indexOf(type) !== -1;
+        } else {
+            return false;
+        }
+    });
+}
+
+function weightedRandomPick(data) {
+    const weights = data.pluck("weight");
+    const sum = weights.reduce((a, b) => a + b);
+
+    const normalizedWeightsMap = new Map();
+    weights.forEach((weight, index) => {
+        normalizedWeightsMap.set(index, parseFloat((weight / sum).toFixed(2)));
+    });
+
+    const table = [];
+    for (const [index, weight] of normalizedWeightsMap) {
+        for (let i = 0; i < weight * 100; i++) {
+            table.push(index);
+        }
+    }
+
+    return data.at(table[Math.floor(Math.random() * table.length)]);
+}
+
 export default {
-    Webhooks: Webhooks,
     WebhookView: WebhookView,
-    add: add
+    load: load
 };
diff --git a/client/galaxy/scripts/onload.js b/client/galaxy/scripts/onload.js
index 7af85c6fe35..232fc87c0ab 100644
--- a/client/galaxy/scripts/onload.js
+++ b/client/galaxy/scripts/onload.js
@@ -25,6 +25,8 @@ window.make_popup_menus = Popupmenu.make_popup_menus;
 import init_tag_click_function from "ui/autocom_tagging";
 window.init_tag_click_function = init_tag_click_function;
 import Tours from "mvc/tours";
+import Webhooks from "mvc/webhooks";
+import Utils from "utils/utils";
 // console.debug( 'galaxy globals loaded' );
 
 // ============================================================================
@@ -176,23 +178,19 @@ $(document).ready(() => {
     Tours.activeGalaxyTourRunner();
 
     function onloadWebhooks() {
-        // Wait until Galaxy.config is loaded.
-        if (Galaxy.config) {
-            if (Galaxy.config.enable_webhooks) {
-                // Load all webhooks with the type 'onload'
-                $.getJSON(`${Galaxy.root}api/webhooks/onload/all`, webhooks => {
-                    _.each(webhooks, webhook => {
+        if (Galaxy.root !== undefined) {
+            // Load all webhooks with the type 'onload'
+            Webhooks.load({
+                type: "onload",
+                callback: function(webhooks) {
+                    webhooks.each(model => {
+                        var webhook = model.toJSON();
                         if (webhook.activate && webhook.script) {
-                            $("<script/>", { type: "text/javascript" })
-                                .text(webhook.script)
-                                .appendTo("head");
-                            $("<style/>", { type: "text/css" })
-                                .text(webhook.styles)
-                                .appendTo("head");
+                            Utils.appendScriptStyle(webhook);
                         }
                     });
-                });
-            }
+                }
+            });
         } else {
             setTimeout(onloadWebhooks, 100);
         }
diff --git a/client/galaxy/scripts/qunit/test-app.js b/client/galaxy/scripts/qunit/test-app.js
index c1f6991aba7..155eb38627c 100644
--- a/client/galaxy/scripts/qunit/test-app.js
+++ b/client/galaxy/scripts/qunit/test-app.js
@@ -1,4 +1,6 @@
 /** Creates a generic/global Galaxy environment, loads shared libraries and a fake server */
+/* global define */
+
 define(
     [
         "jquery",
diff --git a/client/galaxy/scripts/qunit/tests/page_tests.js b/client/galaxy/scripts/qunit/tests/page_tests.js
index d7b4951e7e4..5d70e19653d 100644
--- a/client/galaxy/scripts/qunit/tests/page_tests.js
+++ b/client/galaxy/scripts/qunit/tests/page_tests.js
@@ -1,8 +1,7 @@
-/* global define */
+/* global QUnit */
 
 import testApp from "qunit/test-app";
 import Page from "layout/page";
-import Panel from "layout/panel";
 
 QUnit.module("Page test", {
     beforeEach: function() {
diff --git a/config/plugins/webhooks/demo/search/config/searchover.yaml b/config/plugins/webhooks/demo/search/config.yml
similarity index 82%
rename from config/plugins/webhooks/demo/search/config/searchover.yaml
rename to config/plugins/webhooks/demo/search/config.yml
index f97f5797fc8..92dccea779e 100644
--- a/config/plugins/webhooks/demo/search/config/searchover.yaml
+++ b/config/plugins/webhooks/demo/search/config.yml
@@ -1,4 +1,4 @@
-name: searchover
+id: searchover
 type:
   - masthead
 activate: true
diff --git a/config/plugins/webhooks/demo/search/static/script.js b/config/plugins/webhooks/demo/search/script.js
similarity index 99%
rename from config/plugins/webhooks/demo/search/static/script.js
rename to config/plugins/webhooks/demo/search/script.js
index 8b1a5b5e0b4..339d4b57f43 100644
--- a/config/plugins/webhooks/demo/search/static/script.js
+++ b/config/plugins/webhooks/demo/search/script.js
@@ -38,7 +38,7 @@ $(document).ready(function() {
                 e.stopPropagation();
                 if ( $( '.search-screen-overlay' ).is( ':visible' ) ){
                     self.removeOverlay();
-                } 
+                }
                 else {
                     self.clearSearchResults();
                     self.showOverlay();
diff --git a/config/plugins/webhooks/demo/search/static/styles.css b/config/plugins/webhooks/demo/search/styles.css
similarity index 100%
rename from config/plugins/webhooks/demo/search/static/styles.css
rename to config/plugins/webhooks/demo/search/styles.css
diff --git a/config/plugins/webhooks/demo/tool_list/helper/__init__.py b/config/plugins/webhooks/demo/tool_list/__init__.py
similarity index 100%
rename from config/plugins/webhooks/demo/tool_list/helper/__init__.py
rename to config/plugins/webhooks/demo/tool_list/__init__.py
diff --git a/config/plugins/webhooks/demo/tool_list/config/tool_list.yml b/config/plugins/webhooks/demo/tool_list/config.yml
similarity index 94%
rename from config/plugins/webhooks/demo/tool_list/config/tool_list.yml
rename to config/plugins/webhooks/demo/tool_list/config.yml
index cc3577068b4..d57c1832e6a 100644
--- a/config/plugins/webhooks/demo/tool_list/config/tool_list.yml
+++ b/config/plugins/webhooks/demo/tool_list/config.yml
@@ -1,4 +1,4 @@
-name: tool_list
+id: tool_list
 type:
   - masthead
 activate: true
@@ -13,7 +13,7 @@ function: >
     'be patient, this might take a moment.');
   }, 1);
 
-  $.getJSON(Galaxy.root + "api/webhooks/tool_list/get_data", function(data) {
+  $.getJSON(Galaxy.root + "api/webhooks/tool_list/data", function(data) {
     var popup = window.open('tool_list.html');
     var html = '<!DOCTYPE html><body><h2>' +
       'Create a Docker flavour of this instance:</h2>' +
diff --git a/config/plugins/webhooks/demo/tour_generator/helper/__init__.py b/config/plugins/webhooks/demo/tour_generator/__init__.py
similarity index 100%
rename from config/plugins/webhooks/demo/tour_generator/helper/__init__.py
rename to config/plugins/webhooks/demo/tour_generator/__init__.py
diff --git a/config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml b/config/plugins/webhooks/demo/tour_generator/config.yml
similarity index 95%
rename from config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
rename to config/plugins/webhooks/demo/tour_generator/config.yml
index b510bdb0088..309f1791afa 100644
--- a/config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
+++ b/config/plugins/webhooks/demo/tour_generator/config.yml
@@ -1,4 +1,4 @@
-name: tour_generator
+id: tour_generator
 type:
   - onload
   - tool-menu
diff --git a/config/plugins/webhooks/demo/tour_generator/static/script.js b/config/plugins/webhooks/demo/tour_generator/script.js
similarity index 97%
rename from config/plugins/webhooks/demo/tour_generator/static/script.js
rename to config/plugins/webhooks/demo/tour_generator/script.js
index 4885e37a1bf..b5a499353b1 100644
--- a/config/plugins/webhooks/demo/tour_generator/static/script.js
+++ b/config/plugins/webhooks/demo/tour_generator/script.js
@@ -10,7 +10,7 @@ $(document).ready(function() {
                 $('#execute').attr('tour_id', 'execute');
 
                 Toastr.info('Tour generation might take some time.');
-                $.getJSON('/api/webhooks/tour_generator/get_data/', {
+                $.getJSON('/api/webhooks/tour_generator/data/', {
                     tool_id: me.toolId,
                     tool_version: me.toolVersion
                 }, function(obj) {
diff --git a/config/plugins/webhooks/demo/tour_generator/static/styles.css b/config/plugins/webhooks/demo/tour_generator/styles.css
similarity index 100%
rename from config/plugins/webhooks/demo/tour_generator/static/styles.css
rename to config/plugins/webhooks/demo/tour_generator/styles.css
diff --git a/doc/source/admin/framework_dependencies.rst b/doc/source/admin/framework_dependencies.rst
index d0d293a1539..15b9c88b386 100644
--- a/doc/source/admin/framework_dependencies.rst
+++ b/doc/source/admin/framework_dependencies.rst
@@ -3,55 +3,48 @@
 Framework Dependencies
 ======================
 
-Galaxy is a large Python application with a long list of `Python module
-dependencies`_. As a result, the Galaxy developers have made significant effort
-to provide these dependencies in as simple a method as possible. Prior to the
-16.01 release, this was done by distributing dependencies in Python's old
-standard packaging format (Egg) in a non-standard way. As of the 16.01 release,
-Galaxy now distributes dependencies in Python's new standard packaging format
-(Wheel), albeit still in a non-standard way. Thankfully, the new distribution
-method is far more compatible with the standard package distribution tooling
-(i.e. `pip`_) than the old method.
+Galaxy is a large Python application with a long list of `Python module dependencies`_. As a result, the Galaxy
+developers have made significant effort to provide these dependencies in as simple a method as possible while remaining
+compatible with the `Python packaging best practices`_. Thus, Galaxy's runtime setup procedure makes use of virtualenv_
+for package environment isolation, pip_ for installation, and wheel_ to provide pre-built versions of dependencies.
+
+In addition to framework dependencies, as of Galaxy 18.01, the client (UI) is no longer provided in its built format
+**in the development (``dev``) branch of the source repository**. The built client is still provided in
+``release_YY.MM`` branches and the ``master`` branch.
 
 .. _Python module dependencies: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/dependencies/requirements.txt
-.. _pip: https://pip.pypa.io/
-.. _wheel: https://wheel.readthedocs.org/
+.. _Python packaging best practices: https://packaging.python.org
+.. _virtualenv: https://packaging.python.org/tutorials/installing-packages/#creating-virtual-environments
+.. _pip: https://packaging.python.org/tutorials/installing-packages/#use-pip-for-installing
+.. _wheel: https://packaging.python.org/tutorials/installing-packages/#source-distributions-vs-wheels
 
 How it works
 ------------
 
 Upon startup (with ``run.sh``), the startup scripts will:
 
-1. Create a Python `virtualenv`_ in the directory ``.venv``.
+1. Create a Python virtualenv_ in the directory ``.venv``.
 
-2. Unset the ``$PYTHONPATH`` environment variable (if set) as this can
-   interfere with installing `Galaxy pip`_ and dependencies.
+2. Unset the ``$PYTHONPATH`` environment variable (if set) as this can interfere with installing dependencies.
 
-3. Replace that virtualenv's pip with `Galaxy pip`_.
+3. Download and install packages from the Galaxy project wheel server, wheels.galaxyproject.org_, as well as the `Python
+   Package Index`_ (aka PyPI) , using pip_.
 
-4. If applicable, create a ``binary-compatibility.cfg`` (see the `Galaxy pip
-   and wheel`_ section for an explanation of this file).
+4. Start Galaxy using ``.venv/bin/python``.
 
-5. Download and install wheels from the Galaxy project wheel server,
-   `wheels.galaxyproject.org`_, using pip.
-
-6. Start Galaxy using ``.venv/bin/python``.
-
-.. _virtualenv: https://virtualenv.readthedocs.org/
 .. _wheels.galaxyproject.org: https://wheels.galaxyproject.org/
+.. _Python Package Index: https://pypi.org
 
 Options
 -------
 
 A variety of options to ``run.sh`` are available to control the above behavior:
 
-- ``--skip-venv``: Do not create or use a virtualenv, and do not replace pip
-  with Galaxy pip.
+- ``--skip-venv``: Do not create or use a virtualenv.
 - ``--skip-wheels``: Do not install wheels.
-- ``--no-create-venv``: Do not create a virtualenv, but use one if it exists at
-  ``.venv`` or if ``$VIRTUAL_ENV`` is set (this variable is set by virtualenv's
-  ``activate``)
-- ``--replace-pip/--no-replace-pip``: Do/do not replace pip with Galaxy pip.
+- ``--no-create-venv``: Do not create a virtualenv, but use one if it exists at ``.venv`` or if ``$VIRTUAL_ENV`` is set
+  (this variable is set by virtualenv's ``activate``).
+- ``--replace-pip/--no-replace-pip``: Do/do not upgrade pip if necessary.
 
 Managing dependencies manually
 ------------------------------
@@ -59,29 +52,23 @@ Managing dependencies manually
 Create a virtualenv
 ^^^^^^^^^^^^^^^^^^^
 
-Using a `virtualenv`_ in ``.venv`` under the Galaxy source tree is not
-required. More complicated Galaxy setups may choose to use a virtualenv
-external to the Galaxy source tree, which can be done either by not using
-``run.sh`` directly (an example of this can be found under the `Supervisor`_
-section) or using the ``--no-create-venv`` option, explained in the `Options`_
-section. It is also possible to force Galaxy to start without a virtualenv at
-all, but you should not do this unless you know what you're doing.
+Using a `virtualenv`_ in ``.venv`` under the Galaxy source tree is not required. More complicated Galaxy setups may
+choose to use a virtualenv external to the Galaxy source tree, which can be done either by not using ``run.sh`` directly
+(an example of this can be found under the `Scaling and Load Balancing` documentation) or using the ``--no-create-venv``
+option, explained in the `Options` section. It is also possible to force Galaxy to start without a virtualenv at all,
+but you should not do this unless you know what you're doing.
 
-To manually create a virtualenv, you will first need to obtain virtualenv.
-There are a variety of ways to do this:
+To manually create a virtualenv, you will first need to obtain virtualenv.  There are a variety of ways to do this:
 
 - ``pip install virtualenv``
 - ``brew install virtualenv``
-- Install your Linux distribution's virtualenv package from the system package
-  manager (e.g. ``apt-get install python-virtualenv``).
-- Download the `virtualenv source from PyPI
-  <https://pypi.python.org/pypi/virtualenv>`_, untar, and run the
-  ``virtualenv.py`` script contained within as ``python virtualenv.py
-  /path/to/galaxy/virtualenv``
+- Install your Linux distribution's virtualenv package from the system package manager (e.g. ``apt-get install
+  python-virtualenv``).
+- Download the `virtualenv source from PyPI <https://pypi.python.org/pypi/virtualenv>`_, untar, and run the
+  ``virtualenv.py`` script contained within as ``python virtualenv.py /path/to/galaxy/virtualenv``
 
-Once this is done, create a virtualenv. In our example, the virtualenv will
-live in ``/srv/galaxy/venv`` and the Galaxy source code has been cloned to
-``/srv/galaxy/server``.
+Once this is done, create a virtualenv. In our example, the virtualenv will live in ``/srv/galaxy/venv`` and the Galaxy
+source code has been cloned to ``/srv/galaxy/server``.
 
 .. code-block:: console
 
@@ -91,550 +78,316 @@ live in ``/srv/galaxy/venv`` and the Galaxy source code has been cloned to
     $ . /srv/galaxy/venv/bin/activate
     (venv)$
 
+Next, in ``galaxy.yml``, set the ``virtualenv`` option in the ``uwsgi`` section to point to your new virtualenv:
+
+.. code-block:: yaml
+
+    ---
+    uwsgi:
+        #...
+        virtualenv: /srv/galaxy/venv
+
 Install dependencies
 ^^^^^^^^^^^^^^^^^^^^
 
-Normally, ``run.sh`` calls `common_startup.sh`_, which creates the virtualenv,
-installs Galaxy pip, and installs dependencies. You can call this script
-yourself to set up Galaxy pip and the dependencies without creating a
-virtualenv using the ``--no-create-venv`` option:
+Normally, ``run.sh`` calls `common_startup.sh`_, which creates the virtualenv and installs dependencies. You can call
+this script yourself to set up Galaxy pip and the dependencies without creating a virtualenv using the
+``--no-create-venv`` option:
 
 .. code-block:: console
 
     (venv)$ PYTHONPATH= sh /srv/galaxy/server/scripts/common_startup.sh --no-create-venv
-    Ignoring indexes: https://pypi.python.org/simple
-    Collecting pip
-      Downloading https://wheels.galaxyproject.org/packages/pip-8.0.0+gx1-py2.py3-none-any.whl (1.2MB)
-        100% |████████████████████████████████| 1.2MB 37.8MB/s
-    Installing collected packages: pip
-      Found existing installation: pip 7.1.2
-        Uninstalling pip-7.1.2:
-          Successfully uninstalled pip-7.1.2
-    Successfully installed pip-8.0.0+gx1
-    Collecting bx-python==0.7.3 (from -r requirements.txt (line 2))
-      Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-linux_x86_64.whl (1.7MB)
-        100% |████████████████████████████████| 1.7MB 25.4MB/s
+    Requirement already satisfied: pip>=8.1 in /home/nate/.virtualenvs/test/lib/python2.7/site-packages
+    Collecting numpy==1.9.2 (from -r requirements.txt (line 4))
+      Downloading https://wheels.galaxyproject.org/packages/numpy-1.9.2-cp27-cp27mu-manylinux1_x86_64.whl (10.2MB)
+        100% |████████████████████████████████| 10.2MB 21.7MB/s 
+    Collecting bx-python==0.7.3 (from -r requirements.txt (line 5))
+      Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-manylinux1_x86_64.whl (2.1MB)
+        100% |████████████████████████████████| 2.2MB 97.2MB/s 
 
-    ...
+        ...
 
-    Collecting pysam==0.8.3+gx1 (from -r requirements.txt (line 69))
-      Downloading https://wheels.galaxyproject.org/packages/pysam-0.8.3+gx1-cp27-cp27mu-linux_x86_64.whl (7.4MB)
-        100% |████████████████████████████████| 7.4MB 15.1MB/s
-    Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy,
-      mercurial, numpy, pycrypto, six, Paste, PasteDeploy, docutils, wchartype,
-      repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker,
-      Markdown, Cheetah, requests, requests-toolbelt, boto, bioblend, amqp,
-      anyjson, kombu, pbr, sqlparse, decorator, Tempita, sqlalchemy-migrate,
-      Parsley, nose, svgwrite, ecdsa, paramiko, Fabric, Whoosh, pysam
-    Successfully installed Babel-2.0 Beaker-1.7.0 Cheetah-2.4.4 Fabric-1.10.2
-      Mako-1.0.2 Markdown-2.6.3 MarkupSafe-0.23 Parsley-1.3 Paste-2.0.2
-      PasteDeploy-1.5.2 PyYAML-3.11 Routes-2.2 SQLAlchemy-1.0.8 svgwrite-1.1.6
-      Tempita-0.5.3.dev0 WebHelpers-1.3 WebOb-1.4.1 Whoosh-2.4.1+gx1 amqp-1.4.8
-      anyjson-0.3.3 bioblend-0.6.1 boto-2.38.0 bx-python-0.7.3 decorator-4.0.2
-      docutils-0.12 ecdsa-0.13 kombu-3.0.30 mercurial-3.4.2 nose-1.3.7
-      numpy-1.9.2 paramiko-1.15.2 pbr-1.8.0 pycrypto-2.6.1 pysam-0.8.3+gx1
-      pytz-2015.4 repoze.lru-0.6 requests-2.8.1 requests-toolbelt-0.4.0
-      six-1.9.0 sqlalchemy-migrate-0.10.0 sqlparse-0.1.16 wchartype-0.1
+    Installing collected packages: numpy, bx-python, ...
+    Successfully installed numpy-1.9.2 bx-python-0.7.3 ...
 
-**Warning:** If your ``$PYTHONPATH`` is set, it may interfere with the
-dependency installation process (this will almost certainly be the case if you
-use `virtualenv-burrito`_). Without ``--no-create-venv`` the ``$PYTHONPATH``
-variable will be automatically unset, but we assume you know what you're doing
-and may want it left intact if you are using ``--no-create-venv``. If you
-encounter problems, try unsetting ``$PYTHONPATH`` as shown in the example
-above.
+.. warning::
+
+    If your ``$PYTHONPATH`` is set, it may interfere with the dependency installation process. Without
+    ``--no-create-venv`` the ``$PYTHONPATH`` variable will be automatically unset, but we assume you know what you're
+    doing and may want it left intact if you are using ``--no-create-venv``. If you encounter problems, try unsetting
+    ``$PYTHONPATH`` as shown in the example above.
 
 .. _common_startup.sh: https://github.com/galaxyproject/galaxy/blob/dev/scripts/common_startup.sh
-.. _virtualenv-burrito: https://github.com/brainsik/virtualenv-burrito
 
 Installing unpinned dependencies
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Galaxy's dependencies can be installed either "pinned" (they will be installed
-at exact versions specified for your Galaxy release) or "unpinned" (the latest
-versions of all dependencies will be installed unless there are known
-incompatibilities with new versions). By default, the release branch(es) of
-Galaxy use pinned versions for three reasons:
+Galaxy's dependencies can be installed either "pinned" (they will be installed at exact versions specified for your
+Galaxy release) or "unpinned" (the latest versions of all dependencies will be installed unless there are known
+incompatibilities with new versions). By default, the release branches of Galaxy use pinned versions for three reasons:
 
-1. Using pinned versions insures that the prebuilt wheels on
-   `wheels.galaxyproject.org`_ will be installed, and no compilation will be
-   necesseary.
+1. Using pinned versions insures that the prebuilt wheels on `wheels.galaxyproject.org`_ will be installed, and no
+   compilation will be necesseary.
 
-2. Galaxy releases are tested with the pinned versions and this allows us to
-   give as much assurance as possible that the pinned versions will work with
-   the given Galaxy release (especially as time progresses and newer dependency
-   versions are released while the Galaxy release receives fewer updates.
+2. Galaxy releases are tested with the pinned versions and this allows us to give as much assurance as possible that the
+   pinned versions will work with the given Galaxy release (especially as time progresses and newer dependency versions
+   are released while the Galaxy release receives fewer updates.
 
-3. Pinning furthers Galaxy's goal of reproducibility as differing dependency
-   versions could result in non-reproducible behavior.
+3. Pinning furthers Galaxy's goal of reproducibility as differing dependency versions could result in non-reproducible
+   behavior.
 
-Install dependencies using the `unpinned requirements file`_, and then instruct
-Galaxy to start without attempting to fetch wheels:
+If you would like to install unpinned versions of Galaxy's dependencies, install dependencies using the `unpinned
+requirements file`_, and then instruct Galaxy to start without attempting to fetch wheels:
 
 .. code-block:: console
 
-    (venv)$ pip install --index-url=https://wheels.galaxyproject.org/simple/ -r lib/galaxy/dependencies/requirements.txt
+    (venv)$ pip install -r lib/galaxy/dependencies/requirements.txt
     (venv)$ deactivate
     $ sh run.sh --no-create-venv --skip-wheels
 
-Including ``--index-url=https://wheels.galaxyproject.org/simple/`` is important
-as two dependencies (pysam, Whoosh) include modifications specific to Galaxy
-which are only available on `wheels.galaxyproject.org`_.
+You may be able to save yourself some compiling by adding the argument ``--index-url
+https://wheels.galaxyproject.org/simple/`` to ``pip install``, but it is possible to install all of Galaxy's
+dependencies directly from PyPI_.
 
 .. _unpinned requirements file: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/dependencies/requirements.txt
+.. _PyPI: https://pypi.org
 
-Wheel interaction with other software
--------------------------------------
+Dependency management complications
+-----------------------------------
+
+Certain deployment scenarios or other software may complicate Galaxy dependency management. If you use any of these,
+relevant information can be found in the corresponding subsection below.
 
 Galaxy job handlers
 ^^^^^^^^^^^^^^^^^^^
 
-All Galaxy jobs run a metadata detection step on the job outputs upon
-completion of the tool. The metadata detection step requires many of Galaxy's
-dependencies. Because of this, it's necessary to make sure the metadata
-detection step runs in Galaxy's virtualenv. If you run a relatively simple
-Galaxy setup (e.g. single process, or multiple Python Paste processes started
-using ``run.sh``) then this is assured for you automatically. In more
-complicated setups (supervisor, the "headless" Galaxy handler, and/or the
-virtualenv used to start Galaxy is not a shared filesystem) it may be necessary
-to make sure the handlers know where the virtualenv (or a virtualenv containing
-Galaxy's dependencies) can be found.
+All Galaxy jobs run a metadata detection step on the job outputs upon completion of the tool. The metadata detection
+step requires many of Galaxy's dependencies. Because of this, it's necessary to make sure the metadata detection step
+runs in Galaxy's virtualenv. If you run a relatively simple Galaxy deployment (e.g. ``run.sh``) then this is assured for
+you automatically. In more complicated setups (running under supervisor and/or the virtualenv used to start Galaxy is
+not on a shared filesystem) it may be necessary to make sure the handlers know where the virtualenv (or a virtualenv
+containing Galaxy's dependencies) can be found.
 
-If your jobs are failing due to Python ``ImportError`` exceptions, this is most
-likely the problem. If so, you can use the ``<env>`` tag in ``job_conf.xml`` to
-source the virtualenv. For example:
+If the virtualenv cannot be located, you will see job failures due to Python ``ImportError`` exceptions, like so:
+
+.. code-block:: pytb
+
+	Traceback (most recent call last):
+	  File "/srv/galaxy/tmp/job_working_directory/001/set_metadata_RK41sy.py", line 1, in <module>
+		from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
+	  File "/srv/galaxy/server/lib/galaxy_ext/metadata/set_metadata.py", line 23, in <module>
+		from sqlalchemy.orm import clear_mappers
+	ImportError: No module named sqlalchemy.orm
+
+If this is the case, you can instruct jobs to activate the virtualenv with an ``env`` tag in ``job_conf.xml``:
 
 .. code-block:: xml
 
-    <job_conf>
-        <plugins>
-            ...
-        </plugins>
-        <destinations default="cluster">
-            <destination id="cluster" runner="drmaa">
-                <param id="nativeSpecification"> ...cluster options... </param>
+    <destination id="cluster" runner="drmaa">
+        <!-- ... other destination params -- >
+        <env file="/cluster/galaxy/venv/bin/activate" />
+    </destination>
 
-                <env file="/galaxy/server/.venv/bin/activate" />
-
-            </destination>
-        </destinations>
-    </job_conf>
-
-If your Galaxy server's virtualenv isn't available on the cluster you can
-create one manually using the instructions under `Managing dependencies
-manually`_.
+If your Galaxy server's virtualenv isn't available on the cluster you can create one manually using the instructions
+under `Managing dependencies manually`_.
 
 Pulsar
 ^^^^^^
 
-If using `Pulsar`_'s option to set metadata on the remote server, the same
-conditions as with `Galaxy job handlers`_ apply. You should create a virtualenv
-on the remote resource, install Galaxy's dependencies in to it, and set an
-``<env>`` tag pointing to the virtualenv's ``activate`` as in the `Galaxy job
-handlers`_ section. Instructions on how to create a virtualenv can be found
-under the `Managing dependencies manually`_ section.
+If using `Pulsar`_'s option to set metadata on the remote server, the same conditions as with `Galaxy job handlers`_
+apply. You should create a virtualenv on the remote resource, install Galaxy's dependencies in to it, and set an
+``<env>`` tag pointing to the virtualenv's ``activate`` as in the `Galaxy job handlers`_ section. Instructions on how to
+create a virtualenv can be found under the `Managing dependencies manually`_ section.
 
 .. _Pulsar: http://pulsar.readthedocs.org/
 
 Conda
 ^^^^^
 
-`Conda`_ and `virtualenv`_ are incompatible. However, Conda provides its own
-environment separation functionality in the form of `Conda environments`_.
-Starting Galaxy with Conda Python will cause ``--skip-venv`` to be implicitly
-set, and the currently active Conda environment will be used to install Galaxy
-framework dependencies instaead.  Be sure to create and activate a Conda
-environment for Galaxy prior to installing packages and/or starting Galaxy.
+`Conda`_ and `virtualenv`_ are incompatible. However, Conda provides its own environment separation functionality in the
+form of `Conda environments`_.  Starting Galaxy with Conda Python will cause ``--skip-venv`` to be implicitly set, and
+the currently active Conda environment will be used to install Galaxy framework dependencies instead.
 
-You may choose to install Galaxy's dependencies either at their `pinned`_
-versions using pip or `unpinned`_ using a combination of conda and pip. When
-running under Conda, pip is not replaced with Galaxy pip, so installing pinned
-dependencies will require compilation, will be slower and requires having those
-dependencies' build-time dependencies installed, but has benefits as explained
-under the `Installing unpinned dependencies`_ section.  Installing unpinned
-dependencies allows you to use Conda's binary packages for quick and easy
-installation.
+.. caution::
 
-Pinned dependencies will be installed by default when running ``run.sh``. To
-install unpinned dependencies, the process is similar as to installing unpinned
-versions without Conda, with the extra step of installing as much as possible
-from Conda/Bioconda before installing from pip. Begin by adding the `Bioconda`_
-channel as explained in the `Bioconda instructions`_ and then creating a new
-Conda environment using the provided Conda environment file. Then, install
-remaining dependencies using pip and start Galaxy, instructing it to skip the
-automatic fetching of pinned dependencies.
+    Be sure to create and activate a Conda environment for Galaxy prior to installing packages and/or starting Galaxy or
+    else they will be installed in the Conda root environment.
+
+Because Conda package names typically match PyPI package names, you can install Conda versions of what dependencies are
+available from conda-forge_ and Bioconda_ using a script provided with Galaxy:
 
 .. code-block:: console
 
-    $ conda config --add channels r
+    $ conda config --add channels conda-forge
     $ conda config --add channels bioconda
-    $ conda create --name galaxy --file lib/galaxy/dependencies/conda-environment.txt
-    Fetching package metadata: ........
-    Solving package specifications: ............................................
-    Package plan for installation in environment /home/nate/conda/envs/galaxy:
+    $ conda create --name galaxy --file <(lib/galaxy/dependencies/conda-file.sh)
+    Filtering out requirements not available in conda... done
+    Solving environment: done
 
-    The following packages will be downloaded:
+    ## Package Plan ##
+
+      environment location: /srv/galaxy/conda/envs/galaxy
+
+      added / updated specs: 
+        - anyjson==0.3.3
+        #...
+        - whoosh==2.7.4
 
-        package                    |            build
-        ---------------------------|-----------------
-        boto-2.38.0                |           py27_0         1.3 MB
-        cheetah-2.4.4              |           py27_0         267 KB
-        decorator-4.0.6            |           py27_0          11 KB
-        docutils-0.12              |           py27_0         636 KB
-        ecdsa-0.11                 |           py27_0          73 KB
-        markupsafe-0.23            |           py27_0          30 KB
-        mercurial-3.4.2            |           py27_0         2.9 MB
-        nose-1.3.7                 |           py27_0         194 KB
-        paste-1.7.5.1              |           py27_0         490 KB
-        pytz-2015.7                |           py27_0         174 KB
-        repoze.lru-0.6             |           py27_0          15 KB
-        requests-2.9.1             |           py27_0         605 KB
-        six-1.10.0                 |           py27_0          16 KB
-        sqlalchemy-1.0.11          |           py27_0         1.3 MB
-        sqlparse-0.1.18            |           py27_0          51 KB
-        webob-1.4.1                |           py27_0         108 KB
-        babel-2.1.1                |           py27_0         2.3 MB
-        bx-python-0.7.3            |      np110py27_1         2.1 MB
-        mako-1.0.3                 |           py27_0         105 KB
-        paramiko-1.15.2            |           py27_0         197 KB
-        pastedeploy-1.5.2          |           py27_1          23 KB
-        requests-toolbelt-0.5.0    |           py27_0          83 KB
-        routes-2.2                 |           py27_0          48 KB
-        bioblend-0.7.0             |           py27_0         181 KB
-        fabric-1.10.2              |           py27_0         108 KB
-        ------------------------------------------------------------
-                                               Total:        13.2 MB
 
     The following NEW packages will be INSTALLED:
 
-        babel:             2.1.1-py27_0
-        bioblend:          0.7.0-py27_0
-        boto:              2.38.0-py27_0
-        bx-python:         0.7.3-np110py27_1
-        cheetah:           2.4.4-py27_0
-        decorator:         4.0.6-py27_0
-        docutils:          0.12-py27_0
-        ecdsa:             0.11-py27_0
-        fabric:            1.10.2-py27_0
-        libgfortran:       1.0-0
-        mako:              1.0.3-py27_0
-        markupsafe:        0.23-py27_0
-        mercurial:         3.4.2-py27_0
-        nose:              1.3.7-py27_0
-        numpy:             1.10.2-py27_0
-        openblas:          0.2.14-3
-        openssl:           1.0.2e-0
-        paramiko:          1.15.2-py27_0
-        paste:             1.7.5.1-py27_0
-        pastedeploy:       1.5.2-py27_1
-        pip:               7.1.2-py27_0
-        pycrypto:          2.6.1-py27_0
-        python:            2.7.11-0
-        pytz:              2015.7-py27_0
-        pyyaml:            3.11-py27_1
-        readline:          6.2-2
-        repoze.lru:        0.6-py27_0
-        requests:          2.9.1-py27_0
-        requests-toolbelt: 0.5.0-py27_0
-        routes:            2.2-py27_0
-        setuptools:        19.2-py27_0
-        six:               1.10.0-py27_0
-        sqlalchemy:        1.0.11-py27_0
-        sqlite:            3.9.2-0
-        sqlparse:          0.1.18-py27_0
-        tk:                8.5.18-0
-        webob:             1.4.1-py27_0
-        wheel:             0.26.0-py27_1
-        yaml:              0.1.6-0
-        zlib:              1.2.8-0
+        anyjson:            0.3.3-py27_1            conda-forge
+        #...
+        zlib:               1.2.8-3                 conda-forge
 
-    Proceed ([y]/n)?
+    Proceed ([y]/n)? 
 
-    Fetching packages ...
-    boto-2.38.0-py 100% |############################################| Time: 0:00:00   3.27 MB/s
-    cheetah-2.4.4- 100% |############################################| Time: 0:00:00   1.65 MB/s
-    decorator-4.0. 100% |############################################| Time: 0:00:00  20.38 MB/s
-    docutils-0.12- 100% |############################################| Time: 0:00:00   2.21 MB/s
-    ecdsa-0.11-py2 100% |############################################| Time: 0:00:00 762.58 kB/s
-    markupsafe-0.2 100% |############################################| Time: 0:00:00 931.23 kB/s
-    mercurial-3.4. 100% |############################################| Time: 0:00:00   5.36 MB/s
-    nose-1.3.7-py2 100% |############################################| Time: 0:00:00   1.12 MB/s
-    paste-1.7.5.1- 100% |############################################| Time: 0:00:00   1.91 MB/s
-    pytz-2015.7-py 100% |############################################| Time: 0:00:00   1.08 MB/s
-    repoze.lru-0.6 100% |############################################| Time: 0:00:00 465.26 kB/s
-    requests-2.9.1 100% |############################################| Time: 0:00:00   2.28 MB/s
-    six-1.10.0-py2 100% |############################################| Time: 0:00:00 477.04 kB/s
-    sqlalchemy-1.0 100% |############################################| Time: 0:00:00   4.25 MB/s
-    sqlparse-0.1.1 100% |############################################| Time: 0:00:00 774.57 kB/s
-    webob-1.4.1-py 100% |############################################| Time: 0:00:00 819.13 kB/s
-    babel-2.1.1-py 100% |############################################| Time: 0:00:00   5.53 MB/s
-    bx-python-0.7. 100% |############################################| Time: 0:00:00   5.11 MB/s
-    mako-1.0.3-py2 100% |############################################| Time: 0:00:00 813.04 kB/s
-    paramiko-1.15. 100% |############################################| Time: 0:00:00   1.23 MB/s
-    pastedeploy-1. 100% |############################################| Time: 0:00:00 721.20 kB/s
-    requests-toolb 100% |############################################| Time: 0:00:00 856.06 kB/s
-    routes-2.2-py2 100% |############################################| Time: 0:00:00 666.70 kB/s
-    bioblend-0.7.0 100% |############################################| Time: 0:00:00   1.15 MB/s
-    fabric-1.10.2- 100% |############################################| Time: 0:00:00 843.81 kB/s
-    Extracting packages ...
-    [      COMPLETE      ]|###############################################################| 100%
-    Linking packages ...
-    [      COMPLETE      ]|###############################################################| 100%
+    Preparing transaction: done
+    Verifying transaction: done
+    Executing transaction: done
     #
-    # To activate this environment, use:
-    # $ source activate galaxy
+    # To activate this environment, use
     #
-    # To deactivate this environment, use:
-    # $ source deactivate
+    #     $ conda activate galaxy
     #
-    $ source activate galaxy
-    discarding /home/nate/conda/bin from PATH
-    prepending /home/nate/conda/envs/galaxy/bin to PATH
-    $ pip install --index-url=https://wheels.galaxyproject.org/simple/ -r lib/galaxy/dependencies/requirements.txt
-    Requirement already satisfied (use --upgrade to upgrade): numpy in /home/nate/conda/envs/galaxy/lib/python2.7/site-packages (from -r lib/galaxy/dependencies/requirements.txt (line 1))
+    # To deactivate an active environment, use
+    #
+    #     $ conda deactivate
 
-      ...
+Next, activate the environment and run ``pip`` to fetch the remaining dependencies:
 
-    Collecting WebHelpers (from -r lib/galaxy/dependencies/requirements.txt (line 15))
-      Downloading https://wheels.galaxyproject.org/packages/WebHelpers-1.3-py2-none-any.whl (149kB)
-        100% |████████████████████████████████| 151kB 55.7MB/s
+.. code-block:: console
 
-      ...
+    $ conda activate galaxy
+    $ pip install --index-url https://wheels.galaxyproject.org/simple/ --extra-index-url https://pypi.python.org/simple/ -r requirements.txt
+    Requirement already satisfied: pip>=8.1 in /srv/galaxy/conda/envs/galaxy/lib/python2.7/site-packages
+    #...
+    Collecting SQLAlchemy==1.0.15 (from -r requirements.txt (line 8))
+      Downloading https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.15-cp27-cp27mu-manylinux1_x86_64.whl (1.0MB)
+        100% |████████████████████████████████| 1.0MB 48.6MB/s 
+    #...
+    Installing collected packages: SQLAlchemy, ...
+    Successfully installed SQLAlchemy-1.0.15 ...
 
-    Building wheels for collected packages: pysam
-      Running setup.py bdist_wheel for pysam
+``run.sh`` is not currently compatible with running without a virtualenv. In this case, you should start with uWSGI
+directly. Be sure to uncomment the required options in the ``uwsgi`` section of ``galaxy.yml`` since ``run.sh`` normally
+sets these for you on the command line:
 
-    $ sh run.sh --skip-wheels
+.. code-block:: console
+
+    $ uwsgi --yaml config/galaxy.yml
+    [uWSGI] getting YAML configuration from config/galaxy.yml
+    [uwsgi-static] added mapping for /static/style => static/style/blue
+    [uwsgi-static] added mapping for /static => static
+    *** Starting uWSGI 2.0.15 (64bit) on [Thu Jan 25 11:57:17 2018] ***
+
+You may encounter the following traceback when starting Galaxy:
+
+.. code-block:: pytb
+
+    Traceback (most recent call last):
+      File "lib/galaxy/main.py", line 278, in <module>
+        main()
+      File "lib/galaxy/main.py", line 274, in main
+        app_loop(args, log)
+      File "lib/galaxy/main.py", line 124, in app_loop
+        log=log,
+      File "lib/galaxy/main.py", line 91, in load_galaxy_app
+        from galaxy.app import UniverseApplication
+      File "/srv/galaxy/server/lib/galaxy/app.py", line 30, in <module>
+        from galaxy.visualization.data_providers.registry import DataProviderRegistry
+      File "/srv/galaxy/server/lib/galaxy/visualization/data_providers/registry.py", line 15, in <module>
+        from galaxy.visualization.data_providers import genome
+      File "/srv/galaxy/server/lib/galaxy/visualization/data_providers/genome.py", line 17, in <module>
+        from bx.bbi.bigbed_file import BigBedFile
+    ImportError: cannot import name BigBedFile
+
+If this is the case, uninstall bx-python from Conda and reinstall it from the Galaxy wheel:
+
+.. code-block:: console
+
+    $ conda remove bx-python
+    Solving environment: done
+
+    ## Package Plan ##
+
+      environment location: /srv/galaxy/conda/envs/galaxy
+
+      removed specs: 
+        - bx-python
+
+
+    The following packages will be REMOVED:
+
+        bx-python: 0.7.3-py27_0 bioconda
+
+    Proceed ([y]/n)? 
+
+    Preparing transaction: done
+    Verifying transaction: done
+    Executing transaction: done
+    $ pip install --index-url https://wheels.galaxyproject.org/simple bx-python
+    Collecting bx-python
+      Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-manylinux1_x86_64.whl (2.1MB)
+        100% |████████████████████████████████| 2.2MB 66.1MB/s 
+    Installing collected packages: bx-python
+    Successfully installed bx-python-0.7.3
 
 .. _Conda: http://conda.pydata.org/
 .. _Conda environments: http://conda.pydata.org/docs/using/envs.html
+.. _conda-forge: https://conda-forge.org/
 .. _Bioconda: https://bioconda.github.io/
-.. _Bioconda instructions: Bioconda_
-.. _pinned: `Installing unpinned dependencies`_
-.. _unpinned: pinned_
 
 uWSGI
 ^^^^^
 
-The simplest scenario to using uWSGI with the wheel-based dependencies is to
-install uWSGI into Galaxy virtualenv (by default, ``.venv``) using pip, e.g.:
+``run.sh`` should automatically set ``--virtualenv`` on uWSGI's command line. However, you can override this using the
+``virtualenv`` option in the ``uwsgi`` section of ``galaxy.yml`` as described in the `Managing dependencies manually`_
+section.
 
-.. code-block:: console
+Adding additional Galaxy dependencies
+-------------------------------------
 
-    $ . ./.venv/bin/activate
-    (.venv)$ pip install uwsgi
-    Collecting uwsgi
-      Downloading uwsgi-2.0.12.tar.gz (784kB)
-        100% |████████████████████████████████| 786kB 981kB/s
-    Building wheels for collected packages: uwsgi
-      Running setup.py bdist_wheel for uwsgi
-      Stored in directory: /home/nate/.cache/pip/wheels/a4/7b/7c/8cbe2fe2c2b963173361cc18aa726f165dc4803effbb8195fc
-    Successfully built uwsgi
-    Installing collected packages: uwsgi
-    Successfully installed uwsgi-2.0.12
+New packages can be added to Galaxy, or the versions of existing packages can be updated, using `pipenv`_ and `Galaxy
+Starforge`_, Galaxy's Docker-based build system.
 
-Because uWSGI is installed in the virtualenv, Galaxy's dependencies will be
-found upon startup.
+.. note::
 
-If uWSGI is installed outside of the virtualenv (e.g. from apt) you will need
-to pass the ``-H`` option (or one of `its many aliases
-<http://uwsgi-docs.readthedocs.org/en/latest/Options.html#home>`_) on the uWSGI
-command line:
+    Dependency pinning management is being migrated to pipenv_. As of this release, pinning for packages used for Galaxy
+    development are managed by pipenv_, but pinning for regular runtime packages are still managed with manual changes
+    to ``pinned-requirements.txt``. See `Pull Request #4891`_ for details.
 
-.. code-block:: console
+The process is still under development and will be streamlined and automated over time. For the time being, please use
+the following process to add new packages and have their wheels built:
 
-    $ uwsgi --ini /srv/galaxy/config/uwsgi.ini -H /srv/galaxy/venv
+1. Install `Starforge`_ (e.g. with ``pip install starforge`` or ``python setup.py install`` from the source). You will
+   also need to have Docker installed on your system.
 
-Or in the uWSGI config file:
+2. Obtain `wheels.yml`_ (this file will most likely be moved in to Galaxy in the future) and add/modify the wheel
+   definition.
 
-.. code-block:: ini
+3. Use ``starforge wheel --wheels-config=wheels.yml <wheel-name>`` to build the wheel. If the wheel includes C
+   extensions, you will probably want to also use the ``--no-qemu`` flag to prevent Starforge from attempting to build
+   on Mac OS X using QEMU/KVM.
 
-    [uwsgi]
-    processes = 8
-    threads = 4
-    socket = /srv/galaxy/var/uwgi.sock
-    logto = /srv/galaxy/var/uwsgi.log
-    master = True
-    pythonpath = /srv/galaxy/server/lib
-    pythonhome = /srv/galaxy/venv
-    module = galaxy.webapps.galaxy.buildapp:uwsgi_app_factory()
-    set = galaxy_config_file=/srv/galaxy/config/galaxy.ini
-    set = galaxy_root=/srv/galaxy/server
+4. If the wheel build is successful, submit a pull request to `Starforge`_ with your changes to `wheels.yml`_.
 
-Supervisor
-^^^^^^^^^^
+5. A `Galaxy Committers group`_ member will need to trigger an automated build of the wheel changes in your pull
+   request. Galaxy's Jenkins_ service will build these changes using Starforge.
 
-Many production sites use `supervisord`_ to manage their Galaxy processes
-rather than relying on ``run.sh`` or other means. There's no simple way to
-activate a virtualenv when using supervisor, but you can simulate the effects
-by setting ``$PATH`` and ``$VIRTUAL_ENV`` in your supervisor config:
+6. If the pull request is merged, submit a pull request to Galaxy modifying the files in `lib/galaxy/dependencies`_ as
+   appropriate.
 
-.. code-block:: ini
-
-    [program:galaxy_uwsgi]
-    command         = /srv/galaxy/venv/bin/uwsgi --ini /srv/galaxy/config/uwsgi.ini
-    directory       = /srv/galaxy/server
-    environment     = VIRTUAL_ENV="/srv/galaxy/venv",PATH="/srv/galaxy/venv/bin:%(ENV_PATH)s"
-    numprocs        = 1
-
-    [program:galaxy_handler]
-    command         = /srv/galaxy/venv/bin/python ./scripts/galaxy-main -c /srv/galaxy/config/galaxy.ini --server-name=handler%(process_num)s
-    directory       = /srv/galaxy/server
-    process_name    = handler%(process_num)s
-    numprocs        = 4
-    environment     = VIRTUAL_ENV="/srv/galaxy/venv",PATH="/srv/galaxy/venv/bin:%(ENV_PATH)s"
-
-With supervisor < 3.0 you cannot use the ``%(ENV_PATH)s`` template variable and
-must instead specify the full desired ``$PATH``.
-
-.. _supervisord: http://supervisord.org/
-
-Custom pip/wheel rationale
---------------------------
-
-We chose to use a modified version of the `pip`_ and `wheel`_ packages in order
-to make Galaxy easy to use. People wishing to run Galaxy (especially only for
-tool development) may not be systems or command line experts. Unfortunately,
-Python modules with C extensions may not always compile out of the box
-(typically due to missing compilers, headers, or other system packages) and the
-failure messages generated are typically only decipherable to people
-experienced with software compilation and almost never indicate how to fix the
-problem. In addition, the process of compiling all of Galaxy's C extension
-dependencies can be very long if it does succeed. As a result, we want to
-precompile Galaxy's dependencies. However, the egg format was never prepared
-for doing this on any platform and wheels could not do it on Linux because
-there is no ABI compatibility between Linux distributions or versions.
-
-As a benefit of using the standard tooling (pip), if you choose not to use
-Galaxy pip, all of Galaxy's dependencies should still be installable using
-standard pip. You will still need to point pip at `wheels.galaxyproject.org`_
-in order to fetch some modified packages and ones that aren't available on
-PyPI, but this can be done with the unmodified version of pip.
-
-A good early discussion of these problems can be found in Armin Ronacher's
-`blog post on wheels <http://lucumr.pocoo.org/2014/1/27/python-on-wheels/>`_.
-One of the problems Armin discusses, Python interpreter ABI incompatibilites
-depending on build-time options (UCS2 vs. UCS4), has been fixed by us and
-accepted into pip >= 8.0 in `pip pull request #3075`_. The other major problem
-(the non-portability of wheels between Linux distributions) remains. `Galaxy
-pip`_ provides one solution to this problem.
-
-More recently, the proposed `PEP 513`_ proposes a different solution to the
-cross-distro problem.  PEP 513 also contains a very detailed technical
-explanation of the problem.
-
-.. _PEP 513: https://www.python.org/dev/peps/pep-0513/
-.. _pip pull request #3075: https://github.com/pypa/pip/pull/3075
-
-Galaxy pip and wheel
---------------------
-.. _Galaxy pip:
-.. _Galaxy wheel: `Galaxy pip and wheel`_
-
-`Galaxy pip is a fork <https://github.com/natefoo/pip/tree/linux-wheels>`_ of
-`pip`_ in which we have added support for installing wheels containing C
-extensions (wheels that have compiled binary code) on Linux.  `Galaxy wheel is
-a fork <https://bitbucket.org/natefoo/wheel>`_ of `wheel`_ in which we have
-added support for building wheels installable with Galaxy pip.
-
-Two different types of wheels can be created:
-
-1. "Simple" wheels with very few dependencies outside of libc and libm built on
-   a "suitably old" platform (currently Debian Squeeze) such that they should
-   work on all newer systems (e.g. RHEL 6+, Ubuntu 12.04+). These wheels carry
-   the unmodified ``linux_{arch}`` platform tag (e.g. ``linux_x86_64``) as
-   specified in `PEP 425`_ and that you will find on wheels built with an
-   unmodified `wheel`_.
-
-2. Wheels with specific external dependencies (for example, ``libpq.so``, the
-   PostgreSQL library, used by `psycopg2`_) can be built on each supported
-   Linux distribution and tagged more specifically for each distribution. These
-   wheels carry a ``linux_{arch}_{distro}_{version}`` platform tag (e.g.
-   ``linux_x86_ubuntu_14_04``) and can be created using `Galaxy wheel`_.
-
-The `manylinux`_ project implements the "Simple" wheels in a more clearly
-defined way and allows for the inclusion of "non-standard" external
-dependencies directly into the wheel. Galaxy will officially support any
-standard which allows for Linux wheels in PyPI once such a standard is
-complete.
-
-.. _PEP 425: https://www.python.org/dev/peps/pep-0425/
-.. _manylinux: https://github.com/manylinux/manylinux/
-.. _psycopg2: http://initd.org/psycopg/
-
-Wheel platform compatibility
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Galaxy pip and Galaxy wheel also include support for the proposed
-`binary-compatibility.cfg`_ file. This file allows distributions that are
-binary compatibile (e.g. Red Hat Enterprise Linux 6 and CentOS 6) to use the
-same wheels.
-
-This is a JSON format file which can be installed in ``/etc/python`` or the
-root of a virtualenv (`common_startup.sh`_ creates it here) and provides a
-mapping between `PEP 425`_ platform tags. For example, the following
-``binary-compatibility.cfg`` indicates that wheels built on the platform
-``linux_x86_centos_6_7`` will have their platform tag overridden to
-``linux_x86_rhel_6``. In addition, wheels tagged with ``linux_x86_64_rhel_6_7``
-and ``linux_x86_64_rhel_6`` will be installable on a ``linux_x86_centos_6_7``
-system:
-
-.. code-block:: json
-
-    {
-        "linux_x86_64_centos_6_7": {
-            "build": "linux_x86_64_rhel_6",
-            "install": ["linux_x86_64_rhel_6_7", "linux_x86_64_rhel_6"]
-        }
-    }
-
-Currently, Scientific Linux, CentOS, and Red Hat Enterprise Linux will be set
-as binary compatible by `common_startup.sh`_.
-
-.. _binary-compatibility.cfg: https://mail.python.org/pipermail/distutils-sig/2015-July/026617.html
-
-Adding additional wheels as Galaxy dependencies
------------------------------------------------
-
-New wheels can be added to Galaxy, or the versions of existing wheels can be
-updated, using `Galaxy Starforge`_, Galaxy's Docker-based build system.
-
-The process is still under development and will be streamlined and automated
-over time. For the time being, please use the following process to add new
-wheels:
-
-1. Install `Starforge`_ (e.g. with ``pip install starforge`` or ``python
-   setup.py install`` from the source). You will also need to have Docker
-   installed on your system.
-
-2. Obtain `wheels.yml`_ (this file will most likely be moved in to Galaxy in
-   the future) and add/modify the wheel definition.
-
-3. Use ``starforge wheel --wheels-config=wheels.yml <wheel-name>`` to build the
-   wheel. If the wheel includes C extensions, you will probably want to also
-   use the ``--no-qemu`` flag to prevent Starforge from attempting to build on
-   Mac OS X using QEMU/KVM.
-
-4. If the wheel build is successful, submit a pull request to `Starforge`_ with
-   your changes to `wheels.yml`_.
-
-5. A `Galaxy Committers group`_ member will need to trigger an automated build
-   of the wheel changes in your pull request. Galaxy's Jenkins_ service will
-   build these changes using Starforge.
-
-6. If the pull request is merged, submit a pull request to Galaxy modifying the
-   files in `lib/galaxy/dependencies`_ as appropriate.
-
-You may attempt to skip directly to step 4 and let the Starforge wheel PR
-builder build your wheels for you. This is especially useful if you are simply
-updating an existing wheel's version. However, if you are adding a new C
-extension wheel that is not simple to build, you may need to go through many
-iterations of updating the PR and having a `Galaxy Committers group`_ member
-triggering builds before wheels are successfully built. You can avoid this
-cycle by performing steps 1-3 locally.
+You may attempt to skip directly to step 4 and let the Starforge wheel PR builder build your wheels for you. This is
+especially useful if you are simply updating an existing wheel's version. However, if you are adding a new C extension
+wheel that is not simple to build, you may need to go through many iterations of updating the PR and having a `Galaxy
+Committers group`_ member triggering builds before wheels are successfully built. You can avoid this cycle by performing
+steps 1-3 locally.
 
+.. _pipenv: http://pipenv.readthedocs.io/
 .. _Starforge:
 .. _Galaxy Starforge: https://github.com/galaxyproject/starforge/
+.. _Pull Request #4891: https://github.com/galaxyproject/galaxy/pull/4891
 .. _wheels.yml: https://github.com/galaxyproject/starforge/blob/master/wheels/build/wheels.yml
 .. _Galaxy Committers group: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organization.rst#committers
 .. _Jenkins: https://jenkins.galaxyproject.org/
diff --git a/doc/source/admin/scaling.md b/doc/source/admin/scaling.md
index f504ff0e31f..418807774f9 100644
--- a/doc/source/admin/scaling.md
+++ b/doc/source/admin/scaling.md
@@ -510,7 +510,7 @@ If using the **uWSGI + Webless** scenario, you'll need to addtionally define job
 
 ```ini
 [program:handler]
-command         = python ./scripts/galaxy-main -c /srv/galaxy/config/galaxy.yml --server-name=handler%(process_num)s --pid-file=/srv/galaxy/var/handler%(process_num)s.pid --log-file=/srv/galaxy/log/handler%(process_num)s.log
+command         = /srv/galaxy/venv/bin/python ./scripts/galaxy-main -c /srv/galaxy/config/galaxy.yml --server-name=handler%(process_num)s --pid-file=/srv/galaxy/var/handler%(process_num)s.pid --log-file=/srv/galaxy/log/handler%(process_num)s.log
 directory       = /srv/galaxy/server
 process_name    = handler%(process_num)s
 numprocs        = 3
@@ -519,6 +519,7 @@ autostart       = true
 autorestart     = true
 startsecs       = 15
 user            = galaxy
+environment     = VIRTUAL_ENV="/srv/galaxy/venv",PATH="/srv/galaxy/venv/bin:%(ENV_PATH)s"
 ```
 
 This is similar to the "web" definition above, however, you'll notice that we use `%(process_num)s`. That's a variable
diff --git a/doc/source/admin/special_topics/webhooks.rst b/doc/source/admin/special_topics/webhooks.rst
index 98164fe6ba4..51404cd2971 100644
--- a/doc/source/admin/special_topics/webhooks.rst
+++ b/doc/source/admin/special_topics/webhooks.rst
@@ -64,21 +64,17 @@ Each plugin has the following folder structure:
 .. code-block::
 
    - plugin_name
-      - config
-         - plugin_name.yaml (mandatory)
-      - helper
-         - __init__.py (optional)
-      - static
-         - script.js (optional)
-         - styles.css (optional)
+      - config.yml (mandatory)
+      - __init__.py (optional)
+      - script.js (optional)
+      - styles.css (optional)
 
-
-config
-------
+config.yml
+----------
 
 The configuration file is just a .yml (or .yaml) file with a few options. The following options are mandatory:
 
-- **name** - must be the same as the plugin's root directory name
+- **id** - must be the same as the plugin's root directory name
 - **type** (see Entry points) - can be combined with others
 - **activate** - *true* or *false* - whether show the plugin on a page or not
 - **icon** Icon to show (if masthead)
@@ -88,8 +84,8 @@ The configuration file is just a .yml (or .yaml) file with a few options. The fo
 All other options can be anything used by the plugin and accessed later via *webhook.config['...']*.
 
 
-helper/__init__.py
-------------------
+__init__.py
+-----------
 
 *__init__.py has* to have the **main()** function with the following (or similar) structure:
 
@@ -116,10 +112,8 @@ helper/__init__.py
 As an example please take a look at the *phdcomics* example plugin: https://github.com/galaxyproject/galaxy/blob/release_17.05/test/functional/webhooks/phdcomics/helper/__init__.py
 
 
-static
-------
-
-The *static* folder contains only two files with the specified above names (otherwise, they won’t be read on Galaxy run).
+static files
+------------
 
 - script.js - all JavaScript code (with all third-party dependencies) must be here
 - styles.css - all CSS styles, used by the plugin
@@ -149,41 +143,3 @@ tool/workflow
 If a tool or a workflow plugin has script.js and/or styles.css, the content of these files will be read as two strings and sent to the client and appended to DOM’s <head>.
 
 Such approach is a possible bottleneck if the two files are big (however, this shouldn’t ever happen because plugins are supposed to be small and simple).
-
-masthead
---------
-
-Topbar buttons are hard coded, so they’re rendered only after *make client*.
-
-The plugin system is entirely dynamic. All plugins are detected during Galaxy load and their configs and statics are being saved. So, every plugin must be shown/rendered dynamically.
-
-I found a not very optimal way to add buttons to the topbar (masthead):
-
-.. code-block:: javascript
-
-  $(document).ready(function() {
-     Galaxy.page.masthead.collection.add({
-          id      : ... ,
-          icon    : ... ,
-          url     : ... ,
-          tooltip : ... ,
-          onlick  : function() { ... }
-      });
-  });
-
-history-menu
-------------
-
-History Panel items are again hard coded, but in the current implementation they’re rendered as html elements (so, they’re not even stored in a collection or any other object).
-
-To add new menu items, I do the following:
-
-.. code-block:: javascript
-
-  menu.push({
-    html : _l( ... ),
-    anon : true,
-    func : function() { ... }
-  });
-
-But in order to fetch all plugin menu items before rendering, I get them via API in a synchronous manner. The problem is that History Panel now may load a bit longer.
diff --git a/lib/galaxy/dependencies/conda-file.sh b/lib/galaxy/dependencies/conda-file.sh
new file mode 100755
index 00000000000..397cec1804c
--- /dev/null
+++ b/lib/galaxy/dependencies/conda-file.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+#
+# Conda does not have all of Galaxy's dependencies, and the list of which ones it does is always changing. As a result,
+# it's not possible to keep a conda requirements file up to date. However, with Conda >= 4.4, we can use Conda itself to
+# determine which dependencies it can install. Pip will be used (upon Galaxy startup) to install the rest.
+#
+# You should use this script like so:
+#
+# conda create -n <env> --file <(lib/galaxy/dependencies/conda-file.sh)
+#
+# Ensure you have enabled the bioconda and conda-forge repositories first!:
+#
+# conda config --add channels conda-forge
+# conda config --add channels bioconda
+
+here=$(dirname $0)
+
+if ! command -v conda >/dev/null; then
+    printf "$0: command not found: conda\n" >&2
+    printf "hint: did you run 'conda activate base'?\n" >&2
+    exit 1
+fi
+
+printf "Filtering out Galaxy requirements not available from Conda:" >&2
+egrep -iv $( \
+    conda create -n _gx_test_env --dry-run --file <(sed 's/;.*//' $here/pinned-requirements.txt) python=2.7 2>&1 \
+    | grep '^\s*-' | grep -v https: | awk '{print $NF}' | paste -s -d'|' \
+) $here/pinned-requirements.txt | sed 's/;.*//'
+printf " done\n" >&2
diff --git a/lib/galaxy/webapps/galaxy/api/webhooks.py b/lib/galaxy/webapps/galaxy/api/webhooks.py
index 8b543e77754..48e827cdace 100644
--- a/lib/galaxy/webapps/galaxy/api/webhooks.py
+++ b/lib/galaxy/webapps/galaxy/api/webhooks.py
@@ -3,7 +3,6 @@ API Controller providing Galaxy Webhooks
 """
 import imp
 import logging
-import random
 
 from galaxy.web import _future_expose_api_anonymous_and_sessionless as \
     expose_api_anonymous_and_sessionless
@@ -17,7 +16,7 @@ class WebhooksController(BaseAPIController):
         super(WebhooksController, self).__init__(app)
 
     @expose_api_anonymous_and_sessionless
-    def get_all(self, trans, **kwd):
+    def all_webhooks(self, trans, **kwd):
         """
         *GET /api/webhooks/
         Returns all webhooks
@@ -28,35 +27,9 @@ class WebhooksController(BaseAPIController):
         ]
 
     @expose_api_anonymous_and_sessionless
-    def get_random(self, trans, webhook_type, **kwd):
+    def webhook_data(self, trans, webhook_id, **kwd):
         """
-        *GET /api/webhooks/{webhook_type}
-        Returns a random webhook for a given type
-        """
-        webhooks = [
-            webhook
-            for webhook in self.app.webhooks_registry.webhooks
-            if webhook_type in webhook.type and
-            webhook.activate is True
-        ]
-        return random.choice(webhooks).to_dict() if webhooks else {}
-
-    @expose_api_anonymous_and_sessionless
-    def get_all_by_type(self, trans, webhook_type, **kwd):
-        """
-        *GET /api/webhooks/{webhook_type}/all
-        Returns all webhooks for a given type
-        """
-        return [
-            webhook.to_dict()
-            for webhook in self.app.webhooks_registry.webhooks
-            if webhook_type in webhook.type
-        ]
-
-    @expose_api_anonymous_and_sessionless
-    def get_data(self, trans, webhook_name, **kwd):
-        """
-        *GET /api/webhooks/{webhook_name}/get_data/{params}
+        *GET /api/webhooks/{webhook_id}/data/{params}
         Returns the result of executing helper function
         """
         params = {}
@@ -64,14 +37,12 @@ class WebhooksController(BaseAPIController):
         for key, value in kwd.items():
             params[key] = value
 
-        webhook = [
+        webhook = (
             webhook
             for webhook in self.app.webhooks_registry.webhooks
-            if webhook.name == webhook_name
-        ]
+            if webhook.id == webhook_id
+        ).next()
 
-        return imp.load_source('helper', webhook[0].helper).main(
-            trans,
-            webhook[0],
-            params,
-        ) if webhook and webhook[0].helper != '' else {}
+        return imp.load_source(webhook.path, webhook.helper).main(
+            trans, webhook, params,
+        ) if webhook and webhook.helper != '' else {}
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index fa14db1e806..7103d74b57c 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -609,29 +609,17 @@ def populate_api_routes(webapp, app):
     # ===== WEBHOOKS API =====
     # ========================
 
-    webapp.mapper.connect('get_all',
+    webapp.mapper.connect('get_all_webhooks',
                           '/api/webhooks',
                           controller='webhooks',
-                          action='get_all',
-                          conditions=dict(method=["GET"]))
+                          action='all_webhooks',
+                          conditions=dict(method=['GET']))
 
-    webapp.mapper.connect('get_random',
-                          '/api/webhooks/{webhook_type}',
+    webapp.mapper.connect('get_webhook_data',
+                          '/api/webhooks/{webhook_id}/data',
                           controller='webhooks',
-                          action='get_random',
-                          conditions=dict(method=["GET"]))
-
-    webapp.mapper.connect('get_all_by_type',
-                          '/api/webhooks/{webhook_type}/all',
-                          controller='webhooks',
-                          action='get_all_by_type',
-                          conditions=dict(method=["GET"]))
-
-    webapp.mapper.connect('get_data',
-                          '/api/webhooks/{webhook_name}/get_data',
-                          controller='webhooks',
-                          action='get_data',
-                          conditions=dict(method=["GET"]))
+                          action='webhook_data',
+                          conditions=dict(method=['GET']))
 
     # =======================
     # ===== LIBRARY API =====
diff --git a/lib/galaxy/webhooks/__init__.py b/lib/galaxy/webhooks/__init__.py
index 6cc2c34d9d9..e32ee2d9ba6 100644
--- a/lib/galaxy/webhooks/__init__.py
+++ b/lib/galaxy/webhooks/__init__.py
@@ -12,11 +12,12 @@ log = logging.getLogger(__name__)
 
 
 class Webhook(object):
-    def __init__(self, w_name, w_type, w_activate, w_path):
-        self.name = w_name
-        self.type = w_type
-        self.activate = w_activate
-        self.path = w_path
+    def __init__(self, id, type, activate, weight, path):
+        self.id = id
+        self.type = type
+        self.activate = activate
+        self.weight = weight
+        self.path = path
         self.styles = ''
         self.script = ''
         self.helper = ''
@@ -24,12 +25,13 @@ class Webhook(object):
 
     def to_dict(self):
         return {
-            'name': self.name,
+            'id': self.id,
             'type': self.type,
             'activate': self.activate,
+            'weight': self.weight,
             'styles': self.styles,
             'script': self.script,
-            'config': self.config
+            'config': self.config,
         }
 
 
@@ -48,56 +50,57 @@ class WebhooksRegistry(object):
 
     def load_webhooks(self):
         for directory in self.webhooks_directories:
-            config_dir = os.path.join(directory, 'config')
+            config_file_path = None
+            for config_file in ['config.yml', 'config.yaml']:
+                path = os.path.join(directory, config_file)
+                if os.path.isfile(path):
+                    config_file_path = path
+                    break
 
-            if not os.path.exists(config_dir):
-                log.warning('directory not found: %s', config_dir)
-                continue
+            if config_file_path:
+                try:
+                    self.load_webhook_from_config(directory, config_file_path)
+                except Exception as e:
+                    log.exception(e)
 
-            config_dir_contents = os.listdir(config_dir)
-            # We are assuming that all yml/yaml files in a webhooks'
-            # config directory are webhook config files.
-            for config_file in config_dir_contents:
-                if config_file.endswith('.yml') or config_file.endswith('.yaml'):
-                    self.load_webhook_from_config(config_dir, config_file)
+    def load_webhook_from_config(self, webhook_dir, config_file_path):
+        with open(config_file_path) as file:
+            config = yaml.safe_load(file)
 
-    def load_webhook_from_config(self, config_dir, config_file):
+        weight = config.get('weight', 1)
+        if weight < 1:
+            raise ValueError('Webhook weight must be greater or equal 1.')
+
+        webhook = Webhook(
+            config.get('id'),
+            config.get('type'),
+            config.get('activate', False),
+            weight,
+            webhook_dir,
+        )
+
+        # Read styles into a string, assuming all styles are in a
+        # single file
         try:
-            with open(os.path.join(config_dir, config_file)) as file:
-                config = yaml.safe_load(file)
-                path = os.path.normpath(os.path.join(config_dir, '..'))
-                webhook = Webhook(
-                    config['name'],
-                    config['type'],
-                    config['activate'],
-                    path,
-                )
+            styles_file = os.path.join(webhook_dir, 'styles.css')
+            with open(styles_file, 'r') as file:
+                webhook.styles = file.read().replace('\n', '')
+        except IOError:
+            pass
 
-                # Read styles into a string, assuming all styles are in a
-                # single file
-                try:
-                    styles_file = os.path.join(path, 'static/styles.css')
-                    with open(styles_file, 'r') as file:
-                        webhook.styles = file.read().replace('\n', '')
-                except IOError:
-                    pass
+        # Read script into a string, assuming everything is in a
+        # single file
+        try:
+            script_file = os.path.join(webhook_dir, 'script.js')
+            with open(script_file, 'r') as file:
+                webhook.script = file.read()
+        except IOError:
+            pass
 
-                # Read script into a string, assuming everything is in a
-                # single file
-                try:
-                    script_file = os.path.join(path, 'static/script.js')
-                    with open(script_file, 'r') as file:
-                        webhook.script = file.read()
-                except IOError:
-                    pass
+        # Save helper function path if it exists
+        helper_path = os.path.join(webhook_dir, '__init__.py')
+        if os.path.isfile(helper_path):
+            webhook.helper = helper_path
 
-                # Save helper function path if it exists
-                helper_path = os.path.join(path, 'helper/__init__.py')
-                if os.path.isfile(helper_path):
-                    webhook.helper = helper_path
-
-                webhook.config = config
-                self.webhooks.append(webhook)
-
-        except Exception as e:
-            log.exception(e)
+        webhook.config = config
+        self.webhooks.append(webhook)
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index 74f4f1e8957..e944058321a 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -9,6 +9,8 @@ done
 # Conda Python is in use, do not use virtualenv
 if python -V 2>&1 | grep -q -e 'Anaconda' -e 'Continuum Analytics' ; then
     CONDA_ALREADY_INSTALLED=1
+elif python -c 'import sys; print(sys.version.replace("\n", " "))' | grep -q -e 'packaged by conda-forge' ; then
+    CONDA_ALREADY_INSTALLED=1
 else
     CONDA_ALREADY_INSTALLED=0
 fi
diff --git a/test/api/test_webhooks.py b/test/api/test_webhooks.py
index 73fe9d16feb..62cfb049bc9 100644
--- a/test/api/test_webhooks.py
+++ b/test/api/test_webhooks.py
@@ -14,28 +14,13 @@ class WebhooksApiTestCase(api.ApiTestCase):
 
         self._assert_status_code_is(response, 200)
         webhook_objs = self._assert_are_webhooks(response)
-        names = self._get_webhook_names(webhook_objs)
-        for expected_name in ["history_test1", "history_test2", "masthead_test", "phdcomics", "trans_object", "xkcd"]:
-            assert expected_name in names
-
-    def test_get_random(self):
-        response = self._get('webhooks/tool')
-        self._assert_status_code_is(response, 200)
-        self._assert_is_webhook(response.json())
-
-    def test_get_all_by_type(self):
-        # Ensure tool type filtering include a valid webhook of type tool and excludes a webhook
-        # that isn't of type tool.
-        response = self._get('webhooks/tool/all')
-
-        self._assert_status_code_is(response, 200)
-        webhook_objs = self._assert_are_webhooks(response)
-        names = self._get_webhook_names(webhook_objs)
-        assert "phdcomics" in names
-        assert "trans_object" not in names  # properly filtered out by type
+        ids = self._get_webhook_ids(webhook_objs)
+        for expected_id in ['history_test1', 'history_test2', 'masthead_test',
+                            'phdcomics', 'trans_object', 'xkcd']:
+            assert expected_id in ids
 
     def test_get_data(self):
-        response = self._get('webhooks/trans_object/get_data')
+        response = self._get('webhooks/trans_object/data')
         self._assert_status_code_is(response, 200)
         self._assert_has_keys(response.json(), 'username')
 
@@ -48,8 +33,9 @@ class WebhooksApiTestCase(api.ApiTestCase):
 
     def _assert_is_webhook(self, obj):
         assert isinstance(obj, dict)
-        self._assert_has_keys(obj, 'styles', 'activate', 'name', 'script', 'type', 'config')
+        self._assert_has_keys(obj,
+            'id', 'type', 'activate', 'weight', 'script', 'styles', 'config')
 
-    def _get_webhook_names(self, webhook_objs):
-        names = [w.get("name") for w in webhook_objs]
+    def _get_webhook_ids(self, webhook_objs):
+        names = [w.get('id') for w in webhook_objs]
         return names
diff --git a/test/functional/webhooks/history_test1/config/history_test1.yml b/test/functional/webhooks/history_test1/config.yml
similarity index 71%
rename from test/functional/webhooks/history_test1/config/history_test1.yml
rename to test/functional/webhooks/history_test1/config.yml
index 46d362d8d37..cb581bc8fcd 100644
--- a/test/functional/webhooks/history_test1/config/history_test1.yml
+++ b/test/functional/webhooks/history_test1/config.yml
@@ -1,5 +1,5 @@
-name: history_test1
+id: history_test1
 title: History Menu Webhook Item 1
-type: 
+type:
   - history-menu
 activate: true
diff --git a/test/functional/webhooks/history_test2/config/history_test2.yml b/test/functional/webhooks/history_test2/config.yml
similarity index 71%
rename from test/functional/webhooks/history_test2/config/history_test2.yml
rename to test/functional/webhooks/history_test2/config.yml
index 7b071e4d855..d24dfdd2c80 100644
--- a/test/functional/webhooks/history_test2/config/history_test2.yml
+++ b/test/functional/webhooks/history_test2/config.yml
@@ -1,5 +1,5 @@
-name: history_test2
+id: history_test2
 title: History Menu Webhook Item 2
-type: 
+type:
   - history-menu
 activate: true
diff --git a/test/functional/webhooks/masthead_test/config/masthead_test.yml b/test/functional/webhooks/masthead_test/config.yml
similarity index 84%
rename from test/functional/webhooks/masthead_test/config/masthead_test.yml
rename to test/functional/webhooks/masthead_test/config.yml
index 935da0e8463..dfb14084885 100644
--- a/test/functional/webhooks/masthead_test/config/masthead_test.yml
+++ b/test/functional/webhooks/masthead_test/config.yml
@@ -1,5 +1,5 @@
-name: masthead_test
-type: 
+id: masthead_test
+type:
   - masthead
 activate: true
 
diff --git a/test/functional/webhooks/phdcomics/helper/__init__.py b/test/functional/webhooks/phdcomics/__init__.py
similarity index 100%
rename from test/functional/webhooks/phdcomics/helper/__init__.py
rename to test/functional/webhooks/phdcomics/__init__.py
diff --git a/test/functional/webhooks/phdcomics/config/phdcomics.yaml b/test/functional/webhooks/phdcomics/config.yaml
similarity index 72%
rename from test/functional/webhooks/phdcomics/config/phdcomics.yaml
rename to test/functional/webhooks/phdcomics/config.yaml
index f66a29a432a..d2c57bc8a60 100644
--- a/test/functional/webhooks/phdcomics/config/phdcomics.yaml
+++ b/test/functional/webhooks/phdcomics/config.yaml
@@ -1,4 +1,4 @@
-name: phdcomics
+id: phdcomics
 type:
   - tool
   - workflow
diff --git a/test/functional/webhooks/phdcomics/static/script.js b/test/functional/webhooks/phdcomics/script.js
similarity index 95%
rename from test/functional/webhooks/phdcomics/static/script.js
rename to test/functional/webhooks/phdcomics/script.js
index 73628a260d5..1c036373b8b 100644
--- a/test/functional/webhooks/phdcomics/static/script.js
+++ b/test/functional/webhooks/phdcomics/script.js
@@ -32,7 +32,7 @@ $(document).ready(function() {
 
         getRandomComic: function() {
             var me = this,
-                url = galaxyRoot + 'api/webhooks/phdcomics/get_data';
+                url = galaxyRoot + 'api/webhooks/phdcomics/data';
 
             this.$comicImg.html($('<div/>', {
                 id: 'phdcomics-loader'
diff --git a/test/functional/webhooks/phdcomics/static/styles.css b/test/functional/webhooks/phdcomics/styles.css
similarity index 100%
rename from test/functional/webhooks/phdcomics/static/styles.css
rename to test/functional/webhooks/phdcomics/styles.css
diff --git a/test/functional/webhooks/trans_object/helper/__init__.py b/test/functional/webhooks/trans_object/__init__.py
similarity index 100%
rename from test/functional/webhooks/trans_object/helper/__init__.py
rename to test/functional/webhooks/trans_object/__init__.py
diff --git a/test/functional/webhooks/trans_object/config/trans_object.yaml b/test/functional/webhooks/trans_object/config.yaml
similarity index 56%
rename from test/functional/webhooks/trans_object/config/trans_object.yaml
rename to test/functional/webhooks/trans_object/config.yaml
index 67b2bb8097e..cd8e2d8277f 100644
--- a/test/functional/webhooks/trans_object/config/trans_object.yaml
+++ b/test/functional/webhooks/trans_object/config.yaml
@@ -1,4 +1,4 @@
-name: trans_object
+id: trans_object
 type:
   - masthead
 activate: true
@@ -7,6 +7,6 @@ icon: fa-user
 tooltip: Show Username
 
 function: >
-  $.getJSON(Galaxy.root + "api/webhooks/trans_object/get_data", function(data) {
+  $.getJSON(Galaxy.root + "api/webhooks/trans_object/data", function(data) {
     alert('Username: ' + data.username);
   });
diff --git a/test/functional/webhooks/xkcd/config/xkcd.yml b/test/functional/webhooks/xkcd/config.yml
similarity index 79%
rename from test/functional/webhooks/xkcd/config/xkcd.yml
rename to test/functional/webhooks/xkcd/config.yml
index c8ce604b002..81143a9a44c 100644
--- a/test/functional/webhooks/xkcd/config/xkcd.yml
+++ b/test/functional/webhooks/xkcd/config.yml
@@ -1,4 +1,4 @@
-name: xkcd
+id: xkcd
 type:
   - tool
   - workflow
diff --git a/test/functional/webhooks/xkcd/static/script.js b/test/functional/webhooks/xkcd/script.js
similarity index 100%
rename from test/functional/webhooks/xkcd/static/script.js
rename to test/functional/webhooks/xkcd/script.js
diff --git a/test/functional/webhooks/xkcd/static/styles.css b/test/functional/webhooks/xkcd/styles.css
similarity index 100%
rename from test/functional/webhooks/xkcd/static/styles.css
rename to test/functional/webhooks/xkcd/styles.css
diff --git a/test/selenium_tests/test_tool_describing_tours.py b/test/selenium_tests/test_tool_describing_tours.py
index 7dcb1ee8491..bc54dcdf59b 100644
--- a/test/selenium_tests/test_tool_describing_tours.py
+++ b/test/selenium_tests/test_tool_describing_tours.py
@@ -72,9 +72,9 @@ class ToolDescribingToursTestCase(SeleniumTestCase):
 
     def _ensure_tdt_available(self):
         """ Skip a test if the webhook TDT doesn't appear. """
-        response = self.api_get('webhooks/tool-menu/all', raw=True)
+        response = self.api_get('webhooks', raw=True)
         self.assertEqual(response.status_code, 200)
         data = response.json()
-        webhooks = [x['name'] for x in data]
+        webhooks = [x['id'] for x in data]
         if 'tour_generator' not in webhooks:
             raise unittest.SkipTest('Skipping test, webhook "Tool-Describing-Tours" doesn\'t appear to be configured.')