diff --git a/client/galaxy/scripts/utils/config.js b/client/galaxy/scripts/utils/config.js
index b1a5457eb0e..e060743d978 100644
--- a/client/galaxy/scripts/utils/config.js
+++ b/client/galaxy/scripts/utils/config.js
@@ -1,6 +1,10 @@
 import * as _ from "libs/underscore";
+import * as Backbone from "libs/backbone";
 import util_mod from "viz/trackster/util";
-import config_mod from "utils/config";
+
+/* global $ */
+/* global Galaxy */
+
 /**
  * A configuration setting. Currently key is used as id.
  */
@@ -307,23 +311,22 @@ var ConfigSettingCollectionView = Backbone.View.extend({
                         // No propagation to avoid triggering document click (and tip hiding) above.
                         e.stopPropagation();
                     });
-
-                var // Icon for setting a new random color; behavior set below.
-                new_color_icon = $("<a href='javascript:void(0)'/>")
+                // Icon for setting a new random color; behavior set below.
+                var new_color_icon = $("<a href='javascript:void(0)'/>")
                     .addClass("icon-button arrow-circle")
                     .appendTo(container_div)
                     .attr("title", "Set new random color")
                     .tooltip();
 
-                var // Color picker in tool tip style.
-                tip = $("<div class='tooltip right' style='position: absolute;' />")
+                // Color picker in tool tip style.
+                var tip = $("<div class='tooltip right' style='position: absolute;' />")
                     .appendTo(container_div)
                     .hide();
 
-                var // Inner div for padding purposes
-                tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip);
+                // Inner div for padding purposes
+                var tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip);
 
-                var tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(tip);
+                $("<div class='tooltip-arrow'></div>").appendTo(tip);
 
                 var farb_obj = $.farbtastic(tip_inner, {
                     width: 100,
diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js
index 8640cce51f6..2b85b4a85ef 100644
--- a/client/galaxy/scripts/viz/trackster.js
+++ b/client/galaxy/scripts/viz/trackster.js
@@ -1,15 +1,15 @@
-import _l from "utils/localization";
 /**
  * Top-level trackster code, used for creating/loading visualizations and user interface elements.
  */
-//import * as $ from 'jquery';
+import _l from "utils/localization";
 import * as _ from "libs/underscore";
+import * as Backbone from "libs/backbone";
 import tracks from "viz/trackster/tracks";
 import visualization from "viz/visualization";
-import mod_icon_btn from "mvc/ui/icon-button";
+import IconButton from "mvc/ui/icon-button";
 import query_string from "utils/query-string-parsing";
 import GridView from "mvc/grid/grid-view";
-import mod_utils from "utils/utils";
+import Utils from "utils/utils";
 import "libs/jquery/jquery.event.drag";
 import "libs/jquery/jquery.event.hover";
 import "libs/jquery/jquery.mousewheel";
@@ -20,44 +20,36 @@ import "libs/jquery/jquery.form";
 import "libs/jquery/jquery.rating";
 import "ui/editable-text";
 
-// trackster global variables
-var ui = null;
-var view = null;
-var browser_router = null;
-
-/**
- * Base Object/Model for inhertiance.
- */
-var Base = function() {
-    if (this.initialize) {
-        this.initialize.apply(this, arguments);
-    }
-};
-Base.extend = Backbone.Model.extend;
+/* global Galaxy */
+/* global $ */
 
 /**
  * User interface controls for trackster
  */
-var TracksterUI = Base.extend({
-    initialize: function(baseURL) {
-        mod_utils.cssLoadFile("static/style/jquery.rating.css");
-        mod_utils.cssLoadFile("static/style/autocomplete_tagging.css");
-        mod_utils.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");
-        mod_utils.cssLoadFile("static/style/library.css");
-        mod_utils.cssLoadFile("static/style/trackster.css");
+class TracksterUI extends Backbone.Model {
+    constructor(options) {
+        super(options);
+    }
+
+    initialize(baseURL) {
         this.baseURL = baseURL;
-    },
+        Utils.cssLoadFile("static/style/jquery.rating.css");
+        Utils.cssLoadFile("static/style/autocomplete_tagging.css");
+        Utils.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");
+        Utils.cssLoadFile("static/style/library.css");
+        Utils.cssLoadFile("static/style/trackster.css");
+    }
 
     /**
      * Save visualization, returning a Deferred object for the remote call to save.
      */
-    save_viz: function() {
+    save_viz() {
         // show dialog
         Galaxy.modal.show({ title: "Saving...", body: "progress" });
 
         // Save bookmarks.
         var bookmarks = [];
-        $(".bookmark").each(function() {
+        $(".bookmark").each(() => {
             bookmarks.push({
                 position: $(this)
                     .children(".position")
@@ -69,14 +61,16 @@ var TracksterUI = Base.extend({
         });
 
         // FIXME: give unique IDs to Drawables and save overview as ID.
-        var overview_track_name = view.overview_drawable ? view.overview_drawable.config.get_value("name") : null;
+        var overview_track_name = this.view.overview_drawable
+            ? this.view.overview_drawable.config.get_value("name")
+            : null;
 
         var viz_config = {
-            view: view.to_dict(),
+            view: this.view.to_dict(),
             viewport: {
-                chrom: view.chrom,
-                start: view.low,
-                end: view.high,
+                chrom: this.view.chrom,
+                start: this.view.low,
+                end: this.view.high,
                 overview: overview_track_name
             },
             bookmarks: bookmarks
@@ -88,17 +82,17 @@ var TracksterUI = Base.extend({
             type: "POST",
             dataType: "json",
             data: {
-                id: view.vis_id,
-                title: view.config.get_value("name"),
-                dbkey: view.dbkey,
+                id: this.view.vis_id,
+                title: this.view.config.get_value("name"),
+                dbkey: this.view.dbkey,
                 type: "trackster",
                 vis_json: JSON.stringify(viz_config)
             }
         })
             .success(vis_info => {
                 Galaxy.modal.hide();
-                view.vis_id = vis_info.vis_id;
-                view.has_changes = false;
+                this.view.vis_id = vis_info.vis_id;
+                this.view.has_changes = false;
 
                 // Needed to set URL when first saving a visualization.
                 window.history.pushState({}, "", vis_info.url + window.top.location.hash);
@@ -109,29 +103,27 @@ var TracksterUI = Base.extend({
                     title: _l("Could Not Save"),
                     body: "Could not save visualization. Please try again later.",
                     buttons: {
-                        Cancel: function() {
+                        Cancel: () => {
                             Galaxy.modal.hide();
                         }
                     }
                 });
             });
-    },
+    }
 
     /**
      * Create button menu
      */
-    createButtonMenu: function() {
-        var self = this;
-
-        var menu = mod_icon_btn.create_icon_buttons_menu(
+    createButtonMenu() {
+        var menu = IconButton.create_icon_buttons_menu(
             [
                 {
                     icon_class: "plus-button",
                     title: _l("Add tracks"),
-                    on_click: function() {
-                        visualization.select_datasets({ dbkey: view.dbkey }, new_tracks => {
+                    on_click: () => {
+                        visualization.select_datasets({ dbkey: this.view.dbkey }, new_tracks => {
                             _.each(new_tracks, track => {
-                                view.add_drawable(tracks.object_from_template(track, view, view));
+                                this.view.add_drawable(tracks.object_from_template(track, this.view, this.view));
                             });
                         });
                     }
@@ -139,9 +131,9 @@ var TracksterUI = Base.extend({
                 {
                     icon_class: "block--plus",
                     title: _l("Add group"),
-                    on_click: function() {
-                        view.add_drawable(
-                            new tracks.DrawableGroup(view, view, {
+                    on_click: () => {
+                        this.view.add_drawable(
+                            new tracks.DrawableGroup(this.view, this.view, {
                                 name: "New Group"
                             })
                         );
@@ -150,7 +142,7 @@ var TracksterUI = Base.extend({
                 {
                     icon_class: "bookmarks",
                     title: _l("Bookmarks"),
-                    on_click: function() {
+                    on_click: () => {
                         // HACK -- use style to determine if panel is hidden and hide/show accordingly.
                         window.force_right_panel($("div#right").css("right") == "0px" ? "hide" : "show");
                     }
@@ -158,22 +150,22 @@ var TracksterUI = Base.extend({
                 {
                     icon_class: "globe",
                     title: _l("Circster"),
-                    on_click: function() {
-                        window.top.location = `${self.baseURL}visualization/circster?id=${view.vis_id}`;
+                    on_click: () => {
+                        window.top.location = `${this.baseURL}visualization/circster?id=${this.view.vis_id}`;
                     }
                 },
                 {
                     icon_class: "disk--arrow",
                     title: _l("Save"),
-                    on_click: function() {
-                        self.save_viz();
+                    on_click: () => {
+                        this.save_viz();
                     }
                 },
                 {
                     icon_class: "cross-circle",
                     title: _l("Close"),
-                    on_click: function() {
-                        self.handle_unsaved_changes(view);
+                    on_click: () => {
+                        this.handle_unsaved_changes(this.view);
                     }
                 }
             ],
@@ -184,12 +176,12 @@ var TracksterUI = Base.extend({
 
         this.buttonMenu = menu;
         return menu;
-    },
+    }
 
     /**
      * Add bookmark.
      */
-    add_bookmark: function(position, annotation, editable) {
+    add_bookmark(position, annotation, editable) {
         // Create HTML.
         var bookmarks_container = $("#right .unified-panel-body");
 
@@ -201,11 +193,12 @@ var TracksterUI = Base.extend({
             .addClass("position")
             .appendTo(new_bookmark);
 
-        var position_link = $("<a href=''/>")
+        //position_link
+        $("<a href=''/>")
             .text(position)
             .appendTo(position_div)
             .click(() => {
-                view.go_to(position);
+                this.view.go_to(position);
                 return false;
             });
 
@@ -222,11 +215,12 @@ var TracksterUI = Base.extend({
                     // Remove bookmark.
                     new_bookmark.slideUp("fast");
                     new_bookmark.remove();
-                    view.has_changes = true;
+                    this.view.has_changes = true;
                     return false;
                 });
 
-            var delete_icon = $("<a href=''/>")
+            // delete_icon
+            $("<a href=''/>")
                 .addClass("icon-button delete")
                 .appendTo(delete_icon_container);
 
@@ -239,56 +233,50 @@ var TracksterUI = Base.extend({
                 .addClass("annotation");
         }
 
-        view.has_changes = true;
+        this.view.has_changes = true;
         return new_bookmark;
-    },
+    }
 
     /**
      * Create a complete Trackster visualization. Returns view.
      */
-    create_visualization: function(view_config, viewport_config, drawables_config, bookmarks_config, editable) {
+    create_visualization(view_config, viewport_config, drawables_config, bookmarks_config, editable) {
         // Create view.
-        var self = this;
+        this.view = new tracks.TracksterView(_.extend(view_config, { header: false }));
+        this.view.editor = true;
 
-        view = new tracks.TracksterView(_.extend(view_config, { header: false }));
-
-        view.editor = true;
-        $.when(view.load_chroms_deferred).then(chrom_info => {
+        $.when(this.view.load_chroms_deferred).then(chrom_info => {
+            var overview_drawable_name = null;
             // Viewport config.
             if (viewport_config) {
                 var chrom = viewport_config.chrom;
                 var start = viewport_config.start;
                 var end = viewport_config.end;
-                var overview_drawable_name = viewport_config.overview;
+                overview_drawable_name = viewport_config.overview;
 
                 if (chrom && start !== undefined && end) {
-                    view.change_chrom(chrom, start, end);
+                    this.view.change_chrom(chrom, start, end);
                 } else {
                     // No valid viewport, so use first chromosome.
-                    view.change_chrom(chrom_info[0].chrom);
+                    this.view.change_chrom(chrom_info[0].chrom);
                 }
             } else {
                 // No viewport, so use first chromosome.
-                view.change_chrom(chrom_info[0].chrom);
+                this.view.change_chrom(chrom_info[0].chrom);
             }
 
             // Add drawables to view.
             if (drawables_config) {
                 // FIXME: can from_dict() be used to create view and add drawables?
-                var drawable_config;
-
-                var drawable_type;
-                var drawable;
-                for (var i = 0; i < drawables_config.length; i++) {
-                    view.add_drawable(tracks.object_from_template(drawables_config[i], view, view));
+                for (let i = 0; i < drawables_config.length; i++) {
+                    this.view.add_drawable(tracks.object_from_template(drawables_config[i], this.view, this.view));
                 }
             }
 
             // Set overview.
-            var overview_drawable;
-            for (var i = 0; i < view.drawables.length; i++) {
-                if (view.drawables[i].config.get_value("name") === overview_drawable_name) {
-                    view.set_overview(view.drawables[i]);
+            for (let i = 0; i < this.view.drawables.length; i++) {
+                if (this.view.drawables[i].config.get_value("name") === overview_drawable_name) {
+                    this.view.set_overview(this.view.drawables[i]);
                     break;
                 }
             }
@@ -296,34 +284,35 @@ var TracksterUI = Base.extend({
             // Load bookmarks.
             if (bookmarks_config) {
                 var bookmark;
-                for (var i = 0; i < bookmarks_config.length; i++) {
+                for (let i = 0; i < bookmarks_config.length; i++) {
                     bookmark = bookmarks_config[i];
-                    self.add_bookmark(bookmark["position"], bookmark["annotation"], editable);
+                    this.add_bookmark(bookmark.position, bookmark.annotation, editable);
                 }
             }
 
             // View has no changes as of yet.
-            view.has_changes = false;
+            this.view.has_changes = false;
         });
 
         // Final initialization.
-        this.set_up_router({ view: view });
+        this.set_up_router({ view: this.view });
 
-        return view;
-    },
+        // TODO: This is hopefully not necessary anymore, since we're using the instance view.  Do it for compatibility for now.
+        return this.view;
+    }
 
     /**
      * Set up location router to use hashes as track browser locations.
      */
-    set_up_router: function(options) {
+    set_up_router(options) {
         new visualization.TrackBrowserRouter(options);
         Backbone.history.start();
-    },
+    }
 
     /**
      * Set up keyboard navigation for a visualization.
      */
-    init_keyboard_nav: function(view) {
+    init_keyboard_nav(view) {
         // Keyboard navigation. Scroll ~7% of height when scrolling up/down.
         $(document).keyup(e => {
             // Do not navigate if arrow keys used in input element.
@@ -337,39 +326,38 @@ var TracksterUI = Base.extend({
                     view.move_fraction(0.25);
                     break;
                 case 38:
-                    var change = Math.round(view.viewport_container.height() / 15.0);
+                    // var change = Math.round(view.viewport_container.height() / 15.0);
                     view.viewport_container.scrollTop(view.viewport_container.scrollTop() - 20);
                     break;
                 case 39:
                     view.move_fraction(-0.25);
                     break;
                 case 40:
-                    var change = Math.round(view.viewport_container.height() / 15.0);
+                    // var change = Math.round(view.viewport_container.height() / 15.0);
                     view.viewport_container.scrollTop(view.viewport_container.scrollTop() + 20);
                     break;
             }
         });
-    },
+    }
 
     /**
      * Handle unsaved changes in visualization.
      */
-    handle_unsaved_changes: function(view) {
+    handle_unsaved_changes(view) {
         if (view.has_changes) {
-            var self = this;
             Galaxy.modal.show({
                 title: _l("Close visualization"),
                 body: "There are unsaved changes to your visualization which will be lost if you do not save them.",
                 buttons: {
-                    Cancel: function() {
+                    Cancel: () => {
                         Galaxy.modal.hide();
                     },
-                    "Leave without Saving": function() {
+                    "Leave without Saving": () => {
                         $(window).off("beforeunload");
                         window.top.location = `${Galaxy.root}visualization`;
                     },
-                    Save: function() {
-                        $.when(self.save_viz()).then(() => {
+                    Save: () => {
+                        $.when(this.save_viz()).then(() => {
                             window.top.location = `${Galaxy.root}visualization`;
                         });
                     }
@@ -379,22 +367,25 @@ var TracksterUI = Base.extend({
             window.top.location = `${Galaxy.root}visualization`;
         }
     }
-});
+}
 
-var TracksterView = Backbone.View.extend({
+class TracksterUIView extends Backbone.View {
+    constructor(options) {
+        super(options);
+    }
     // initalize trackster
-    initialize: function() {
+    initialize() {
         // load ui
-        ui = new TracksterUI(Galaxy.root);
+        this.ui = new TracksterUI(Galaxy.root);
 
         // create button menu
-        ui.createButtonMenu();
+        this.ui.createButtonMenu();
 
         // attach the button menu to the panel header and float it left
-        ui.buttonMenu.$el.attr("style", "float: right");
+        this.ui.buttonMenu.$el.attr("style", "float: right");
 
         // add to center panel
-        $("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);
+        $("#center .unified-panel-header-inner").append(this.ui.buttonMenu.$el);
 
         // configure right panel
         $("#right .unified-panel-title").append("Bookmarks");
@@ -404,7 +395,7 @@ var TracksterView = Backbone.View.extend({
 
         // resize view when showing/hiding right panel (bookmarks for now).
         $("#right-border").click(() => {
-            view.resize_window();
+            this.ui.view.resize_window();
         });
 
         // hide right panel
@@ -418,10 +409,9 @@ var TracksterView = Backbone.View.extend({
         } else {
             this.view_new();
         }
-    },
+    }
 
-    choose_existing_or_new: function() {
-        var self = this;
+    choose_existing_or_new() {
         var dbkey = query_string.get("dbkey");
         var listTracksParams = {};
 
@@ -442,21 +432,21 @@ var TracksterView = Backbone.View.extend({
             body: `<p><ul style='list-style: disc inside none'>You can add this dataset as:<li>a new track to one of your existing, saved Trackster sessions if they share the genome build: <b>${dbkey ||
                 "Not available."}</b></li><li>or create a new session with this dataset as the only track</li></ul></p>`,
             buttons: {
-                Cancel: function() {
+                Cancel: () => {
                     window.top.location = `${Galaxy.root}visualizations/list`;
                 },
-                "View in saved visualization": function() {
-                    self.view_in_saved(dataset_params);
+                "View in saved visualization": () => {
+                    this.view_in_saved(dataset_params);
                 },
-                "View in new visualization": function() {
-                    self.view_new();
+                "View in new visualization": () => {
+                    this.view_new();
                 }
             }
         });
-    },
+    }
 
     // view
-    view_in_saved: function(dataset_params) {
+    view_in_saved(dataset_params) {
         var tracks_grid = new GridView({
             url_base: `${Galaxy.root}visualization/list_tracks`,
             embedded: true
@@ -465,28 +455,28 @@ var TracksterView = Backbone.View.extend({
             title: _l("Add Data to Saved Visualization"),
             body: tracks_grid.$el,
             buttons: {
-                Cancel: function() {
+                Cancel: () => {
                     window.top.location = `${Galaxy.root}visualizations/list`;
                 },
-                "Add to visualization": function() {
-                    $(parent.document)
+                "Add to visualization": () => {
+                    $(window.parent.document)
                         .find("input[name=id]:checked")
-                        .each(function() {
+                        .each(() => {
                             dataset_params.id = $(this).val();
                             window.top.location = `${Galaxy.root}visualization/trackster?${$.param(dataset_params)}`;
                         });
                 }
             }
         });
-    },
+    }
 
     // view
-    view_existing: function() {
+    view_existing() {
         // get config
         var viz_config = window.galaxy_config.app.viz_config;
 
         // view
-        view = ui.create_visualization(
+        this.ui.create_visualization(
             {
                 container: $("#center .unified-panel-body"),
                 name: viz_config.title,
@@ -501,31 +491,28 @@ var TracksterView = Backbone.View.extend({
 
         // initialize editor
         this.init_editor();
-    },
+    }
 
     // view
-    view_new: function() {
-        // reference this
-        var self = this;
-
+    view_new() {
         // ajax
         $.ajax({
             url: `${Galaxy.root}api/genomes?chrom_info=True`,
             data: {},
-            error: function() {
+            error: () => {
                 alert("Couldn't create new browser.");
             },
-            success: function(response) {
+            success: response => {
                 // show dialog
                 Galaxy.modal.show({
                     title: _l("New Visualization"),
-                    body: self.template_view_new(response),
+                    body: this.template_view_new(response),
                     buttons: {
-                        Cancel: function() {
+                        Cancel: () => {
                             window.top.location = `${Galaxy.root}visualizations/list`;
                         },
-                        Create: function() {
-                            self.create_browser($("#new-title").val(), $("#new-dbkey").val());
+                        Create: () => {
+                            this.create_browser($("#new-title").val(), $("#new-dbkey").val());
                             Galaxy.modal.hide();
                         }
                     }
@@ -548,10 +535,10 @@ var TracksterView = Backbone.View.extend({
                 $("#overlay").css("overflow", "auto");
             }
         });
-    },
+    }
 
     // new browser form
-    template_view_new: function(response) {
+    template_view_new(response) {
         // start template
         var html =
             '<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;">' +
@@ -568,7 +555,7 @@ var TracksterView = Backbone.View.extend({
             '<select name="dbkey" id="new-dbkey">';
 
         // add dbkeys
-        for (var i = 0; i < response.length; i++) {
+        for (let i = 0; i < response.length; i++) {
             html += `<option value="${response[i][1]}">${response[i][0]}</option>`;
         }
 
@@ -579,13 +566,48 @@ var TracksterView = Backbone.View.extend({
 
         // return
         return html;
-    },
+    }
+
+    // initialization for editor-specific functions.
+    init_editor() {
+        // set title
+        $("#center .unified-panel-title").text(`${this.ui.view.config.get_value("name")} (${this.ui.view.dbkey})`);
+
+        // add dataset
+        if (window.galaxy_config.app.add_dataset)
+            $.ajax({
+                url: `${Galaxy.root}api/datasets/${window.galaxy_config.app.add_dataset}`,
+                data: { hda_ldda: "hda", data_type: "track_config" },
+                dataType: "json",
+                success: track_data => {
+                    this.ui.view.add_drawable(tracks.object_from_template(track_data, this.ui.view, this.ui.view));
+                }
+            });
+
+        // initialize icons
+        $("#add-bookmark-button").click(() => {
+            // add new bookmark.
+            var position = `${this.ui.view.chrom}:${this.ui.view.low}-${this.ui.view.high}`;
+
+            var annotation = "Bookmark description";
+            return this.ui.add_bookmark(position, annotation, true);
+        });
+
+        // initialize keyboard
+        this.ui.init_keyboard_nav(this.ui.view);
+
+        $(window).on("beforeunload", () => {
+            if (this.ui.view.has_changes) {
+                return "There are unsaved changes to your visualization that will be lost if you leave this page.";
+            }
+        });
+    }
 
     // create
-    create_browser: function(name, dbkey) {
+    create_browser(name, dbkey) {
         $(document).trigger("convert_to_values");
 
-        view = ui.create_visualization(
+        this.ui.create_visualization(
             {
                 container: $("#center .unified-panel-body"),
                 name: name,
@@ -598,46 +620,11 @@ var TracksterView = Backbone.View.extend({
         this.init_editor();
 
         // modify view setting
-        view.editor = true;
-    },
-
-    // initialization for editor-specific functions.
-    init_editor: function() {
-        // set title
-        $("#center .unified-panel-title").text(`${view.config.get_value("name")} (${view.dbkey})`);
-
-        // add dataset
-        if (window.galaxy_config.app.add_dataset)
-            $.ajax({
-                url: `${Galaxy.root}api/datasets/${window.galaxy_config.app.add_dataset}`,
-                data: { hda_ldda: "hda", data_type: "track_config" },
-                dataType: "json",
-                success: function(track_data) {
-                    view.add_drawable(tracks.object_from_template(track_data, view, view));
-                }
-            });
-
-        // initialize icons
-        $("#add-bookmark-button").click(() => {
-            // add new bookmark.
-            var position = `${view.chrom}:${view.low}-${view.high}`;
-
-            var annotation = "Bookmark description";
-            return ui.add_bookmark(position, annotation, true);
-        });
-
-        // initialize keyboard
-        ui.init_keyboard_nav(view);
-
-        $(window).on("beforeunload", () => {
-            if (view.has_changes) {
-                return "There are unsaved changes to your visualization that will be lost if you leave this page.";
-            }
-        });
+        this.ui.view.editor = true;
     }
-});
+}
 
 export default {
     TracksterUI: TracksterUI,
-    GalaxyApp: TracksterView
+    GalaxyApp: TracksterUIView
 };
diff --git a/client/galaxy/scripts/viz/trackster/filters.js b/client/galaxy/scripts/viz/trackster/filters.js
index 4cac685ab98..3abc219a983 100644
--- a/client/galaxy/scripts/viz/trackster/filters.js
+++ b/client/galaxy/scripts/viz/trackster/filters.js
@@ -151,7 +151,7 @@ var NumberFilter = function(obj_dict) {
         .addClass("elt-label")
         .appendTo(filter.parent_div);
 
-    var name_span = $("<span/>")
+    $("<span/>")
         .addClass("slider-name")
         .text(`${filter.name}  `)
         .appendTo(filter_label);
@@ -341,9 +341,6 @@ extend(NumberFilter.prototype, {
             return true;
         }
 
-        // Keep value function.
-        var filter = this;
-
         // Do filtering.
         var to_filter = element[this.index];
         if (to_filter instanceof Array) {
@@ -482,7 +479,7 @@ var FiltersManager = function(track, obj_dict) {
                     filter.height_icon.addClass("active").show();
                 }
             } else {
-                console.log("ERROR: unsupported filter: ", name, type);
+                console.log("ERROR: unsupported filter: ", filters_dict[i]);
             }
         }
 
@@ -656,6 +653,7 @@ extend(FiltersManager.prototype, {
             // Remove current filter.
             filters = filters.slice(1);
 
+            // DBTODO: This will never work, run_tool_url doesn't exist?
             $.getJSON(run_tool_url, url_params, response => {
                 if (response.error) {
                     // General error.
diff --git a/client/galaxy/scripts/viz/trackster/painters.js b/client/galaxy/scripts/viz/trackster/painters.js
index 4c81e1b9bd5..c3e48e2a1bd 100644
--- a/client/galaxy/scripts/viz/trackster/painters.js
+++ b/client/galaxy/scripts/viz/trackster/painters.js
@@ -1,4 +1,23 @@
 import * as _ from "libs/underscore";
+// Constants specific to feature tracks moved here (HACKING, these should
+// basically all be configuration options)
+const BEFORE = 1001;
+const CONTAINS = 1002;
+const OVERLAP_START = 1003;
+const OVERLAP_END = 1004;
+const CONTAINED_BY = 1005;
+const AFTER = 1006;
+
+const DENSE_TRACK_HEIGHT = 10;
+const NO_DETAIL_TRACK_HEIGHT = 3;
+const SQUISH_TRACK_HEIGHT = 5;
+const PACK_TRACK_HEIGHT = 10;
+const NO_DETAIL_FEATURE_HEIGHT = 1;
+const DENSE_FEATURE_HEIGHT = 9;
+const SQUISH_FEATURE_HEIGHT = 3;
+const PACK_FEATURE_HEIGHT = 9;
+const LABEL_SPACING = 2;
+const CONNECTOR_COLOR = "#ccc";
 
 /**
  * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig.
@@ -6,14 +25,7 @@ import * as _ from "libs/underscore";
  * region overlaps the start (but not the end) of the second region.
  * NOTE: Coordinates are assumed to be in BED format: half open (start is closed, end is open).
  */
-var BEFORE = 1001;
-
-var CONTAINS = 1002;
-var OVERLAP_START = 1003;
-var OVERLAP_END = 1004;
-var CONTAINED_BY = 1005;
-var AFTER = 1006;
-var compute_overlap = (first_region, second_region) => {
+function compute_overlap(first_region, second_region) {
     var first_start = first_region[0];
     var first_end = first_region[1];
     var second_start = second_region[0];
@@ -38,17 +50,16 @@ var compute_overlap = (first_region, second_region) => {
             overlap = OVERLAP_END;
         }
     }
-
     return overlap;
-};
+}
 
 /**
  * Returns true if regions overlap.
  */
-var is_overlap = (first_region, second_region) => {
+function is_overlap(first_region, second_region) {
     var overlap = compute_overlap(first_region, second_region);
     return overlap !== BEFORE && overlap !== AFTER;
-};
+}
 
 /**
  * Draw a dashed line on a canvas using filled rectangles. This function is based on:
@@ -56,7 +67,7 @@ var is_overlap = (first_region, second_region) => {
  * However, that approach uses lines, which don't seem to render as well, so use
  * rectangles instead.
  */
-var dashedLine = (ctx, x1, y1, x2, y2, dashLen) => {
+function dashedLine(ctx, x1, y1, x2, y2, dashLen) {
     if (dashLen === undefined) {
         dashLen = 4;
     }
@@ -73,12 +84,12 @@ var dashedLine = (ctx, x1, y1, x2, y2, dashLen) => {
         }
         ctx.fillRect(x1, y1, dashLen, 1);
     }
-};
+}
 
 /**
  * Draw an isosceles triangle that points down.
  */
-var drawDownwardEquilateralTriangle = function(ctx, down_vertex_x, down_vertex_y, side_len) {
+function drawDownwardEquilateralTriangle(ctx, down_vertex_x, down_vertex_y, side_len) {
     // Compute other two points of triangle.
     var x1 = down_vertex_x - side_len / 2;
 
@@ -96,302 +107,317 @@ var drawDownwardEquilateralTriangle = function(ctx, down_vertex_x, down_vertex_y
     ctx.fill();
     ctx.stroke();
     ctx.closePath();
-};
+}
 
 /**
  * Base class for all scalers. Scalers produce values that are used to change (scale) drawing attributes.
  */
-var Scaler = function(default_val) {
-    this.default_val = default_val ? default_val : 1;
-};
+class Scaler {
+    constructor(default_val) {
+        this.default_val = default_val ? default_val : 1;
+    }
 
-/**
- * Produce a scaling value.
- */
-Scaler.prototype.gen_val = function(input) {
-    return this.default_val;
-};
+    /**
+     * Produce a scaling value.
+     */
+    gen_val(input) {
+        return this.default_val;
+    }
+}
 
 /**
  * Results from painter.draw()
  */
-var DrawResults = function(options) {
-    this.incomplete_features = options.incomplete_features;
-    this.feature_mapper = options.feature_mapper;
-};
+class DrawResults {
+    constructor(options) {
+        this.incomplete_features = options.incomplete_features;
+        this.feature_mapper = options.feature_mapper;
+    }
+}
 
 /**
  * Base class for painters
  *
  * -- Mode and prefs are both optional
  */
-var Painter = function(data, view_start, view_end, prefs, mode) {
-    // Data and data properties
-    this.data = data;
-    // View
-    this.view_start = view_start;
-    this.view_end = view_end;
-    // Drawing prefs
-    this.prefs = _.extend({}, this.default_prefs, prefs);
-    this.mode = mode;
-};
-
-Painter.prototype.default_prefs = {};
-
-/**
- * Draw on the context using a rectangle of width x height using scale w_scale.
- */
-Painter.prototype.draw = (ctx, width, height, w_scale) => {};
-
-/**
- * Get starting drawing position, which is offset a half-base left of coordinate.
- */
-Painter.prototype.get_start_draw_pos = function(chrom_pos, w_scale) {
-    return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, -0.5);
-};
-
-/**
- * Get end drawing position, which is offset a half-base right of coordinate.
- */
-Painter.prototype.get_end_draw_pos = function(chrom_pos, w_scale) {
-    return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0.5);
-};
-
-/**
- * Get drawing position.
- */
-Painter.prototype.get_draw_pos = function(chrom_pos, w_scale) {
-    return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0);
-};
-
-/**
- * Convert chromosome position to drawing position.
- */
-Painter.prototype._chrom_pos_to_draw_pos = function(chrom_pos, w_scale, offset) {
-    return Math.floor(w_scale * (Math.max(0, chrom_pos - this.view_start) + offset));
-};
-
-var LinePainter = function(data, view_start, view_end, prefs, mode) {
-    Painter.call(this, data, view_start, view_end, prefs, mode);
-};
-
-LinePainter.prototype.default_prefs = {
-    min_value: undefined,
-    max_value: undefined,
-    mode: "Histogram",
-    color: "#000",
-    overflow_color: "#F66"
-};
-
-LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
-    var in_path = false;
-    var min_value = this.prefs.min_value;
-    var max_value = this.prefs.max_value;
-    var vertical_range = max_value - min_value;
-    var height_px = height;
-    var view_start = this.view_start;
-    var mode = this.mode;
-    var data = this.data;
-
-    ctx.save();
-
-    // Pixel position of 0 on the y axis
-    var y_zero = Math.round(height + min_value / vertical_range * height);
-
-    // Horizontal line to denote x-axis
-    if (mode !== "Intensity") {
-        ctx.fillStyle = "#aaa";
-        ctx.fillRect(0, y_zero, width, 1);
+class Painter {
+    constructor(data, view_start, view_end, prefs, mode) {
+        // Data and data properties
+        this.data = data;
+        this.default_prefs = {};
+        // View
+        this.view_start = view_start;
+        this.view_end = view_end;
+        // Drawing prefs
+        this.prefs = _.extend({}, this.default_prefs, prefs);
+        this.mode = mode;
     }
 
-    ctx.beginPath();
-    var x_scaled;
-    var y;
-    var delta_x_pxs;
-    if (data.length > 1) {
-        delta_x_pxs = _.map(data.slice(0, -1), (d, i) => Math.ceil((data[i + 1][0] - data[i][0]) * w_scale));
-    } else {
-        delta_x_pxs = [10];
+    static get default_prefs() {
+        return {};
     }
 
-    // Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack).
-    var painter_color = this.prefs.block_color || this.prefs.color;
+    /**
+     * Draw on the context using a rectangle of width x height using scale w_scale.
+     */
+    draw(ctx, width, height, w_scale) {}
 
-    var // Extract RGB from preference color.
-    pref_color = parseInt(painter_color.slice(1), 16);
+    /**
+     * Get starting drawing position, which is offset a half-base left of coordinate.
+     */
+    get_start_draw_pos(chrom_pos, w_scale) {
+        return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, -0.5);
+    }
 
-    var pref_r = (pref_color & 0xff0000) >> 16;
-    var pref_g = (pref_color & 0x00ff00) >> 8;
-    var pref_b = pref_color & 0x0000ff;
-    var top_overflow = false;
-    var bot_overflow = false;
+    /**
+     * Get end drawing position, which is offset a half-base right of coordinate.
+     */
+    get_end_draw_pos(chrom_pos, w_scale) {
+        return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0.5);
+    }
 
-    // Paint track.
-    var delta_x_px;
-    for (var i = 0, len = data.length; i < len; i++) {
-        // Reset attributes for next point.
-        ctx.fillStyle = ctx.strokeStyle = painter_color;
-        top_overflow = bot_overflow = false;
-        delta_x_px = delta_x_pxs[i];
+    /**
+     * Get drawing position.
+     */
+    get_draw_pos(chrom_pos, w_scale) {
+        return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0);
+    }
 
-        x_scaled = Math.floor((data[i][0] - view_start - 0.5) * w_scale);
-        y = data[i][1];
+    /**
+     * Convert chromosome position to drawing position.
+     */
+    _chrom_pos_to_draw_pos(chrom_pos, w_scale, offset) {
+        return Math.floor(w_scale * (Math.max(0, chrom_pos - this.view_start) + offset));
+    }
+}
 
-        // Process Y (scaler) value.
-        if (y === null) {
-            if (in_path && mode === "Filled") {
-                ctx.lineTo(x_scaled, height_px);
-            }
-            in_path = false;
-            continue;
+class LinePainter extends Painter {
+    constructor(data, view_start, view_end, prefs, mode) {
+        super(data, view_start, view_end, prefs, mode);
+    }
+
+    static get default_prefs() {
+        return {
+            min_value: undefined,
+            max_value: undefined,
+            mode: "Histogram",
+            color: "#000",
+            overflow_color: "#F66"
+        };
+    }
+
+    draw(ctx, width, height, w_scale) {
+        var in_path = false;
+        var min_value = this.prefs.min_value;
+        var max_value = this.prefs.max_value;
+        var vertical_range = max_value - min_value;
+        var height_px = height;
+        var view_start = this.view_start;
+        var mode = this.mode;
+        var data = this.data;
+
+        ctx.save();
+
+        // Pixel position of 0 on the y axis
+        var y_zero = Math.round(height + min_value / vertical_range * height);
+
+        // Horizontal line to denote x-axis
+        if (mode !== "Intensity") {
+            ctx.fillStyle = "#aaa";
+            ctx.fillRect(0, y_zero, width, 1);
         }
 
-        // Bound Y value by min, max.
-        if (y < min_value) {
-            bot_overflow = true;
-            y = min_value;
-        } else if (y > max_value) {
-            top_overflow = true;
-            y = max_value;
-        }
-
-        // Draw point.
-        if (mode === "Histogram") {
-            // y becomes the bar height in pixels, which is the negated for canvas coords
-            y = Math.round(y / vertical_range * height_px);
-            ctx.fillRect(x_scaled, y_zero, delta_x_px, -y);
-        } else if (mode === "Intensity") {
-            var saturation = (y - min_value) / vertical_range;
-
-            var // Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color
-            new_r = Math.round(pref_r + (255 - pref_r) * (1 - saturation));
-
-            var new_g = Math.round(pref_g + (255 - pref_g) * (1 - saturation));
-            var new_b = Math.round(pref_b + (255 - pref_b) * (1 - saturation));
-            ctx.fillStyle = `rgb(${new_r},${new_g},${new_b})`;
-            ctx.fillRect(x_scaled, 0, delta_x_px, height_px);
+        ctx.beginPath();
+        var x_scaled;
+        var y;
+        var delta_x_pxs;
+        if (data.length > 1) {
+            delta_x_pxs = _.map(data.slice(0, -1), (d, i) => Math.ceil((data[i + 1][0] - data[i][0]) * w_scale));
         } else {
-            // mode is Coverage/Line or Filled.
+            delta_x_pxs = [10];
+        }
 
-            // Scale Y value.
-            y = Math.round(height_px - (y - min_value) / vertical_range * height_px);
-            if (in_path) {
-                ctx.lineTo(x_scaled, y);
+        // Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack).
+        var painter_color = this.prefs.block_color || this.prefs.color;
+
+        var // Extract RGB from preference color.
+        pref_color = parseInt(painter_color.slice(1), 16);
+        var pref_r = (pref_color & 0xff0000) >> 16;
+        var pref_g = (pref_color & 0x00ff00) >> 8;
+        var pref_b = pref_color & 0x0000ff;
+        var top_overflow = false;
+        var bot_overflow = false;
+
+        // Paint track.
+        var delta_x_px;
+        for (var i = 0, len = data.length; i < len; i++) {
+            // Reset attributes for next point.
+            ctx.fillStyle = ctx.strokeStyle = painter_color;
+            top_overflow = bot_overflow = false;
+            delta_x_px = delta_x_pxs[i];
+
+            x_scaled = Math.floor((data[i][0] - view_start - 0.5) * w_scale);
+            y = data[i][1];
+
+            // Process Y (scaler) value.
+            if (y === null) {
+                if (in_path && mode === "Filled") {
+                    ctx.lineTo(x_scaled, height_px);
+                }
+                in_path = false;
+                continue;
+            }
+
+            // Bound Y value by min, max.
+            if (y < min_value) {
+                bot_overflow = true;
+                y = min_value;
+            } else if (y > max_value) {
+                top_overflow = true;
+                y = max_value;
+            }
+
+            // Draw point.
+            if (mode === "Histogram") {
+                // y becomes the bar height in pixels, which is the negated for canvas coords
+                y = Math.round(y / vertical_range * height_px);
+                ctx.fillRect(x_scaled, y_zero, delta_x_px, -y);
+            } else if (mode === "Intensity") {
+                var saturation = (y - min_value) / vertical_range;
+
+                var // Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color
+                new_r = Math.round(pref_r + (255 - pref_r) * (1 - saturation));
+
+                var new_g = Math.round(pref_g + (255 - pref_g) * (1 - saturation));
+                var new_b = Math.round(pref_b + (255 - pref_b) * (1 - saturation));
+                ctx.fillStyle = `rgb(${new_r},${new_g},${new_b})`;
+                ctx.fillRect(x_scaled, 0, delta_x_px, height_px);
             } else {
-                in_path = true;
-                if (mode === "Filled") {
-                    ctx.moveTo(x_scaled, height_px);
+                // mode is Coverage/Line or Filled.
+
+                // Scale Y value.
+                y = Math.round(height_px - (y - min_value) / vertical_range * height_px);
+                if (in_path) {
                     ctx.lineTo(x_scaled, y);
                 } else {
-                    ctx.moveTo(x_scaled, y);
-                    // Use this approach (note: same as for filled) to draw line from 0 to
-                    // first data point.
-                    //ctx.moveTo(x_scaled, height_px);
-                    //ctx.lineTo(x_scaled, y);
+                    in_path = true;
+                    if (mode === "Filled") {
+                        ctx.moveTo(x_scaled, height_px);
+                        ctx.lineTo(x_scaled, y);
+                    } else {
+                        ctx.moveTo(x_scaled, y);
+                        // Use this approach (note: same as for filled) to draw line from 0 to
+                        // first data point.
+                        //ctx.moveTo(x_scaled, height_px);
+                        //ctx.lineTo(x_scaled, y);
+                    }
                 }
             }
+
+            // Draw lines at boundaries if overflowing min or max
+            ctx.fillStyle = this.prefs.overflow_color;
+            if (top_overflow || bot_overflow) {
+                var overflow_x;
+                if (mode === "Histogram" || mode === "Intensity") {
+                    overflow_x = delta_x_px;
+                } else {
+                    // Line and Filled, which are points
+                    x_scaled -= 2; // Move it over to the left so it's centered on the point
+                    overflow_x = 4;
+                }
+                if (top_overflow) {
+                    ctx.fillRect(x_scaled, 0, overflow_x, 3);
+                }
+                if (bot_overflow) {
+                    ctx.fillRect(x_scaled, height_px - 3, overflow_x, 3);
+                }
+            }
+            ctx.fillStyle = painter_color;
+        }
+        if (mode === "Filled") {
+            if (in_path) {
+                ctx.lineTo(x_scaled, y_zero);
+                ctx.lineTo(0, y_zero);
+            }
+            ctx.fill();
+        } else {
+            ctx.stroke();
         }
 
-        // Draw lines at boundaries if overflowing min or max
-        ctx.fillStyle = this.prefs.overflow_color;
-        if (top_overflow || bot_overflow) {
-            var overflow_x;
-            if (mode === "Histogram" || mode === "Intensity") {
-                overflow_x = delta_x_px;
-            } else {
-                // Line and Filled, which are points
-                x_scaled -= 2; // Move it over to the left so it's centered on the point
-                overflow_x = 4;
-            }
-            if (top_overflow) {
-                ctx.fillRect(x_scaled, 0, overflow_x, 3);
-            }
-            if (bot_overflow) {
-                ctx.fillRect(x_scaled, height_px - 3, overflow_x, 3);
-            }
-        }
-        ctx.fillStyle = painter_color;
+        ctx.restore();
     }
-    if (mode === "Filled") {
-        if (in_path) {
-            ctx.lineTo(x_scaled, y_zero);
-            ctx.lineTo(0, y_zero);
-        }
-        ctx.fill();
-    } else {
-        ctx.stroke();
-    }
-
-    ctx.restore();
-};
+}
 
 /**
  * Mapper that contains information about feature locations and data.
  */
-var FeaturePositionMapper = function(slot_height) {
-    this.feature_positions = {};
-    this.slot_height = slot_height;
-    this.translation = 0;
-    this.y_translation = 0;
-};
-
-/**
- * Map feature data to a position defined by <slot, x_start, x_end>.
- */
-FeaturePositionMapper.prototype.map_feature_data = function(feature_data, slot, x_start, x_end) {
-    if (!this.feature_positions[slot]) {
-        this.feature_positions[slot] = [];
-    }
-    this.feature_positions[slot].push({
-        data: feature_data,
-        x_start: x_start,
-        x_end: x_end
-    });
-};
-
-/**
- * Get feature data for position <x, y>
- */
-FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
-    // Find slot using Y.
-    var slot = Math.floor((y - this.y_translation) / this.slot_height);
-
-    var feature_dict;
-
-    // May not be over a slot due to padding, margin, etc.
-    if (!this.feature_positions[slot]) {
-        return null;
+class FeaturePositionMapper {
+    constructor(slot_height) {
+        this.feature_positions = {};
+        this.slot_height = slot_height;
+        this.translation = 0;
+        this.y_translation = 0;
     }
 
-    // Find feature using X.
-    x += this.translation;
-    for (var i = 0; i < this.feature_positions[slot].length; i++) {
-        feature_dict = this.feature_positions[slot][i];
-        if (x >= feature_dict.x_start && x <= feature_dict.x_end) {
-            return feature_dict.data;
+    /**
+     * Map feature data to a position defined by <slot, x_start, x_end>.
+     */
+    map_feature_data(feature_data, slot, x_start, x_end) {
+        if (!this.feature_positions[slot]) {
+            this.feature_positions[slot] = [];
+        }
+        this.feature_positions[slot].push({
+            data: feature_data,
+            x_start: x_start,
+            x_end: x_end
+        });
+    }
+
+    /**
+     * Get feature data for position <x, y>
+     */
+    get_feature_data(x, y) {
+        // Find slot using Y.
+        var slot = Math.floor((y - this.y_translation) / this.slot_height);
+
+        var feature_dict;
+
+        // May not be over a slot due to padding, margin, etc.
+        if (!this.feature_positions[slot]) {
+            return null;
+        }
+
+        // Find feature using X.
+        x += this.translation;
+        for (var i = 0; i < this.feature_positions[slot].length; i++) {
+            feature_dict = this.feature_positions[slot][i];
+            if (x >= feature_dict.x_start && x <= feature_dict.x_end) {
+                return feature_dict.data;
+            }
         }
     }
-};
+}
 
 /**
  * Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work.
  * Painter uses a 0-based, half-open coordinate system; start coordinate is closed--included--and the end is open.
  * This coordinate system matches the BED format.
  */
-var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
-    Painter.call(this, data, view_start, view_end, prefs, mode);
-    this.alpha_scaler = alpha_scaler ? alpha_scaler : new Scaler();
-    this.height_scaler = height_scaler ? height_scaler : new Scaler();
-    this.max_label_length = 200;
-};
+class FeaturePainter extends Painter {
+    constructor(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
+        super(data, view_start, view_end, prefs, mode);
+        this.alpha_scaler = alpha_scaler ? alpha_scaler : new Scaler();
+        this.height_scaler = height_scaler ? height_scaler : new Scaler();
+        this.max_label_length = 200;
+    }
 
-FeaturePainter.prototype.default_prefs = {
-    block_color: "#FFF",
-    connector_color: "#FFF"
-};
-
-_.extend(FeaturePainter.prototype, {
-    get_required_height: function(rows_required, width) {
+    static get default_prefs() {
+        return {
+            block_color: "#FFF",
+            connector_color: "#FFF"
+        };
+    }
+    get_required_height(rows_required, width) {
         // y_scale is the height per row
         var required_height = this.get_row_height();
 
@@ -402,24 +428,19 @@ _.extend(FeaturePainter.prototype, {
             required_height = rows_required * y_scale;
         }
         return required_height + this.get_top_padding(width);
-    },
+    }
 
     /** Extra padding before first row of features */
-    get_top_padding: function(width) {
+    get_top_padding(width) {
         return 0;
-    },
+    }
 
     /**
      * Draw data on ctx using slots and within the rectangle defined by width and height. Returns
      * a FeaturePositionMapper object with information about where features were drawn.
      */
-    draw: function(ctx, width, height, w_scale, slots) {
-        var data = this.data;
-        var view_start = this.view_start;
-        var view_end = this.view_end;
-
+    draw(ctx, width, height, w_scale, slots) {
         ctx.save();
-
         ctx.fillStyle = this.prefs.block_color;
         ctx.textAlign = "right";
 
@@ -428,26 +449,29 @@ _.extend(FeaturePainter.prototype, {
         var x_draw_coords;
         var incomplete_features = [];
 
-        for (var i = 0, len = data.length; i < len; i++) {
-            var feature = data[i];
+        for (var i = 0, len = this.data.length; i < len; i++) {
+            var feature = this.data[i];
             var feature_uid = feature[0];
             var feature_start = feature[1];
             var feature_end = feature[2];
 
-            var // Slot valid only if features are slotted and this feature is slotted;
+            // Slot valid only if features are slotted and this feature is slotted;
             // feature may not be due to lack of space.
-            slot = slots && slots[feature_uid] !== undefined ? slots[feature_uid].slot : null;
+            var slot = slots && slots[feature_uid] !== undefined ? slots[feature_uid].slot : null;
 
             // Draw feature if (a) mode is dense or feature is slotted (as it must be for all non-dense modes) and
             // (b) there's overlap between the feature and drawing region.
-            if ((this.mode === "Dense" || slot !== null) && (feature_start < view_end && feature_end > view_start)) {
+            if (
+                (this.mode === "Dense" || slot !== null) &&
+                (feature_start < this.view_end && feature_end > this.view_start)
+            ) {
                 x_draw_coords = this.draw_element(
                     ctx,
                     this.mode,
                     feature,
                     slot,
-                    view_start,
-                    view_end,
+                    this.view_start,
+                    this.view_end,
                     w_scale,
                     y_scale,
                     width
@@ -455,7 +479,7 @@ _.extend(FeaturePainter.prototype, {
                 feature_mapper.map_feature_data(feature, slot, x_draw_coords[0], x_draw_coords[1]);
 
                 // Add to incomplete features if it's not drawn completely in region.
-                if (feature_start < view_start || feature_end > view_end) {
+                if (feature_start < this.view_start || feature_end > this.view_end) {
                     incomplete_features.push(feature);
                 }
             }
@@ -468,43 +492,29 @@ _.extend(FeaturePainter.prototype, {
             incomplete_features: incomplete_features,
             feature_mapper: feature_mapper
         });
-    },
+    }
 
     /**
      * Abstract function for drawing an individual feature.
      */
-    draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
+    draw_element(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
         return [0, 0];
     }
-});
+}
 
-// Constants specific to feature tracks moved here (HACKING, these should
-// basically all be configuration options)
-var DENSE_TRACK_HEIGHT = 10;
+class LinkedFeaturePainter extends FeaturePainter {
+    constructor(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
+        super(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
+        // Whether to draw a single connector in the background that spans the entire feature (the intron fishbone)
+        this.draw_background_connector = true;
+        // Whether to call draw_connector for every pair of blocks
+        this.draw_individual_connectors = false;
+    }
 
-var NO_DETAIL_TRACK_HEIGHT = 3;
-var SQUISH_TRACK_HEIGHT = 5;
-var PACK_TRACK_HEIGHT = 10;
-var NO_DETAIL_FEATURE_HEIGHT = 1;
-var DENSE_FEATURE_HEIGHT = 9;
-var SQUISH_FEATURE_HEIGHT = 3;
-var PACK_FEATURE_HEIGHT = 9;
-var LABEL_SPACING = 2;
-var CONNECTOR_COLOR = "#ccc";
-
-var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
-    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
-    // Whether to draw a single connector in the background that spans the entire feature (the intron fishbone)
-    this.draw_background_connector = true;
-    // Whether to call draw_connector for every pair of blocks
-    this.draw_individual_connectors = false;
-};
-
-_.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
     /**
      * Height of a single row, depends on mode
      */
-    get_row_height: function() {
+    get_row_height() {
         var mode = this.mode;
         var height;
         if (mode === "Dense") {
@@ -518,40 +528,32 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             height = PACK_TRACK_HEIGHT;
         }
         return height;
-    },
+    }
 
     /**
      * Draw a feature. Returns an array with feature's start and end X coordinates.
      */
-    draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
-        var feature_uid = feature[0];
+    draw_element(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
+        // var feature_uid = feature[0];
         var feature_start = feature[1];
         var feature_end = feature[2];
         var feature_name = feature[3];
         var feature_strand = feature[4];
-
-        var // -0.5 to offset region between bases.
-        f_start = Math.floor(Math.max(0, (feature_start - tile_low - 0.5) * w_scale));
-
+        // -0.5 to offset region between bases.
+        var f_start = Math.floor(Math.max(0, (feature_start - tile_low - 0.5) * w_scale));
         var f_end = Math.ceil(Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)));
-
         var draw_start = f_start;
         var draw_end = f_end;
-
         var y_start = (mode === "Dense" ? 0 : 0 + slot) * y_scale + this.get_top_padding(width);
-
-        var thickness;
-        var y_start;
         var thick_start = null;
         var thick_end = null;
 
-        var // TODO: is there any reason why block, label color cannot be set at the Painter level?
+        // TODO: is there any reason why block, label color cannot be set at the Painter level?
         // For now, assume '.' === '+'
-        block_color =
+        var block_color =
             !feature_strand || feature_strand === "+" || feature_strand === "."
                 ? this.prefs.block_color
                 : this.prefs.reverse_strand_color;
-
         var label_color = this.prefs.label_color;
 
         // Set global alpha.
@@ -660,7 +662,6 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 }
 
                 // Draw blocks.
-                var start_and_height;
                 for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
                     var block = feature_blocks[k];
 
@@ -771,29 +772,18 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
 
         return [draw_start, draw_end];
     }
-});
+}
 
-var ReadPainter = function(
-    data,
-    view_start,
-    view_end,
-    prefs,
-    mode,
-    alpha_scaler,
-    height_scaler,
-    ref_seq,
-    base_color_fn
-) {
-    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
-    this.ref_seq = ref_seq ? ref_seq.data : null;
-    this.base_color_fn = base_color_fn;
-};
-
-_.extend(ReadPainter.prototype, FeaturePainter.prototype, {
+class ReadPainter extends FeaturePainter {
+    constructor(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq, base_color_fn) {
+        super(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
+        this.ref_seq = ref_seq ? ref_seq.data : null;
+        this.base_color_fn = base_color_fn;
+    }
     /**
      * Returns height based on mode.
      */
-    get_row_height: function() {
+    get_row_height() {
         var height;
         var mode = this.mode;
         if (mode === "Dense") {
@@ -808,14 +798,14 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
             }
         }
         return height;
-    },
+    }
 
     /**
      * Parse CIGAR string to get (a) a list of contiguous drawing blocks (MD=X) and
      * (b) an array of [ op_index, op_len ] pairs where op_index is an index into the
      * string 'MIDNSHP=X' Return value is a dictionary with two entries, blocks and cigar
      */
-    _parse_cigar: function(cigar_str) {
+    _parse_cigar(cigar_str) {
         var cigar_ops = "MIDNSHP=X";
 
         // Parse cigar.
@@ -852,12 +842,12 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
             blocks: blocks,
             cigar: parsed_cigar
         };
-    },
+    }
 
     /**
      * Draw a single read from reference-based read sequence and cigar.
      */
-    draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) {
+    draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) {
         // Helper function to update base and sequnence offsets.
         var update_base_offset = (offset, cig_op, cig_len) => {
             if ("M=NXD".indexOf(cig_op) !== -1) {
@@ -988,11 +978,11 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
 
                     // Draw sequence. Because cur_seq starts and read/tile start, go to there to start writing.
                     var start_pos = Math.max(seq_start, tile_low);
-                    for (var c = 0; c < cur_seq.length; c++) {
+                    for (let c = 0; c < cur_seq.length; c++) {
                         // 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.
-                            var c_start = Math.floor(Math.max(0, (start_pos + c - tile_low) * w_scale));
+                            let 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);
@@ -1066,8 +1056,8 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
                                         break;
                                 }
                                 // Draw sequence.
-                                for (var c = 0, str_len = seq.length; c < str_len; c++) {
-                                    var c_start = Math.floor(Math.max(0, (seq_start + c - tile_low) * w_scale));
+                                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));
                                     ctx.fillText(seq[c], c_start - (s_end - s_start) / 2, y_start);
                                 }
                             } else {
@@ -1110,7 +1100,7 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
         var item;
         var type;
         var data;
-        for (var i = 0; i < draw_last.length; i++) {
+        for (let i = 0; i < draw_last.length; i++) {
             item = draw_last[i];
             type = item.type;
             data = item.data;
@@ -1123,15 +1113,14 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
                 drawDownwardEquilateralTriangle(ctx, data[0], data[1], data[2]);
             }
         }
-    },
+    }
 
     /**
      * Draw a complete read pair
      */
-    draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
+    draw_element(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
         // All features need a start, end, and vertical center.
-        var feature_uid = feature[0];
-
+        // var feature_uid = feature[0];
         var feature_start = feature[1];
         var feature_end = feature[2];
         var feature_name = feature[3];
@@ -1145,8 +1134,6 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
 
         var draw_height = mode === "Pack" ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT;
 
-        var label_color = this.prefs.label_color;
-
         // Draw read.
         if (feature[5] instanceof Array) {
             // Read is paired.
@@ -1234,79 +1221,74 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
         // FIXME: provide actual coordinates for drawn read.
         return [0, 0];
     }
-});
+}
 
-var ArcLinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
-    LinkedFeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
-    // Need to know the longest feature length for adding spacing
-    this.longest_feature_length = this.calculate_longest_feature_length();
-    this.draw_background_connector = false;
-    this.draw_individual_connectors = true;
-};
+class ArcLinkedFeaturePainter extends LinkedFeaturePainter {
+    constructor(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
+        super(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
+        // Need to know the longest feature length for adding spacing
+        this.longest_feature_length = this.calculate_longest_feature_length();
+        this.draw_background_connector = false;
+        this.draw_individual_connectors = true;
+    }
 
-_.extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeaturePainter.prototype, {
-    calculate_longest_feature_length: function() {
+    calculate_longest_feature_length() {
         var longest_feature_length = 0;
-        for (var i = 0, len = this.data.length; i < len; i++) {
+        for (let i = 0, len = this.data.length; i < len; i++) {
             var feature = this.data[i];
             var feature_start = feature[1];
             var feature_end = feature[2];
             longest_feature_length = Math.max(longest_feature_length, feature_end - feature_start);
         }
         return longest_feature_length;
-    },
+    }
 
-    get_top_padding: function(width) {
+    get_top_padding(width) {
         var view_range = this.view_end - this.view_start;
         var w_scale = width / view_range;
         return Math.min(128, Math.ceil(this.longest_feature_length / 2 * w_scale));
-    },
+    }
 
-    draw_connector: function(ctx, block1_start, block1_end, block2_start, block2_end, y_start) {
+    draw_connector(ctx, block1_start, block1_end, block2_start, block2_end, y_start) {
         // Arc drawing -- from closest endpoints
         var x_center = (block1_end + block2_start) / 2;
-
         var radius = block2_start - x_center;
-
-        // For full half circles
-        var angle1 = Math.PI;
-
-        var angle2 = 0;
         if (radius > 0) {
             ctx.beginPath();
             ctx.arc(x_center, y_start, block2_start - x_center, Math.PI, 0);
             ctx.stroke();
         }
     }
-});
+}
 
 // Color stuff from less.js
 
-var Color = function(rgb, a) {
-    /**
-     * The end goal here, is to parse the arguments
-     * into an integer triplet, such as `128, 255, 0`
-     *
-     * This facilitates operations and conversions.
-     */
-    if (Array.isArray(rgb)) {
-        this.rgb = rgb;
-    } else if (rgb.length == 6) {
-        this.rgb = rgb.match(/.{2}/g).map(c => parseInt(c, 16));
-    } else if (rgb.length == 7) {
-        this.rgb = rgb
-            .substring(1, 7)
-            .match(/.{2}/g)
-            .map(c => parseInt(c, 16));
-    } else {
-        this.rgb = rgb.split("").map(c => parseInt(c + c, 16));
+class Color {
+    constructor(rgb, a) {
+        /**
+         * The end goal here, is to parse the arguments
+         * into an integer triplet, such as `128, 255, 0`
+         *
+         * This facilitates operations and conversions.
+         */
+        if (Array.isArray(rgb)) {
+            this.rgb = rgb;
+        } else if (rgb.length == 6) {
+            this.rgb = rgb.match(/.{2}/g).map(c => parseInt(c, 16));
+        } else if (rgb.length == 7) {
+            this.rgb = rgb
+                .substring(1, 7)
+                .match(/.{2}/g)
+                .map(c => parseInt(c, 16));
+        } else {
+            this.rgb = rgb.split("").map(c => parseInt(c + c, 16));
+        }
+        this.alpha = typeof a === "number" ? a : 1;
     }
-    this.alpha = typeof a === "number" ? a : 1;
-};
-Color.prototype = {
-    eval: function() {
+
+    eval() {
         return this;
-    },
+    }
 
     //
     // If we have some transparency, the only way to represent it
@@ -1314,7 +1296,7 @@ Color.prototype = {
     // which has better compatibility with older browsers.
     // Values are capped between `0` and `255`, rounded and zero-padded.
     //
-    toCSS: function() {
+    toCSS() {
         if (this.alpha < 1.0) {
             return `rgba(${this.rgb
                 .map(c => Math.round(c))
@@ -1329,9 +1311,9 @@ Color.prototype = {
                 })
                 .join("")}`;
         }
-    },
+    }
 
-    toHSL: function() {
+    toHSL() {
         var r = this.rgb[0] / 255;
         var g = this.rgb[1] / 255;
         var b = this.rgb[2] / 255;
@@ -1362,9 +1344,9 @@ Color.prototype = {
             h /= 6;
         }
         return { h: h * 360, s: s, l: l, a: a };
-    },
+    }
 
-    toARGB: function() {
+    toARGB() {
         var argb = [Math.round(this.alpha * 255)].concat(this.rgb);
         return `#${argb
             .map(i => {
@@ -1373,9 +1355,9 @@ Color.prototype = {
                 return i.length === 1 ? `0${i}` : i;
             })
             .join("")}`;
-    },
+    }
 
-    mix: function(color2, weight) {
+    mix(color2, weight) {
         var color1 = this;
 
         var p = weight; // .value / 100.0;
@@ -1395,161 +1377,165 @@ Color.prototype = {
 
         return new Color(rgb, alpha);
     }
-};
+}
 
 // End colors from less.js
 
-var LinearRamp = function(start_color, end_color, start_value, end_value) {
-    /**
-     * Simple linear gradient
-     */
-    this.start_color = new Color(start_color);
-    this.end_color = new Color(end_color);
-    this.start_value = start_value;
-    this.end_value = end_value;
-    this.value_range = end_value - start_value;
-};
-
-LinearRamp.prototype.map_value = function(value) {
-    value = Math.max(value, this.start_value);
-    value = Math.min(value, this.end_value);
-    value = (value - this.start_value) / this.value_range;
-    // HACK: just red for now
-    // return "hsl(0,100%," + (value * 100) + "%)"
-    return this.start_color.mix(this.end_color, 1 - value).toCSS();
-};
-
-var SplitRamp = function(start_color, middle_color, end_color, start_value, end_value) {
-    /**
-     * Two gradients split away from 0
-     */
-    this.positive_ramp = new LinearRamp(middle_color, end_color, 0, end_value);
-    this.negative_ramp = new LinearRamp(middle_color, start_color, 0, -start_value);
-    this.start_value = start_value;
-    this.end_value = end_value;
-};
-
-SplitRamp.prototype.map_value = function(value) {
-    value = Math.max(value, this.start_value);
-    value = Math.min(value, this.end_value);
-    if (value >= 0) {
-        return this.positive_ramp.map_value(value);
-    } else {
-        return this.negative_ramp.map_value(-value);
+class LinearRamp {
+    constructor(start_color, end_color, start_value, end_value) {
+        /**
+         * Simple linear gradient
+         */
+        this.start_color = new Color(start_color);
+        this.end_color = new Color(end_color);
+        this.start_value = start_value;
+        this.end_value = end_value;
+        this.value_range = end_value - start_value;
     }
-};
 
-var DiagonalHeatmapPainter = function(data, view_start, view_end, prefs, mode) {
-    Painter.call(this, data, view_start, view_end, prefs, mode);
-    var i;
-    var len;
+    map_value(value) {
+        value = Math.max(value, this.start_value);
+        value = Math.min(value, this.end_value);
+        value = (value - this.start_value) / this.value_range;
+        // HACK: just red for now
+        // return "hsl(0,100%," + (value * 100) + "%)"
+        return this.start_color.mix(this.end_color, 1 - value).toCSS();
+    }
+}
 
-    if (this.prefs.min_value === undefined) {
-        var min_value = Infinity;
-        for (i = 0, len = this.data.length; i < len; i++) {
-            min_value = Math.min(min_value, this.data[i][6]);
+class SplitRamp {
+    constructor(start_color, middle_color, end_color, start_value, end_value) {
+        /**
+         * Two gradients split away from 0
+         */
+        this.positive_ramp = new LinearRamp(middle_color, end_color, 0, end_value);
+        this.negative_ramp = new LinearRamp(middle_color, start_color, 0, -start_value);
+        this.start_value = start_value;
+        this.end_value = end_value;
+    }
+
+    map_value(value) {
+        value = Math.max(value, this.start_value);
+        value = Math.min(value, this.end_value);
+        if (value >= 0) {
+            return this.positive_ramp.map_value(value);
+        } else {
+            return this.negative_ramp.map_value(-value);
         }
-        this.prefs.min_value = min_value;
     }
-    if (this.prefs.max_value === undefined) {
-        var max_value = -Infinity;
-        for (i = 0, len = this.data.length; i < len; i++) {
-            max_value = Math.max(max_value, this.data[i][6]);
+}
+
+class DiagonalHeatmapPainter extends Painter {
+    constructor(data, view_start, view_end, prefs, mode) {
+        super(data, view_start, view_end, prefs, mode);
+        var i;
+        var len;
+
+        if (this.prefs.min_value === undefined) {
+            var min_value = Infinity;
+            for (i = 0, len = this.data.length; i < len; i++) {
+                min_value = Math.min(min_value, this.data[i][6]);
+            }
+            this.prefs.min_value = min_value;
+        }
+        if (this.prefs.max_value === undefined) {
+            var max_value = -Infinity;
+            for (i = 0, len = this.data.length; i < len; i++) {
+                max_value = Math.max(max_value, this.data[i][6]);
+            }
+            this.prefs.max_value = max_value;
         }
-        this.prefs.max_value = max_value;
-    }
-};
-
-DiagonalHeatmapPainter.prototype.default_prefs = {
-    min_value: undefined,
-    max_value: undefined,
-    mode: "Heatmap",
-    pos_color: "#FF8C00",
-    neg_color: "#4169E1"
-};
-
-DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
-    var min_value = this.prefs.min_value;
-    var max_value = this.prefs.max_value;
-    var value_range = max_value - min_value;
-    var height_px = height;
-    var view_start = this.view_start;
-    var mode = this.mode;
-    var data = this.data;
-    var invsqrt2 = 1 / Math.sqrt(2);
-
-    var ramp = new SplitRamp(this.prefs.neg_color, "#FFFFFF", this.prefs.pos_color, min_value, max_value);
-
-    var d;
-    var s1;
-    var e1;
-    var s2;
-    var e2;
-    var value;
-
-    var scale = p => (p - view_start) * w_scale;
-
-    ctx.save();
-
-    // Draw into triangle, then rotate and scale
-    ctx.rotate(-45 * Math.PI / 180);
-    ctx.scale(invsqrt2, invsqrt2);
-
-    // Paint track.
-    for (var i = 0, len = data.length; i < len; i++) {
-        d = data[i];
-
-        s1 = scale(d[1]);
-        e1 = scale(d[2]);
-        s2 = scale(d[4]);
-        e2 = scale(d[5]);
-        value = d[6];
-
-        ctx.fillStyle = ramp.map_value(value);
-        ctx.fillRect(s1, s2, e1 - s1, e2 - s2);
     }
 
-    ctx.restore();
-};
+    static get default_prefs() {
+        return {
+            min_value: undefined,
+            max_value: undefined,
+            mode: "Heatmap",
+            pos_color: "#FF8C00",
+            neg_color: "#4169E1"
+        };
+    }
+
+    draw(ctx, width, height, w_scale) {
+        var min_value = this.prefs.min_value;
+        var max_value = this.prefs.max_value;
+        var view_start = this.view_start;
+        var invsqrt2 = 1 / Math.sqrt(2);
+
+        var ramp = new SplitRamp(this.prefs.neg_color, "#FFFFFF", this.prefs.pos_color, min_value, max_value);
+
+        var d;
+        var s1;
+        var e1;
+        var s2;
+        var e2;
+        var value;
+
+        var scale = p => (p - view_start) * w_scale;
+
+        ctx.save();
+
+        // Draw into triangle, then rotate and scale
+        ctx.rotate(-45 * Math.PI / 180);
+        ctx.scale(invsqrt2, invsqrt2);
+
+        // Paint track.
+        for (var i = 0, len = this.data.length; i < len; i++) {
+            d = this.data[i];
+
+            s1 = scale(d[1]);
+            e1 = scale(d[2]);
+            s2 = scale(d[4]);
+            e2 = scale(d[5]);
+            value = d[6];
+
+            ctx.fillStyle = ramp.map_value(value);
+            ctx.fillRect(s1, s2, e1 - s1, e2 - s2);
+        }
+
+        ctx.restore();
+    }
+}
 
 /**
  * Utilities for painting reads.
  */
-var ReadPainterUtils = function(ctx, row_height, px_per_base, mode) {
-    this.ctx = ctx;
-    this.row_height = row_height;
-    this.px_per_base = px_per_base;
-    this.draw_details = (mode === "Pack" || mode === "Auto") && px_per_base >= ctx.canvas.manager.char_width_px;
-    this.delete_details_thickness = 0.2;
-};
+class ReadPainterUtils {
+    constructor(ctx, row_height, px_per_base, mode) {
+        this.ctx = ctx;
+        this.row_height = row_height;
+        this.px_per_base = px_per_base;
+        this.draw_details = (mode === "Pack" || mode === "Auto") && px_per_base >= ctx.canvas.manager.char_width_px;
+        this.delete_details_thickness = 0.2;
+    }
 
-_.extend(ReadPainterUtils.prototype, {
     /**
      * Draw deletion of base(s).
      * @param draw_detail if true, drawing in detail and deletion is drawn more subtly
      */
-    draw_deletion: function(x, y, len) {
+    draw_deletion(x, y, len) {
         this.ctx.fillStyle = "black";
         var thickness = (this.draw_details ? this.delete_details_thickness : 1) * this.row_height;
         y += 0.5 * (this.row_height - thickness);
         this.ctx.fillRect(x, y, len * this.px_per_base, thickness);
     }
-});
+}
 
 /**
  * Paints variant data onto canvas.
  */
-var VariantPainter = function(data, view_start, view_end, prefs, mode, base_color_fn) {
-    Painter.call(this, data, view_start, view_end, prefs, mode);
-    this.base_color_fn = base_color_fn;
-    this.divider_height = 1;
-};
+class VariantPainter extends Painter {
+    constructor(data, view_start, view_end, prefs, mode, base_color_fn) {
+        super(data, view_start, view_end, prefs, mode);
+        this.base_color_fn = base_color_fn;
+        this.divider_height = 1;
+    }
 
-_.extend(VariantPainter.prototype, Painter.prototype, {
     /**
      * Height of a single row, depends on mode
      */
-    get_row_height: function() {
+    get_row_height() {
         var mode = this.mode;
         var height;
         if (mode === "Dense") {
@@ -1561,12 +1547,12 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
             height = PACK_TRACK_HEIGHT;
         }
         return height;
-    },
+    }
 
     /**
      * Returns required height to draw a particular number of samples in a given mode.
      */
-    get_required_height: function(num_samples) {
+    get_required_height(num_samples) {
         // FIXME: for single-sample data, height should be summary_height when zoomed out and
         // row_height when zoomed in.
         var height = this.prefs.summary_height;
@@ -1576,12 +1562,12 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
             height += this.divider_height + num_samples * this.get_row_height();
         }
         return height;
-    },
+    }
 
     /**
      * Draw on the context using a rectangle of width x height with scale w_scale.
      */
-    draw: function(ctx, width, height, w_scale) {
+    draw(ctx, width, height, w_scale) {
         ctx.save();
 
         var /**
@@ -1618,11 +1604,8 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
         var locus_data;
 
         var pos;
-        var id;
         var ref;
         var alt;
-        var qual;
-        var filter;
         var sample_gts;
         var allele_counts;
         var variant;
@@ -1764,7 +1747,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
 
         ctx.restore();
     }
-});
+}
 
 export default {
     Scaler: Scaler,
diff --git a/client/galaxy/scripts/viz/trackster/slotting.js b/client/galaxy/scripts/viz/trackster/slotting.js
index 62fca2451b5..c4b4095ce93 100644
--- a/client/galaxy/scripts/viz/trackster/slotting.js
+++ b/client/galaxy/scripts/viz/trackster/slotting.js
@@ -45,7 +45,7 @@ extend(FeatureSlotter.prototype, {
 
         var draw_end = Math.ceil(feature[2] * this.w_scale);
         var f_name = feature[3];
-        var text_align;
+        //var text_align;
 
         // Update start, end drawing locations to include feature name.
         // Try to put the name on the left, if not, put on right.
@@ -55,10 +55,10 @@ extend(FeatureSlotter.prototype, {
             var text_len = this.measureText(f_name).width + (LABEL_SPACING + PACK_SPACING);
             if (draw_start - text_len >= 0) {
                 draw_start -= text_len;
-                text_align = "left";
+                //text_align = "left";
             } else {
                 draw_end += text_len;
-                text_align = "right";
+                //text_align = "right";
             }
         }
 
@@ -130,7 +130,7 @@ extend(FeatureSlotter.prototype, {
         // Loop through features to (a) find those that are not yet slotted and (b) update
         // those that are slotted if new information is availabe. For (a), features already
         // slotted (based on slotting from other tiles) will retain their current slot.
-        for (var i = 0, len = features.length; i < len; i++) {
+        for (let i = 0, len = features.length; i < len; i++) {
             feature = features[i];
             feature_uid = feature[0];
             var slotted_info = this.slots[feature_uid];
@@ -163,7 +163,7 @@ extend(FeatureSlotter.prototype, {
         // Slot unslotted features.
 
         // Do slotting.
-        for (var i = 0, len = undone.length; i < len; i++) {
+        for (let i = 0, len = undone.length; i < len; i++) {
             feature = features[undone[i]];
             feature_uid = feature[0];
             var draw_coords = this._get_draw_coords(feature);
diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js
index dbcb9821ddb..0c1973d4930 100644
--- a/client/galaxy/scripts/viz/trackster/tracks.js
+++ b/client/galaxy/scripts/viz/trackster/tracks.js
@@ -1,5 +1,6 @@
 import _l from "utils/localization";
 import * as _ from "libs/underscore";
+import * as Backbone from "libs/backbone";
 import visualization from "viz/visualization";
 import viz_views from "viz/viz_views";
 import util from "viz/trackster/util";
@@ -13,6 +14,9 @@ import bbi from "viz/bbi-data-manager";
 import "ui/editable-text";
 var extend = _.extend;
 
+/* global $ */
+/* global Galaxy */
+
 // ---- Web UI specific utilities ----
 
 /**
@@ -24,9 +28,9 @@ var html_elt_js_obj_dict = {};
 /**
  * Designates an HTML as a container.
  */
-var is_container = (element, obj) => {
+function is_container(element, obj) {
     html_elt_js_obj_dict[element.attr("id")] = obj;
-};
+}
 
 /**
  * Make `element` moveable within parent and sibling elements by dragging `handle` (a selector).
@@ -37,7 +41,7 @@ var is_container = (element, obj) => {
  * @param container_selector selector used to identify possible containers for this element
  * @param element_js_obj JavaScript object associated with element; used
  */
-var moveable = (element, handle_class, container_selector, element_js_obj) => {
+function moveable(element, handle_class, container_selector, element_js_obj) {
     // HACK: set default value for container selector.
     container_selector = ".group";
 
@@ -48,11 +52,9 @@ var moveable = (element, handle_class, container_selector, element_js_obj) => {
     element
         .bind("drag", { handle: `.${handle_class}`, relative: true }, function(e, d) {
             var element = $(this);
-            var parent = $(this).parent();
-
-            var // Only sorting amongst tracks and groups.
-            children = parent.children(".track,.group");
-
+            var parent = element.parent();
+            // Only sorting amongst tracks and groups.
+            var children = parent.children(".track,.group");
             var this_obj = html_elt_js_obj_dict[$(this).attr("id")];
             var child;
             var container;
@@ -144,46 +146,47 @@ var moveable = (element, handle_class, container_selector, element_js_obj) => {
         .bind("dragend", function() {
             $(this).removeClass("dragging");
         });
-};
+}
 
 /**
  * Init constants & functions used throughout trackster.
  */
-var // Padding at the top of tracks for error messages
-ERROR_PADDING = 20;
 
-var // Maximum number of rows un a slotted track
-MAX_FEATURE_DEPTH = 100;
+// Padding at the top of tracks for error messages
+const ERROR_PADDING = 20;
 
-var // Minimum width for window for squish to be used.
-MIN_SQUISH_VIEW_WIDTH = 12000;
+// Maximum number of rows un a slotted track
+const MAX_FEATURE_DEPTH = 100;
 
-var // Number of pixels per tile, not including left offset.
-TILE_SIZE = 400;
+// Minimum width for window for squish to be used.
+const MIN_SQUISH_VIEW_WIDTH = 12000;
 
-var DEFAULT_DATA_QUERY_WAIT = 5000;
+// Number of pixels per tile, not including left offset.
+const TILE_SIZE = 400;
 
-var // Maximum number of chromosomes that are selectable at any one time.
-MAX_CHROMS_SELECTABLE = 100;
+const DEFAULT_DATA_QUERY_WAIT = 5000;
 
-var DATA_ERROR = "Cannot display dataset due to an error. ";
+// Maximum number of chromosomes that are selectable at any one time.
+const MAX_CHROMS_SELECTABLE = 100;
 
-var DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.";
+const DATA_ERROR = "Cannot display dataset due to an error. ";
 
-var DATA_NONE = "No data for this chrom/contig.";
+const DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.";
 
-var DATA_PENDING =
+const DATA_NONE = "No data for this chrom/contig.";
+
+const DATA_PENDING =
     "Preparing data. This can take a while for a large dataset. " +
     "If the visualization is saved and closed, preparation will continue in the background.";
 
-var DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ";
-var DATA_LOADING = "Loading data...";
-var DATA_OK = "Ready for display";
-var TILE_CACHE_SIZE = 10;
-var DATA_CACHE_SIZE = 20;
-
-var // Numerical/continuous data display modes.
-CONTINUOUS_DATA_MODES = ["Histogram", "Line", "Filled", "Intensity"];
+const DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ";
+//var DATA_LOADING = "Loading data...";
+const DATA_OK = "Ready for display";
+const TILE_CACHE_SIZE = 10;
+//var DATA_CACHE_SIZE = 20;
+//
+// Numerical/continuous data display modes.
+const CONTINUOUS_DATA_MODES = ["Histogram", "Line", "Filled", "Intensity"];
 
 /**
  * Round a number to a given number of decimal places.
@@ -248,7 +251,10 @@ var Drawable = function(view, container, obj_dict) {
     this.action_icons = {};
 
     // -- Set up drawable configuration. --
-    this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values(this.config_params, obj_dict.prefs);
+    this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values(
+        this.build_config_params(),
+        obj_dict.prefs
+    );
 
     // If there's no saved name, use object name.
     if (!this.config.get_value("name")) {
@@ -342,6 +348,10 @@ extend(Drawable.prototype, {
         }
     ],
 
+    build_config_params: function() {
+        return this.config_params;
+    },
+
     config_onchange: function() {},
 
     init: function() {},
@@ -723,7 +733,6 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
             for (i = 0; i < num_drawables; i++) {
                 drawable = this.drawables[i];
                 if (drawable.get_type() !== a_type) {
-                    can_composite = false;
                     break;
                 }
                 if (drawable instanceof FeatureTrack) {
@@ -772,16 +781,12 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
                 // manager.
                 //
                 this.filters_manager.remove_all();
-                var filters;
-                var new_filter;
-                var min;
-                var max;
                 for (var filter_name in shared_filters) {
-                    filters = shared_filters[filter_name];
+                    let filters = shared_filters[filter_name];
                     if (filters.length === num_feature_tracks) {
                         // Add new filter.
                         // FIXME: can filter.copy() be used?
-                        new_filter = new filters_mod.NumberFilter({
+                        let new_filter = new filters_mod.NumberFilter({
                             name: filters[0].name,
                             index: filters[0].index
                         });
@@ -834,7 +839,7 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
             name: this.config.get_value("name"),
             drawables: this.drawables
         });
-        var index = this.container.replace_drawable(this, composite_track, true);
+        this.container.replace_drawable(this, composite_track, true);
         composite_track.request_draw();
     },
 
@@ -981,7 +986,8 @@ var TracksterView = Backbone.View.extend({
         this.intro_div = $("<div/>")
             .addClass("intro")
             .appendTo(this.viewport_container);
-        var add_tracks_button = $("<div/>")
+        // Add tracks button
+        $("<div/>")
             .text("Add Datasets to Visualization")
             .addClass("action-button")
             .appendTo(this.intro_div)
@@ -1270,11 +1276,11 @@ var TracksterView = Backbone.View.extend({
         $(window).bind("resize", function() {
             // Stop previous timer.
             if (this.resize_timer) {
-                clearTimeout(this.resize_timer);
+                window.clearTimeout(this.resize_timer);
             }
 
             // When function activated, resize window and redraw.
-            this.resize_timer = setTimeout(() => {
+            this.resize_timer = window.setTimeout(() => {
                 view.resize_window();
             }, 500);
         });
@@ -1309,18 +1315,17 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
     trigger_navigate: function(new_chrom, new_low, new_high, delay) {
         // Stop previous timer.
         if (this.timer) {
-            clearTimeout(this.timer);
+            window.clearTimeout(this.timer);
         }
 
         if (delay) {
             // To aggregate calls, use timer and only navigate once
             // location has stabilized.
-            var self = this;
-            this.timer = setTimeout(() => {
-                self.trigger("navigate", `${new_chrom}:${new_low}-${new_high}`);
+            this.timer = window.setTimeout(() => {
+                this.trigger("navigate", `${new_chrom}:${new_low}-${new_high}`);
             }, 500);
         } else {
-            view.trigger("navigate", `${new_chrom}:${new_low}-${new_high}`);
+            this.trigger("navigate", `${new_chrom}:${new_low}-${new_high}`);
         }
     },
 
@@ -1343,13 +1348,12 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
     load_chroms: function(url_parms) {
         url_parms.num = MAX_CHROMS_SELECTABLE;
 
-        var view = this;
         var chrom_data = $.Deferred();
         $.ajax({
             url: `${Galaxy.root}api/genomes/${this.dbkey}`,
             data: url_parms,
             dataType: "json",
-            success: function(result) {
+            success: result => {
                 // Do nothing if could not load chroms.
                 if (result.chrom_info.length === 0) {
                     return;
@@ -1357,34 +1361,34 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
 
                 // Load chroms.
                 if (result.reference) {
-                    var ref_track = new ReferenceTrack(view);
-                    view.add_label_track(ref_track);
-                    view.reference_track = ref_track;
+                    var ref_track = new ReferenceTrack(this);
+                    this.add_label_track(ref_track);
+                    this.reference_track = ref_track;
                 }
-                view.chrom_data = result.chrom_info;
+                this.chrom_data = result.chrom_info;
 
-                view.chrom_select.html("");
-                view.chrom_select.append($('<option value="">Select Chrom/Contig</option>'));
+                this.chrom_select.html("");
+                this.chrom_select.append($('<option value="">Select Chrom/Contig</option>'));
 
-                for (var i = 0, len = view.chrom_data.length; i < len; i++) {
-                    var chrom = view.chrom_data[i].chrom;
+                for (var i = 0, len = this.chrom_data.length; i < len; i++) {
+                    var chrom = this.chrom_data[i].chrom;
                     var chrom_option = $("<option>");
                     chrom_option.text(chrom);
                     chrom_option.val(chrom);
-                    view.chrom_select.append(chrom_option);
+                    this.chrom_select.append(chrom_option);
                 }
                 if (result.prev_chroms) {
-                    view.chrom_select.append($(`<option value="previous">Previous ${MAX_CHROMS_SELECTABLE}</option>`));
+                    this.chrom_select.append($(`<option value="previous">Previous ${MAX_CHROMS_SELECTABLE}</option>`));
                 }
                 if (result.next_chroms) {
-                    view.chrom_select.append($(`<option value="next">Next ${MAX_CHROMS_SELECTABLE}</option>`));
+                    this.chrom_select.append($(`<option value="next">Next ${MAX_CHROMS_SELECTABLE}</option>`));
                 }
-                view.chrom_start_index = result.start_index;
+                this.chrom_start_index = result.start_index;
 
                 chrom_data.resolve(result.chrom_info);
             },
             error: function() {
-                alert(`Could not load chroms for this dbkey: ${view.dbkey}`);
+                alert(`Could not load chroms for this dbkey: ${this.dbkey}`);
             }
         });
         return chrom_data;
@@ -1491,7 +1495,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         str = str.replace(/,/g, "");
 
         // Replace colons and hyphens with space for easy parsing.
-        str = str.replace(/:|\-/g, " ");
+        str = str.replace(/:|-/g, " ");
 
         // Parse new location.
         var chrom_pos = str.split(/\s+/);
@@ -1537,10 +1541,10 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
 
         // Set up timeout to redraw with more data when moving stops.
         if (this.redraw_on_move_fn) {
-            clearTimeout(this.redraw_on_move_fn);
+            window.clearTimeout(this.redraw_on_move_fn);
         }
 
-        this.redraw_on_move_fn = setTimeout(() => {
+        this.redraw_on_move_fn = window.setTimeout(() => {
             view.request_redraw();
         }, 200);
 
@@ -1617,7 +1621,7 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
 
         // Set up redraw if it has not been requested since last redraw.
         if (!this.requested_redraw) {
-            requestAnimationFrame(() => {
+            window.requestAnimationFrame(() => {
                 view._redraw();
             });
             this.requested_redraw = true;
@@ -1779,8 +1783,8 @@ extend(TracksterView.prototype, DrawableCollection.prototype, {
         this.overview_box.height(this.default_overview_height);
         this.overview_close.hide();
         this.overview_highlight.hide();
-        view.resize_window();
-        view.overview_drawable = null;
+        this.resize_window();
+        this.overview_drawable = null;
     }
 });
 
@@ -1828,7 +1832,7 @@ var ToolParameterView = Backbone.View.extend({
         var param = this.model;
 
         // Param label.
-        var label_div = $("<div>")
+        $("<div>")
             .addClass("param-label")
             .text(param.get("label"))
             .appendTo(param_div);
@@ -1881,7 +1885,7 @@ var TracksterToolView = Backbone.View.extend({
             });
 
         // Add name, inputs.
-        var name_div = $("<div class='tool-name'>")
+        $("<div class='tool-name'>")
             .appendTo(parent_div)
             .text(tool.get("name"));
         tool.get("inputs").each(param => {
@@ -1989,44 +1993,42 @@ var TracksterToolView = Backbone.View.extend({
             regions: [region.toJSON()]
         };
 
-        var current_track = track;
-
-        var // Set name of track to include tool name, parameters, and region used.
-        track_name = tool.get("name") + current_track.tool_region_and_parameters_str(region);
+        // Set name of track to include tool name, parameters, and region used.
+        var track_name = tool.get("name") + track.tool_region_and_parameters_str(region);
 
         var container;
 
         // If track not in a group, create a group for it and add new track to group. If track
         // already in group, add track to group.
-        if (current_track.container === view) {
+        if (track.container === track.view) {
             // Create new group.
-            var group = new DrawableGroup(view, view, {
+            var group = new DrawableGroup(track.view, track.view, {
                 name: track.config.get_value("name")
             });
 
             // Replace track with group.
-            var index = current_track.container.replace_drawable(current_track, group, false);
+            var index = track.container.replace_drawable(track, group, false);
 
             // Update HTML.
             // FIXME: this is ugly way to replace a track with a group -- make this easier via
             // a Drawable or DrawableCollection function.
-            group.container_div.insertBefore(current_track.view.content_div.children()[index]);
-            group.add_drawable(current_track);
-            current_track.container_div.appendTo(group.content_div);
+            group.container_div.insertBefore(track.view.content_div.children()[index]);
+            group.add_drawable(track);
+            track.container_div.appendTo(group.content_div);
             container = group;
         } else {
             // Use current group.
-            container = current_track.container;
+            container = track.container;
         }
 
         // Create and init new track.
-        var new_track = new current_track.constructor(view, container, {
+        var new_track = new track.constructor(track.view, container, {
             name: track_name,
             hda_ldda: "hda"
         });
         new_track.init_for_tool_data();
-        new_track.change_mode(current_track.mode);
-        new_track.set_filters_manager(current_track.filters_manager.copy(new_track));
+        new_track.change_mode(track.mode);
+        new_track.set_filters_manager(track.filters_manager.copy(new_track));
         new_track.update_icons();
         container.add_drawable(new_track);
         new_track.tiles_div.text("Starting job.");
@@ -2441,12 +2443,17 @@ extend(Track.prototype, Drawable.prototype, {
             name: "param_space_viz_icon",
             title: _l("Tool parameter space visualization"),
             css_class: "arrow-split",
-            on_click_fn: function(track) {
-                var html = `<strong>Tool</strong>:${track.tool.get(
-                    "name"
-                )}<br/><strong>Dataset</strong>:${track.config.get_value(
-                    "name"
-                )}<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>`;
+            on_click_fn: track => {
+                var html = `
+                    <strong>Tool</strong>:${track.tool.get("name")}<br/>
+                    <strong>Dataset</strong>:${track.config.get_value("name")}<br/>
+                    <strong>Region(s)</strong>:
+                        <select name="regions">
+                            <option value="cur">current viewing area</option>
+                            <option value="bookmarks">bookmarks</option>
+                            <option value="both">current viewing area and bookmarks</option>
+                        </select>
+                    `;
 
                 var cancel_fn = () => {
                     Galaxy.modal.hide();
@@ -2454,22 +2461,22 @@ extend(Track.prototype, Drawable.prototype, {
                 };
 
                 var ok_fn = () => {
-                    var regions_to_use = $('select[name="regions"] option:selected').val(),
-                        regions,
-                        view_region = new visualization.GenomeRegion({
-                            chrom: view.chrom,
-                            start: view.low,
-                            end: view.high
-                        }),
-                        bookmarked_regions = _.map(
-                            $(".bookmark"),
-                            elt =>
-                                new visualization.GenomeRegion({
-                                    from_str: $(elt)
-                                        .children(".position")
-                                        .text()
-                                })
-                        );
+                    var regions_to_use = $('select[name="regions"] option:selected').val();
+                    var regions;
+                    var view_region = new visualization.GenomeRegion({
+                        chrom: this.view.chrom,
+                        start: this.view.low,
+                        end: this.view.high
+                    });
+                    var bookmarked_regions = _.map(
+                        $(".bookmark"),
+                        elt =>
+                            new visualization.GenomeRegion({
+                                from_str: $(elt)
+                                    .children(".position")
+                                    .text()
+                            })
+                    );
 
                     // Get regions for visualization.
                     if (regions_to_use === "cur") {
@@ -2493,6 +2500,8 @@ extend(Track.prototype, Drawable.prototype, {
                     })}`;
                 };
 
+                /*
+                 * TODO: Re-enable this when functional.
                 var check_enter_esc = e => {
                     if ((e.keyCode || e.which) === 27) {
                         // Escape key
@@ -2502,6 +2511,7 @@ extend(Track.prototype, Drawable.prototype, {
                         ok_fn();
                     }
                 };
+                */
 
                 // show dialog
                 Galaxy.modal.show({
@@ -2732,7 +2742,7 @@ extend(Track.prototype, Drawable.prototype, {
                 track.container_div.addClass("pending");
                 track.show_message(DATA_PENDING);
                 //$("<img/>").attr("src", image_path + "/yui/rel_interstitial_loading.gif").appendTo(track.tiles_div);
-                setTimeout(() => {
+                window.setTimeout(() => {
                     track.init();
                 }, track.data_query_wait);
             } else if (result === "data" || result.status === "data") {
@@ -3040,7 +3050,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         var clear_after = options && options.clear_after;
         var low = this.view.low;
         var high = this.view.high;
-        var range = high - low;
+        //var range = high - low;
         var width = this.view.container.width();
         var w_scale = this.view.resolution_px_b;
         var resolution = 1 / w_scale;
@@ -3049,7 +3059,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         if (this.is_overview) {
             low = this.view.max_low;
             high = this.view.max_high;
-            w_scale = width / (view.max_high - view.max_low);
+            w_scale = width / (this.view.max_high - this.view.max_low);
             resolution = 1 / w_scale;
         }
 
@@ -3105,17 +3115,16 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         }
 
         // When all tiles are drawn, call post-draw actions.
-        var track = this;
         $.when.apply($, tile_promises).then(() => {
             // Step (c) for (re)moving tiles when clear_after is true:
-            track.tiles_div.children(".remove").remove();
+            this.tiles_div.children(".remove").remove();
 
             // Only do postdraw actions for tiles; instances where tiles may not be drawn include:
             // (a) ReferenceTrack without sufficient resolution;
             // (b) data_fetch = false.
             tiles = _.filter(tiles, t => t !== null);
             if (tiles.length !== 0) {
-                track.postdraw_actions(tiles, width, w_scale, clear_after);
+                this.postdraw_actions(tiles, width, w_scale, clear_after);
             }
         });
     },
@@ -3124,18 +3133,17 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * Add a maximum/minimum label to track.
      */
     _add_yaxis_label: function(type, on_change) {
-        var track = this;
         var css_class = type === "max" ? "top" : "bottom";
         var text = type === "max" ? "max" : "min";
         var pref_name = type === "max" ? "max_value" : "min_value";
         var label = this.container_div.find(`.yaxislabel.${css_class}`);
-        var value = round(track.config.get_value(pref_name), 1);
+        var value = round(this.config.get_value(pref_name), 1);
 
         // Default action for on_change is to redraw track.
         on_change =
             on_change ||
             (() => {
-                track.request_draw({ clear_tile_cache: true });
+                this.request_draw({ clear_tile_cache: true });
             });
 
         if (label.length !== 0) {
@@ -3149,7 +3157,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                     num_cols: 12,
                     on_finish: function(new_val) {
                         $(".tooltip").remove();
-                        track.config.set_value(pref_name, round(new_val, 1));
+                        this.config.set_value(pref_name, round(new_val, 1));
                         on_change();
                     },
                     help_text: `Set ${text} value`
@@ -3176,18 +3184,17 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
 
             // Clear because this is set when drawing.
             this.max_height_px = 0;
-            var track = this;
             _.each(tiles, tile => {
                 if (!(tile instanceof LineTrackTile)) {
                     tile.html_elt.remove();
-                    track.draw_helper(tile.region, w_scale, {
+                    this.draw_helper(tile.region, w_scale, {
                         force: true,
                         mode: "Coverage"
                     });
                 }
             });
 
-            track._add_yaxis_label("max");
+            this._add_yaxis_label("max");
         } else {
             // -- Drawing in non-Coverage mode. --
 
@@ -3247,19 +3254,16 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         var mode = options.mode || this.mode;
         var resolution = 1 / w_scale;
 
-        var // Useful vars.
-        track = this;
-
         var drawables = this._get_drawables();
         var key = this._gen_tile_cache_key(w_scale, region);
 
         var is_tile = o => o && "track" in o;
 
         // Check tile cache, if found show existing tile in correct position
-        var tile = force ? undefined : track.tile_cache.get_elt(key);
+        var tile = force ? undefined : this.tile_cache.get_elt(key);
         if (tile) {
             if (is_tile(tile)) {
-                track.show_tile(tile, w_scale);
+                this.show_tile(tile, w_scale);
             }
             return tile;
         }
@@ -3277,16 +3281,16 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             // Map drawable object to data needed for drawing.
             var tile_data = _.map(drawables, (
                 d // Get the track data/promise.
-            ) => d.data_manager.get_data(region, data_mode, resolution, track.data_url_extra_params));
+            ) => d.data_manager.get_data(region, data_mode, resolution, this.data_url_extra_params));
 
             // Get reference data/promise.
-            if (view.reference_track) {
+            if (this.view.reference_track) {
                 tile_data.push(
-                    view.reference_track.data_manager.get_data(
+                    this.view.reference_track.data_manager.get_data(
                         region,
                         mode,
                         resolution,
-                        view.reference_track.data_url_extra_params
+                        this.view.reference_track.data_url_extra_params
                     )
                 );
             }
@@ -3298,7 +3302,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         // When data is available, draw tile.
         //
         var tile_drawn = $.Deferred();
-        track.tile_cache.set_elt(key, tile_drawn);
+        this.tile_cache.set_elt(key, tile_drawn);
         $.when.apply($, get_tile_data()).then(() => {
             var tile_data = get_tile_data();
             var tracks_data = tile_data;
@@ -3309,41 +3313,36 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the
             // GenomeDataManager in visualization module.
             if (_.find(tile_data, d => util.is_deferred(d))) {
-                track.tile_cache.set_elt(key, undefined);
-                $.when(track.draw_helper(region, w_scale, options)).then(tile => {
+                this.tile_cache.set_elt(key, undefined);
+                $.when(this.draw_helper(region, w_scale, options)).then(tile => {
                     tile_drawn.resolve(tile);
                 });
                 return;
             }
 
             // If sequence data is available, subset to get only data in region.
-            if (view.reference_track) {
-                seq_data = view.reference_track.data_manager.subset_entry(tile_data.pop(), region);
+            if (this.view.reference_track) {
+                seq_data = this.view.reference_track.data_manager.subset_entry(tile_data.pop(), region);
             }
 
             // Get drawing modes, heights for all tracks.
             var drawing_modes = [];
-
             var drawing_heights = [];
 
             _.each(drawables, (d, i) => {
-                var mode = d.mode;
                 var data = tracks_data[i];
-                if (mode === "Auto") {
-                    mode = d.get_mode(data);
-                    d.update_auto_mode(mode);
+                if (d.mode === "Auto") {
+                    d.mode = d.get_mode(data);
+                    d.update_auto_mode(d.mode);
                 }
-                drawing_modes.push(mode);
-                drawing_heights.push(d.get_canvas_height(data, mode, w_scale, width));
+                drawing_modes.push(d.mode);
+                drawing_heights.push(d.get_canvas_height(data, d.mode, w_scale, width));
             });
 
-            var canvas = track.view.canvas_manager.new_canvas();
+            var canvas = this.view.canvas_manager.new_canvas();
             var tile_low = region.get("start");
             var tile_high = region.get("end");
-            var all_data_index = 0;
-
-            var width = Math.ceil((tile_high - tile_low) * w_scale) + track.left_offset;
-
+            var width = Math.ceil((tile_high - tile_low) * w_scale) + this.left_offset;
             var height = _.max(drawing_heights);
             var tile;
 
@@ -3354,7 +3353,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             // Height is specified in options or is the height found above.
             canvas.height = options.height || height;
             var ctx = canvas.getContext("2d");
-            ctx.translate(track.left_offset, 0);
+            ctx.translate(this.left_offset, 0);
             if (drawables.length > 1) {
                 ctx.globalAlpha = 0.5;
                 ctx.globalCompositeOperation = "source-over";
@@ -3365,8 +3364,8 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
 
             // Don't cache, show if no tile.
             if (tile !== undefined) {
-                track.tile_cache.set_elt(key, tile);
-                track.show_tile(tile, w_scale);
+                this.tile_cache.set_elt(key, tile);
+                this.show_tile(tile, w_scale);
             }
 
             tile_drawn.resolve(tile);
@@ -3428,7 +3427,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * an existing tile rather than reshowing it.
      */
     show_tile: function(tile, w_scale) {
-        var track = this;
         var tile_element = tile.html_elt;
 
         // -- Show/move tile element. --
@@ -3785,7 +3783,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
         }
 
         // Replace track with group.
-        var index = this.container.replace_drawable(this, group, true);
+        this.container.replace_drawable(this, group, true);
         group.request_draw({ clear_tile_cache: true });
     },
 
@@ -3819,7 +3817,6 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
      * Update minimum, maximum for component tracks.
      */
     update_all_min_max: function() {
-        var track = this;
         var min_value = this.config.get_value("min_value");
         var max_value = this.config.get_value("max_value");
         _.each(this.drawables, d => {
@@ -4127,7 +4124,8 @@ extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype,
                 hda_ldda: track.dataset.get("hda_ldda")
             },
             result => {
-                var data = result.data;
+                // What does this do?  Is it meant to be attached to some higher scope state object?
+                // var data = result.data;
             }
         );
     },
@@ -4163,10 +4161,9 @@ var FeatureTrack = function(view, container, obj_dict) {
     this.slotters = {};
     this.start_end_dct = {};
     this.left_offset = 200;
-
-    // this.painter = painters.LinkedFeaturePainter;
     this.set_painter_from_config();
 };
+
 extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
 
@@ -4258,9 +4255,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     postdraw_actions: function(tiles, width, w_scale, clear_after) {
         TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
 
-        var track = this;
-        var i;
-
         var line_track_tiles = _.filter(tiles, t => t instanceof LineTrackTile);
 
         //
@@ -4277,7 +4271,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             });
 
             // Draw incomplete features on each tile.
-            var self = this;
             _.each(tiles, tile => {
                 // Remove features already drawn on tile originally.
                 var tile_incomplete_features = _.omit(
@@ -4296,16 +4289,16 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                         data: _.values(tile_incomplete_features)
                     };
 
-                    var new_canvas = self.view.canvas_manager.new_canvas();
+                    var new_canvas = this.view.canvas_manager.new_canvas();
                     var new_canvas_ctx = new_canvas.getContext("2d");
                     new_canvas.height = Math.max(
                         tile.canvas.height,
-                        self.get_canvas_height(features, tile.mode, tile.w_scale, 100)
+                        this.get_canvas_height(features, tile.mode, tile.w_scale, 100)
                     );
                     new_canvas.width = tile.canvas.width;
                     new_canvas_ctx.drawImage(tile.canvas, 0, 0);
-                    new_canvas_ctx.translate(track.left_offset, 0);
-                    var new_tile = self.draw_tile(
+                    new_canvas_ctx.translate(this.left_offset, 0);
+                    var new_tile = this.draw_tile(
                         features,
                         new_canvas_ctx,
                         tile.mode,
@@ -4348,8 +4341,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         //
 
         // Update filtering UI.
-        if (track.filters_manager) {
-            var filters = track.filters_manager.filters;
+        if (this.filters_manager) {
+            var filters = this.filters_manager.filters;
             var f;
             for (f = 0; f < filters.length; f++) {
                 filters[f].update_ui_elt();
@@ -4361,7 +4354,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 
             var example_feature;
             var filter;
-            for (i = 0; i < tiles.length; i++) {
+            for (let i = 0; i < tiles.length; i++) {
                 if (tiles[i].data.length) {
                     example_feature = tiles[i].data[0];
                     for (f = 0; f < filters.length; f++) {
@@ -4375,12 +4368,12 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             }
 
             // If filter availability changed, hide filter div if necessary and update menu.
-            if (track.filters_available !== filters_available) {
-                track.filters_available = filters_available;
-                if (!track.filters_available) {
-                    track.filters_manager.hide();
+            if (this.filters_available !== filters_available) {
+                this.filters_available = filters_available;
+                if (!this.filters_available) {
+                    this.filters_manager.hide();
                 }
-                track.update_icons();
+                this.update_icons();
             }
         }
 
@@ -4389,7 +4382,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         //
         if (tiles[0] instanceof FeatureTrackTile) {
             var all_slotted = true;
-            for (i = 0; i < tiles.length; i++) {
+            for (let i = 0; i < tiles.length; i++) {
                 if (!tiles[i].all_slotted) {
                     all_slotted = false;
                     break;
@@ -4557,6 +4550,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         );
 
         var feature_mapper = null;
+        var incomplete_features = null;
 
         ctx.fillStyle = this.config.get_value("block_color");
         ctx.font = ctx.canvas.manager.default_font;
diff --git a/client/galaxy/scripts/viz/visualization.js b/client/galaxy/scripts/viz/visualization.js
index 7ba8c775ad3..b3140462fe8 100644
--- a/client/galaxy/scripts/viz/visualization.js
+++ b/client/galaxy/scripts/viz/visualization.js
@@ -5,7 +5,6 @@ import util_mod from "viz/trackster/util";
 import config_mod from "utils/config";
 import GridView from "mvc/grid/grid-view";
 import Tabs from "mvc/ui/ui-tabs";
-import Ui from "mvc/ui/ui-misc";
 /**
  * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes
  * to include in the representation; to_json_mappers defines mappers for returned objects.
@@ -1109,12 +1108,11 @@ var TrackBrowserRouter = Backbone.Router.extend({
         // Can't put regular expression in routes dictionary.
         // NOTE: parentheses are used to denote parameters returned to callback.
         this.route(/([\w]+)$/, "change_location");
-        this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/, "change_location");
+        this.route(/([\w+]+:[\d,]+-[\d,]+)$/, "change_location");
 
         // Handle navigate events from view.
-        var self = this;
-        self.view.on("navigate", new_loc => {
-            self.navigate(new_loc);
+        this.view.on("navigate", new_loc => {
+            this.navigate(new_loc);
         });
     },
 
diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index a6b87e2c82c..4da482becf8 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -21,7 +21,7 @@
     </datatype>
     <datatype extension="qname_sorted.bam" type="galaxy.datatypes.binary:BamQuerynameSorted" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted by queryname." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
     </datatype>
-    <datatype extension="bam_native" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
+    <datatype extension="unsorted.bam" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
       <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
       <converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
@@ -299,7 +299,7 @@
     <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
     <datatype extension="roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
     <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
-        <converter file="sam_to_bam_native.xml" target_datatype="bam_native"/>
+        <converter file="sam_to_unsorted_bam.xml" target_datatype="unsorted.bam"/>
         <converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
         <converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
         <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
diff --git a/doc/source/releases/18.01.rst b/doc/source/releases/18.01.rst
new file mode 100644
index 00000000000..cd507ddc8d2
--- /dev/null
+++ b/doc/source/releases/18.01.rst
@@ -0,0 +1,1184 @@
+
+.. to_doc
+
+18.01
+===============================
+
+.. announce_start
+
+Enhancements
+-------------------------------
+
+.. major_feature
+
+.. _list of related performance pull requests:
+
+* Performance and User Experience Improvements
+  `Pull Request 5514`_, `Pull Request 5515`_, `Pull Request 5542`_,
+  `Pull Request 5574`_, `Pull Request 5576`_, `Pull Request 5582`_,
+  `Pull Request 5533`_, `Pull Request 5615`_, `Pull Request 5616`_
+
+.. _list of related client pull requests:
+
+* Client Architecture
+  `Pull Request 4435`_, `Pull Request 4978`_, `Pull Request 4436`_, `Pull Request 5173`_
+  `Pull Request 5293`_, `Pull Request 5191`_, `Pull Request 5190`_,
+  `Pull Request 4827`_, `Pull Request 4964`_, `Pull Request 5371`_,
+  `Pull Request 5128`_, `Pull Request 5262`_, `Pull Request 5081`_, `Pull Request 5054`_
+  `Pull Request 5093`_, `Pull Request 5001`_, `Pull Request 5261`_, `Pull Request 5278`_,
+  `Pull Request 5294`_
+
+.. feature
+
+* Add option to clone tool steps in the workflow editor
+  (thanks to `@anatskiy <https://github.com/anatskiy>`__).
+  `Pull Request 5087`_, `Pull Request 5124`_, `Pull Request 5185`_
+* Implement a generic Cloud ObjectStore using multi-cloud support from
+  `cloudbridge <https://github.com/gvlproject/cloudbridge>`__
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 4487`_
+* Reload tools immediately if a macro changes
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4635`_
+* Add an interactive environment for `AskOmics <https://github.com/askomics/askomics>`__
+  a visual SPARQL query builder for RDF databases
+  (thanks to `@xgaia <https://github.com/xgaia>`__).
+  `Pull Request 4737`_
+* Implement a Github error report backend for
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 4765`_
+* Add maintenance script to simplify setting up a cleanup cron job
+  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
+  `Pull Request 4916`_
+* Create the ``$GALAXY_MEMORY_MB`` job environment variable for tools.
+  `Pull Request 4958`_
+* Improved home and temp directory handling for tools and jobs.
+  `Pull Request 5193`_
+* Tool-based annotation of out of memory errors.
+  `Pull Request 5196`_
+* Added support for recursively discovering output datasets
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 5240`_
+* Add an API endpoint that allows admins to decode galaxy object IDs.
+  `Pull Request 5018`_
+* Add sorting options for data library folders.
+  `Pull Request 4877`_
+* Add option to auto create ``user_library_import_dir`` directories upon user
+  login.
+  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
+  `Pull Request 5138`_
+* Add option to check file permissions for the user library imports
+  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
+  `Pull Request 5154`_
+* Add an admin form to pre-populate an LDAP user
+  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
+  `Pull Request 5238`_
+* Add a CRAM to BAM datatype converter
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4939`_
+* Add infernal-cm datatype
+  (thanks to `@mmiladi <https://github.com/mmiladi>`__).
+  `Pull Request 4977`_
+* Add ICM datatype for glimmer
+  (thanks to `@abretaud <https://github.com/abretaud>`__).
+  `Pull Request 5042`_
+* Add Analyze75 datatype
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 4841`_
+* Add Classical linkage and haplotype datatypes
+  (thanks to `@mtekman <https://github.com/mtekman>`__).
+  `Pull Request 4894`_
+* Add ideaspre datatype
+  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
+  `Pull Request 5445`_
+* Add compressed fasta support.
+  `Pull Request 5561`_
+* Add ``cool`` datatype
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 5023`_
+* Add neostore zip datatype
+  (thanks to `@zipho <https://github.com/zipho>`__).
+  `Pull Request 4178`_
+* Add fast5_archive datatype
+  (thanks to `@jvolkening <https://github.com/jvolkening>`__).
+  `Pull Request 4569`_
+* Add postgresql datatype
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 4730`_
+* Add IQtree datatypes
+  (thanks to `@mtekman <https://github.com/mtekman>`__).
+  `Pull Request 4849`_
+* Add Phylip datatype
+  (thanks to `@khillion <https://github.com/khillion>`__).
+  `Pull Request 5301`_
+.. enhancement
+
+* Option to group Galaxy Tours for viewing clarity
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 4829`_
+* Allow users to upload multiple FTP files within a single request
+  `Pull Request 4513`_
+* Replaces the admin form builder grid and forms
+  `Pull Request 4480`_
+* Update pysam dependency to 0.14 and eliminate the need to have
+  samtools on Galaxy's ``PATH`` (with huge help from `@mvdbeek
+  <https://github.com/mvdbeek>`__)
+  `Pull Request 4497`_, `Pull Request 5512`_, `Pull Request 5037`_
+* Expand and improve Selenium testing of the web UI (with help from
+  `@anatskiy <https://github.com/anatskiy>`__).
+  `Pull Request 4543`_, `Pull Request 4655`_, `Pull Request 4676`_,
+  `Pull Request 4753`_, `Pull Request 4732`_, `Pull Request 4909`_,
+  `Pull Request 4935`_, `Pull Request 4925`_,
+  `Pull Request 4687`_, `Pull Request 4660`_, `Pull Request 5333`_,
+  `Pull Request 5068`_, `Pull Request 4757`_, `Pull Request 4971`_,
+  `Pull Request 4653`_
+* Allow multiple simultaneous uploads via single POST.
+  `Pull Request 4563`_
+* Various bits of proactive security-related hardening
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 4604`_
+* Move test helper ``wait_for_dataset_collection`` for reuse
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4658`_
+* Extend job search for hdcas
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4665`_
+* Add a custom ``TRACE`` log level for even more verbosity.
+  `Pull Request 4672`_
+* Migrate various mako templates to modern JavaScript driven views.
+  `Pull Request 4681`_, `Pull Request 4682`_, `Pull Request 4711`_,
+  `Pull Request 4755`_, `Pull Request 4661`_, `Pull Request 4993`_,
+  `Pull Request 4664`_, `Pull Request 4996`_, `Pull Request 5014`_,
+  `Pull Request 4833`_, `Pull Request 5212`_, `Pull Request 5114`_
+* More HDCA copying tests, add option to copy HDAs into new history.
+  `Pull Request 5004`_
+* Use only latest publication in ``CITATION``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4688`_
+* Nicer logging message for sentry
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 4693`_
+* Use enumeration to provide history input index names.
+  `Pull Request 4700`_
+* Cleanup delayed action in ``history-view.js``.
+  `Pull Request 4704`_
+* Add logging during for script integrity exceptions
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 4720`_
+* Fix to respect ``galaxy.json`` supplied metadata for empty outputs.
+  `Pull Request 4722`_
+* Update ``reports.md`` with a link to the community hub
+  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
+  `Pull Request 4723`_
+* Typo fixes and small cleanups
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4725`_
+* Fix that implements stricter checks for SDF datatype sniffing
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4729`_
+* When reloading the toolbox, use the existing dependency manager if possible
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4739`_
+* Many more upload tests - big improvements to uploads will be coming to Galaxy 18.05.
+  `Pull Request 4746`_, `Pull Request 4762`_, `Pull Request 4790`_,
+  `Pull Request 4863`_, `Pull Request 5266`_, `Pull Request 5209`_
+* Kubernetes resources requests/limits support
+  (thanks to `@pcm32 <https://github.com/pcm32>`__ and the `@phnmnl <https://github.com/phnmnl>`__ project).
+  `Pull Request 4751`_
+* Send all influxdb stats to a single bucket
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 4758`_
+* PEP-8 fixes in random doctests.
+  `Pull Request 4764`_
+* Avoid circular import when determining max metadata value size.
+  `Pull Request 4770`_
+* Remove unused concept of dataset children.
+  `Pull Request 4771`_
+* Allow dataset attribute changes without refreshing the page.
+  `Pull Request 4779`_
+* Include check for updates to dependencies in tox, Makefile, Travis.
+  `Pull Request 4788`_
+* Add labels to selection options of the collection flattening tool.
+  `Pull Request 4791`_
+* Expose ``state``, ``stdout``, ``stderr``, ``uuid`` in the library API
+  `Pull Request 4839`_
+* Significant improvements to client QUnit tests including new
+  `Karma <https://karma-runner.github.io/>`__ based test driver.
+  `Pull Request 4855`_, `Pull Request 5066`_, `Pull Request 5063`_,
+  `Pull Request 5074`_
+* Remove tool reloading buttons and packaging endpoint, revise admin labels
+  `Pull Request 4866`_
+* Add various elements to the Tool XML doc page
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4871`_
+* Absolute pins on linting dependencies.
+  `Pull Request 4876`_
+* Update various Galaxy requirements.
+  `Pull Request 4884`_
+* Updates and enhancements for the testing ``Dockerfile``.
+  `Pull Request 4885`_, `Pull Request 4879`_, `Pull Request 4900`_
+* Add nicer composite dataset names by default
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 4886`_
+* Improved initialization and isolation of Postgres databases used in integration testing.
+  `Pull Request 4887`_, `Pull Request 4914`_
+* Rework dev dependencies to be Pipfile generated, locked, and hashed.
+  `Pull Request 4891`_
+* Install dev and regular dependencies at the same time.
+  `Pull Request 4903`_
+* More structured app shutdown.
+  `Pull Request 4910`_
+* Touch up issue labels in repository procedures document.
+  `Pull Request 4912`_
+* Improve error handling for incorrect datatype upload.
+  `Pull Request 4922`_
+* Activate mulled dependencies once per job
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4945`_
+* Remove invalid user preferences beta (no longer a beta, always enabled)
+  `Pull Request 4957`_
+* Add ``DELETE /api/jobs/<job_id>`` as a job cancellation API endpoint.
+  `Pull Request 4961`_
+* Kill off processes when stopping the local job runner.
+  `Pull Request 4962`_
+* Test both endpoints for collection creation in history contents API.
+  `Pull Request 4965`_
+* Add @flakey test annotation and "skip" them if the fail on Jenkins.
+  `Pull Request 4972`_
+* Include path in job script integrity errors
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4991`_
+* Fix tox envlist to contain all envs that should pass
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4992`_
+* Changes made while working on uWSGI mules that don't belong in the mules PR
+  `Pull Request 4994`_
+* Add warning for sort-of-defunct workflow options in galaxy.ini.
+  `Pull Request 5002`_
+* Fix Python import order everywhere
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4697`_, `Pull Request 5005`_
+* dataset info: present decoded IDs for admins and add peek
+  `Pull Request 5006`_
+* Removed unneeded skip_install tags in tox.ini.
+  `Pull Request 5011`_
+* Add metric to the core plugin to collect $GALAXY_MEMORY_MB
+  `Pull Request 5016`_
+* Test renaming multiple different outputs in workflows.
+  `Pull Request 5017`_
+* Render arbitrarily nested lists in the UI
+  `Pull Request 5038`_
+* Expose proper element_identifier in tool action template expansions
+  `Pull Request 5049`_
+* Document fastest way to iterate on client & client tests together.
+  `Pull Request 5051`_
+* Support separate DSN for job sentry error reports
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 5056`_
+* Build endpoint separation
+  `Pull Request 5058`_
+* Remove ``wchartype`` dependency and ``is_multi_byte`` attribute
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5062`_, `Pull Request 5088`_
+* Implement multilingualization support on workflow page
+  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
+  `Pull Request 5077`_
+* Update Jupyter IE default image
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 5095`_
+* Determine dynamically if an extension corresponds to an unsniffable binary
+  datatype
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5109`_
+* Update to flake8-import-order 0.16
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4869`_, `Pull Request 5110`_
+* Change the default to not add tags based on filename
+  `Pull Request 5115`_
+* Improve tool validation and metadata generation
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5119`_
+* Download button fixes.
+  `Pull Request 5125`_
+* Datatype conversion check optimization
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5137`_
+* Test resubmit for dynamic JobDestination structures.
+  `Pull Request 5139`_
+* Various dataset hashtag display improvements.
+  `Pull Request 5155`_
+* i18n improvements for French localization
+  (thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
+  `Pull Request 5089`_, `Pull Request 5157`_
+* Change hicexplorer image name
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 5177`_
+* Fix `#3002 <https://github.com/galaxyproject/galaxy/issues/3002>`__ with update to
+  newer version of virtualenv.
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 5202`_
+* Huge steps toward Python 3 compatiblity
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5215`_, `Pull Request 5221`_, `Pull Request 5225`_, `Pull Request 5228`_,
+  `Pull Request 5200`_, `Pull Request 5199`_, `Pull Request 4799`_, `Pull Request 4811`_
+* Add chinese support
+  (thanks to `@istevenshen <https://github.com/istevenshen>`__).
+  `Pull Request 5232`_
+* Make ``pam`` a conditional dependency
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5251`_
+* Update api quickstart doc to use default port, with a little bit of extra
+  guidance.
+  `Pull Request 5260`_
+* Allow sorting collection elements based on file
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5273`_
+* Add Biostar configuration options to the configuration sample file.
+  `Pull Request 5276`_
+* Update Japanese translation
+  (thanks to `@istevenshen <https://github.com/istevenshen>`__).
+  `Pull Request 5288`_
+* Improve the migration message when having to downgrade the database
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5299`_
+* Allow ``message`` attribute to be modified on a library dataset.
+  `Pull Request 5312`_
+* Enforce a size constraint on the tag editor.
+  `Pull Request 5337`_
+* Various webhooks improvements.
+  `Pull Request 5342`_
+* Make ``TabularToolDataTable._deduplicate_data()`` faster
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5383`_
+* Add ``--skip_flakey_fails`` flag to CI script for API tests
+  `Pull Request 5455`_
+* Fix for toolbox filters
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 5526`_
+* Fix missing job stdout/stderr on Pulsar transfer failures.
+  `Pull Request 5535`_
+* Optimization to fix repeated fetching dataset permissions in dynamic output collection.
+  `Pull Request 5578`_
+* Backport toolbox cache
+  `Pull Request 5583`_
+* Replace distutils.version with packaging.version (fixing lineage handling for
+  freebayes among other things).
+  `Pull Request 5588`_
+* Move the cache from toolbox level to the tool level.
+  `Pull Request 5600`_
+
+.. small_enhancement
+
+* Removes Sample request and External services makos/controllers
+  `Pull Request 4526`_, `Pull Request 4872`_, `Pull Request 5103`_,
+  `Pull Request 5204`_
+* Remove unused abstraction layers from Visualizations Registry.
+  `Pull Request 4620`_
+* Visible keys standardization in model classes.
+  `Pull Request 4744`_
+* Remove legacy library interface
+  `Pull Request 4908`_
+* ES6 client/galaxy/scripts/utils/ajax-queue.js
+  `Pull Request 4933`_
+* Remove unused galaxy-side set_tool_version code
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4986`_
+* Fix ``allow-register`` option in ``auth`` module
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4989`_
+* Tried to fix issue with Conda environment building failing jobs that
+  had to be rolled back.
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5036`_, `Pull Request 5470`_
+* Add packed symlink back pending a deprecation cycle.
+  `Pull Request 5094`_
+* Onload webhook toggles.
+  `Pull Request 5116`_
+* Re-organize edge case upload options for greater readability.
+  `Pull Request 5206`_
+* Refactor ``upload.py`` toward reuse.
+  `Pull Request 5229`_
+* JavaScript router cleanup.
+  `Pull Request 5235`_
+* Comment PlantTribes datatypes
+  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
+  `Pull Request 5254`_
+* Dataset error interface cleanup.
+  `Pull Request 5279`_
+* Mention how to specify the config file location
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5297`_
+* Uninstall a tool by default (vs. deactivating it).
+  `Pull Request 5300`_
+
+
+
+Fixes
+-------------------------------
+
+.. major_bug
+
+.. bug
+
+* Allow mapping over collections when discovering dataset collections in tools
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5413`_
+* Make liftover tool use data tables
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4645`_
+* Pass job output file unqualified names to Pulsar so that it can create them
+  before running the job.
+  `Pull Request 4662`_
+* Fix transiently failing saved histories due to success message disappearing.
+  `Pull Request 4669`_
+* Update CITATION file with 2016 paper
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4686`_
+* Stop running common_startup.sh twice when starting from run.sh
+  `Pull Request 4759`_
+* Fix docstring linting.
+  `Pull Request 4766`_
+* Mothur.freq sniffer more stringent
+  (thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__).
+  `Pull Request 4781`_
+* MacOS X fix for a test tool.
+  `Pull Request 4806`_
+* Minor architecture slides fixes for typos/grammar.
+  `Pull Request 4822`_
+* Fix two invalid targets in dataset list item.
+  `Pull Request 4823`_
+* Fix double return in form-parameters.
+  `Pull Request 4826`_
+* Fix the case where 'Labels' in a docker node inspect exists but is null.
+  `Pull Request 4838`_
+* Fix all E722 errors and ignore E741
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4847`_
+* Fix jsutils time - fixes charts visualize.
+  `Pull Request 4852`_
+* Bugfix during error handling with linked files during upload
+  (thanks to `@ieguinoa <https://github.com/ieguinoa>`__).
+  `Pull Request 4858`_
+* Add a gulp plumber.
+  `Pull Request 4867`_
+* Minor admin panel fixes.
+  `Pull Request 4895`_
+* Fix list collection creator dragdrop event bindings.
+  `Pull Request 4901`_
+* Fix status handling for grids.
+  `Pull Request 4913`_
+* Fix revision selection during (beta) repository installation
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4944`_
+* Fix Trackster styles bleeding into the app (the slightly off-center upload
+  .icon buttons).
+  `Pull Request 4948`_
+* Fix multiple selections for grid operations redirecting to center panel.
+  `Pull Request 4951`_
+* Fix visualization link in import success message.
+  `Pull Request 4952`_
+* Fix up reports JavaScript.
+  `Pull Request 4967`_
+* Run ``hg clone`` in a subprocess instead of using the Mercurial API
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4979`_
+* Tolerate ``IOError`` in tool and data table watcher
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4981`_
+* Install numpy before bx-python in case you are installing from sdists
+  `Pull Request 4982`_
+* Specify ``TagAssociation`` class when copying a tag
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4984`_
+* Fix initialization of named ajax queue.
+  `Pull Request 4985`_
+* Encode file content with utf-8
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 4987`_
+* Revert export to file.
+  `Pull Request 4988`_
+* Remove extraneous subclass for DMND datatype
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 4990`_
+* Fix to allow ``get_history`` calls with ``create=False`` when evaluating workflows.
+  `Pull Request 4997`_
+* Add missing ``ipaddress`` requirement
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5000`_
+* Use github instead of NCBI for problematic data manager test FASTA.
+  `Pull Request 5007`_
+* Fix for history contents API to remove the default flag override.
+  `Pull Request 5008`_
+* Fix to avoid visiting child inputs of invalid conditionals.
+  `Pull Request 5010`_
+* Fix for ``parse_interpreter`` - log a warning only if interpreter is set
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5015`_
+* Fix a few stray wiki links.
+  `Pull Request 5020`_
+* Workflow editor outputs fixes.
+  `Pull Request 5021`_
+* Fix workflow editor output attributes.
+  `Pull Request 5022`_
+* Metadata parameters rely on their own optional setting not on the field
+  attribute.
+  `Pull Request 5027`_
+* A Python 3 fix for the gsummary tool
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 5043`_
+* Cleanup SA objects between workflow invocation scheduling attempts.
+  `Pull Request 5045`_
+* Safely handle possible ``None`` value encountered in processing and execution of
+  post-job action arguments
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 5050`_
+* Restore admin form routes.
+  `Pull Request 5065`_
+* Fixes galaxy startup when ``LC_TYPE=UTF-8`` on OS X
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5070`_
+* Ignore ``OSError`` when chmod'ing integrated_tool_panel_conf.xml
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5071`_
+* Fix metadata setting for ``otu`` datatypes
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5072`_
+* Fix exception in admin panel
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5079`_
+* Always fill ``message`` to avoid ``KeyError`` for sentry ``ERROR_TEMPLATE``
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5086`_
+* Attempt to make data manager integration test more robust.
+  `Pull Request 5098`_
+* Toolshed install stability improvements
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5099`_
+* Fix Trackster link to custom builds view.
+  `Pull Request 5104`_
+* Improve resilience of filter detection, add error messages, fix identifiers.
+  `Pull Request 5106`_
+* Fix ICM datatype sniffer config
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5121`_
+* Fix attribute error that was missed during refactor of sentry
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 5122`_
+* Fix connecting non-input modules to subworkflow inputs.
+  `Pull Request 5140`_
+* Fix for history copy.
+  `Pull Request 5144`_
+* Fixes for handling delayed steps within subworkflows.
+  `Pull Request 5145`_
+* Fix localization and build client.
+  `Pull Request 5156`_
+* Resolve broken link for "all workflows"
+  (thanks to `@mmiladi <https://github.com/mmiladi>`__).
+  `Pull Request 5161`_
+* Fix workflow collection attachments.
+  `Pull Request 5166`_
+* Provide UI collection output information for subworkflows.
+  `Pull Request 5172`_
+* Remove legacy request controller from reports app.
+  `Pull Request 5182`_
+* Fixes genome decode handling.
+  `Pull Request 5198`_
+* Remove broken Yahoo OpenID support
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 5208`_
+* Force window jQuery access for charts.
+  `Pull Request 5210`_
+* Mark transiently failing ``test_run_data`` as flakey.
+  `Pull Request 5211`_
+* Fail job if tools that use ``galaxy.json`` write to stderr
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5217`_
+* Allow shell plugins with different parameters to co-exist
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5223`_
+* paster.pid/log to galaxy.pid/log reference update
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5226`_
+* Refine Conda version numbers allowed for using ``--offline`` flag again
+  (thanks to `@NCEichner <https://github.com/NCEichner>`__).
+  `Pull Request 5233`_
+* Workflow list show-in-tool-panel callback bugfix.
+  `Pull Request 5234`_
+* Fix image proxy prefix in tool form.
+  `Pull Request 5237`_
+* Fix wrong tool id after switching versions
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5249`_
+* Catch and display error when displaying broken BAM file
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5253`_
+* Fix for getmicrobedata tool
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 5258`_
+* Adjust note about nginx enabled sites configuration
+  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
+  `Pull Request 5259`_
+* Mark the test ``rerun_with_use_cached_job`` as flakey
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5286`_
+* Fix dataset edit link.
+  `Pull Request 5289`_
+* Fix link to getgalaxy.org
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 5295`_
+* Fix tool report submission with sentry
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5303`_
+* Fix ``common_startup.sh`` bash-isms
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5304`_
+* Fix Galaxy instance startup error
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 5306`_
+* Fix link to library from history structure view.
+  `Pull Request 5327`_
+* Prevent reloading when data table is being modified
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5331`_
+* Work around (temporarily) wrong ``getsize()`` output
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5335`_
+* Disable galaxy tour 'path' navigation.
+  `Pull Request 5340`_
+* Fix ``tool-shed-config-validate`` ``Makefile`` target.
+  (thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
+  `Pull Request 5343`_
+* History import fixes
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5344`_
+* Fix dataset purging, dataset cleanup script and db_shell script
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5346`_
+* Fix BAM conversion test tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5351`_
+* Remove charlimit for fetching URLs.
+  `Pull Request 5353`_
+* Use ``print()`` function in common_startup.sh
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5357`_
+* Handle ``None`` in job owner in API
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 5358`_
+* Fix form logic in deactivate or uninstall.
+  `Pull Request 5363`_
+* History multipanel fixes.
+  `Pull Request 5364`_
+* Remove additional checkbox workarounds.
+  `Pull Request 5367`_
+* Workflow tool menu fix for deleted workflows.
+  `Pull Request 5368`_
+* Bump conditional ``Pygments`` version to 2.2.0 so it matches the dev.
+  `Pull Request 5376`_
+* Fix ``make docs`` when the virtualenv is not ``.venv`` .
+  `Pull Request 5377`_
+* Force a fixed node image version when building client for Jenkins.
+  `Pull Request 5382`_
+* Install latest Conda and don't use ``shell=True``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5397`_
+* Fix for subworkflow creation
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5398`_
+* Follow IUC and drop ``r`` channel from the default Conda channels
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5406`_
+* Implement workaround for extra metadata revision creation.
+  `Pull Request 5433`_
+* Don't silently fail rest of multi-action queue when attempting to purge a
+  collection.
+  `Pull Request 5443`_
+* Ensure ``jobStateSummariesCollection`` exists.
+  `Pull Request 5444`_
+* Fix ``server_name`` when config is a ``dict``.
+  `Pull Request 5447`_
+* Fixes for workflow sharing links.
+  `Pull Request 5467`_
+* Fix workflow execution post action - rename
+  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
+  `Pull Request 5485`_
+* Fix ``common_startup.sh`` for galaxy tarballs
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5491`_
+* Close ``tempfile`` handles.
+  `Pull Request 5506`_, `Pull Request 5552`_
+* Do not allow ``codefiles`` during tool shed tool loading.
+  `Pull Request 5510`_
+* Fix for GenomeSpace importer/exporter
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 5528`_
+* Fix search overlay JS errors
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 5531`_
+* Allow LDAP options not starting with ``OPT_``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5556`_
+* Fix broken admin ``create new user`` when ``registration =='challenge'``
+  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
+  `Pull Request 5569`_
+* Do not remove external path files during library uploads
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 5573`_
+* Bump sqlite3 dependency for web proxy.
+  `Pull Request 5575`_
+* Fix small bam (header-only) infinite fetching.
+  `Pull Request 5579`_
+* Fix migration 0137's downgrade.
+  `Pull Request 5605`_
+* Conda fix for commands using stdout redirection.
+  `Pull Request 5620`_
+* Move `Extract genomic DNA 1` to list of versioned galaxy tools requiring
+  galaxy to be importable
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5626`_
+* Changed GenomeSpace token handling to use manual OpenID association only.
+  `Pull Request 5631`_
+* Use sample file path when adding missing indexes
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5650`_
+* Fix exception if user preference value undefined
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5662`_
+* Fix exception if email is not specified or email is wrong
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5663`_
+* Show error message if user tries purging datasets
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5664`_
+* Show error message if history structure can't be shown
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5665`_
+* Consistent sniffing regardless of in_place.
+  `Pull Request 5643`_
+
+.. github_links
+.. _Pull Request 4178: https://github.com/galaxyproject/galaxy/pull/4178
+.. _Pull Request 4435: https://github.com/galaxyproject/galaxy/pull/4435
+.. _Pull Request 4436: https://github.com/galaxyproject/galaxy/pull/4436
+.. _Pull Request 4475: https://github.com/galaxyproject/galaxy/pull/4475
+.. _Pull Request 4480: https://github.com/galaxyproject/galaxy/pull/4480
+.. _Pull Request 4487: https://github.com/galaxyproject/galaxy/pull/4487
+.. _Pull Request 4497: https://github.com/galaxyproject/galaxy/pull/4497
+.. _Pull Request 4513: https://github.com/galaxyproject/galaxy/pull/4513
+.. _Pull Request 4526: https://github.com/galaxyproject/galaxy/pull/4526
+.. _Pull Request 4543: https://github.com/galaxyproject/galaxy/pull/4543
+.. _Pull Request 4563: https://github.com/galaxyproject/galaxy/pull/4563
+.. _Pull Request 4569: https://github.com/galaxyproject/galaxy/pull/4569
+.. _Pull Request 4604: https://github.com/galaxyproject/galaxy/pull/4604
+.. _Pull Request 4620: https://github.com/galaxyproject/galaxy/pull/4620
+.. _Pull Request 4635: https://github.com/galaxyproject/galaxy/pull/4635
+.. _Pull Request 4645: https://github.com/galaxyproject/galaxy/pull/4645
+.. _Pull Request 4649: https://github.com/galaxyproject/galaxy/pull/4649
+.. _Pull Request 4653: https://github.com/galaxyproject/galaxy/pull/4653
+.. _Pull Request 4655: https://github.com/galaxyproject/galaxy/pull/4655
+.. _Pull Request 4658: https://github.com/galaxyproject/galaxy/pull/4658
+.. _Pull Request 4660: https://github.com/galaxyproject/galaxy/pull/4660
+.. _Pull Request 4661: https://github.com/galaxyproject/galaxy/pull/4661
+.. _Pull Request 4662: https://github.com/galaxyproject/galaxy/pull/4662
+.. _Pull Request 4664: https://github.com/galaxyproject/galaxy/pull/4664
+.. _Pull Request 4665: https://github.com/galaxyproject/galaxy/pull/4665
+.. _Pull Request 4669: https://github.com/galaxyproject/galaxy/pull/4669
+.. _Pull Request 4672: https://github.com/galaxyproject/galaxy/pull/4672
+.. _Pull Request 4673: https://github.com/galaxyproject/galaxy/pull/4673
+.. _Pull Request 4676: https://github.com/galaxyproject/galaxy/pull/4676
+.. _Pull Request 4679: https://github.com/galaxyproject/galaxy/pull/4679
+.. _Pull Request 4681: https://github.com/galaxyproject/galaxy/pull/4681
+.. _Pull Request 4682: https://github.com/galaxyproject/galaxy/pull/4682
+.. _Pull Request 4686: https://github.com/galaxyproject/galaxy/pull/4686
+.. _Pull Request 4687: https://github.com/galaxyproject/galaxy/pull/4687
+.. _Pull Request 4688: https://github.com/galaxyproject/galaxy/pull/4688
+.. _Pull Request 4689: https://github.com/galaxyproject/galaxy/pull/4689
+.. _Pull Request 4690: https://github.com/galaxyproject/galaxy/pull/4690
+.. _Pull Request 4693: https://github.com/galaxyproject/galaxy/pull/4693
+.. _Pull Request 4697: https://github.com/galaxyproject/galaxy/pull/4697
+.. _Pull Request 4699: https://github.com/galaxyproject/galaxy/pull/4699
+.. _Pull Request 4700: https://github.com/galaxyproject/galaxy/pull/4700
+.. _Pull Request 4704: https://github.com/galaxyproject/galaxy/pull/4704
+.. _Pull Request 4711: https://github.com/galaxyproject/galaxy/pull/4711
+.. _Pull Request 4720: https://github.com/galaxyproject/galaxy/pull/4720
+.. _Pull Request 4722: https://github.com/galaxyproject/galaxy/pull/4722
+.. _Pull Request 4723: https://github.com/galaxyproject/galaxy/pull/4723
+.. _Pull Request 4725: https://github.com/galaxyproject/galaxy/pull/4725
+.. _Pull Request 4729: https://github.com/galaxyproject/galaxy/pull/4729
+.. _Pull Request 4730: https://github.com/galaxyproject/galaxy/pull/4730
+.. _Pull Request 4732: https://github.com/galaxyproject/galaxy/pull/4732
+.. _Pull Request 4737: https://github.com/galaxyproject/galaxy/pull/4737
+.. _Pull Request 4739: https://github.com/galaxyproject/galaxy/pull/4739
+.. _Pull Request 4744: https://github.com/galaxyproject/galaxy/pull/4744
+.. _Pull Request 4746: https://github.com/galaxyproject/galaxy/pull/4746
+.. _Pull Request 4751: https://github.com/galaxyproject/galaxy/pull/4751
+.. _Pull Request 4753: https://github.com/galaxyproject/galaxy/pull/4753
+.. _Pull Request 4755: https://github.com/galaxyproject/galaxy/pull/4755
+.. _Pull Request 4757: https://github.com/galaxyproject/galaxy/pull/4757
+.. _Pull Request 4758: https://github.com/galaxyproject/galaxy/pull/4758
+.. _Pull Request 4759: https://github.com/galaxyproject/galaxy/pull/4759
+.. _Pull Request 4762: https://github.com/galaxyproject/galaxy/pull/4762
+.. _Pull Request 4764: https://github.com/galaxyproject/galaxy/pull/4764
+.. _Pull Request 4765: https://github.com/galaxyproject/galaxy/pull/4765
+.. _Pull Request 4766: https://github.com/galaxyproject/galaxy/pull/4766
+.. _Pull Request 4770: https://github.com/galaxyproject/galaxy/pull/4770
+.. _Pull Request 4771: https://github.com/galaxyproject/galaxy/pull/4771
+.. _Pull Request 4778: https://github.com/galaxyproject/galaxy/pull/4778
+.. _Pull Request 4779: https://github.com/galaxyproject/galaxy/pull/4779
+.. _Pull Request 4781: https://github.com/galaxyproject/galaxy/pull/4781
+.. _Pull Request 4787: https://github.com/galaxyproject/galaxy/pull/4787
+.. _Pull Request 4788: https://github.com/galaxyproject/galaxy/pull/4788
+.. _Pull Request 4789: https://github.com/galaxyproject/galaxy/pull/4789
+.. _Pull Request 4790: https://github.com/galaxyproject/galaxy/pull/4790
+.. _Pull Request 4791: https://github.com/galaxyproject/galaxy/pull/4791
+.. _Pull Request 4792: https://github.com/galaxyproject/galaxy/pull/4792
+.. _Pull Request 4796: https://github.com/galaxyproject/galaxy/pull/4796
+.. _Pull Request 4799: https://github.com/galaxyproject/galaxy/pull/4799
+.. _Pull Request 4806: https://github.com/galaxyproject/galaxy/pull/4806
+.. _Pull Request 4811: https://github.com/galaxyproject/galaxy/pull/4811
+.. _Pull Request 4814: https://github.com/galaxyproject/galaxy/pull/4814
+.. _Pull Request 4822: https://github.com/galaxyproject/galaxy/pull/4822
+.. _Pull Request 4823: https://github.com/galaxyproject/galaxy/pull/4823
+.. _Pull Request 4826: https://github.com/galaxyproject/galaxy/pull/4826
+.. _Pull Request 4827: https://github.com/galaxyproject/galaxy/pull/4827
+.. _Pull Request 4829: https://github.com/galaxyproject/galaxy/pull/4829
+.. _Pull Request 4833: https://github.com/galaxyproject/galaxy/pull/4833
+.. _Pull Request 4838: https://github.com/galaxyproject/galaxy/pull/4838
+.. _Pull Request 4839: https://github.com/galaxyproject/galaxy/pull/4839
+.. _Pull Request 4841: https://github.com/galaxyproject/galaxy/pull/4841
+.. _Pull Request 4847: https://github.com/galaxyproject/galaxy/pull/4847
+.. _Pull Request 4849: https://github.com/galaxyproject/galaxy/pull/4849
+.. _Pull Request 4850: https://github.com/galaxyproject/galaxy/pull/4850
+.. _Pull Request 4852: https://github.com/galaxyproject/galaxy/pull/4852
+.. _Pull Request 4855: https://github.com/galaxyproject/galaxy/pull/4855
+.. _Pull Request 4858: https://github.com/galaxyproject/galaxy/pull/4858
+.. _Pull Request 4863: https://github.com/galaxyproject/galaxy/pull/4863
+.. _Pull Request 4866: https://github.com/galaxyproject/galaxy/pull/4866
+.. _Pull Request 4867: https://github.com/galaxyproject/galaxy/pull/4867
+.. _Pull Request 4869: https://github.com/galaxyproject/galaxy/pull/4869
+.. _Pull Request 4871: https://github.com/galaxyproject/galaxy/pull/4871
+.. _Pull Request 4872: https://github.com/galaxyproject/galaxy/pull/4872
+.. _Pull Request 4876: https://github.com/galaxyproject/galaxy/pull/4876
+.. _Pull Request 4877: https://github.com/galaxyproject/galaxy/pull/4877
+.. _Pull Request 4879: https://github.com/galaxyproject/galaxy/pull/4879
+.. _Pull Request 4884: https://github.com/galaxyproject/galaxy/pull/4884
+.. _Pull Request 4885: https://github.com/galaxyproject/galaxy/pull/4885
+.. _Pull Request 4886: https://github.com/galaxyproject/galaxy/pull/4886
+.. _Pull Request 4887: https://github.com/galaxyproject/galaxy/pull/4887
+.. _Pull Request 4891: https://github.com/galaxyproject/galaxy/pull/4891
+.. _Pull Request 4894: https://github.com/galaxyproject/galaxy/pull/4894
+.. _Pull Request 4895: https://github.com/galaxyproject/galaxy/pull/4895
+.. _Pull Request 4900: https://github.com/galaxyproject/galaxy/pull/4900
+.. _Pull Request 4901: https://github.com/galaxyproject/galaxy/pull/4901
+.. _Pull Request 4903: https://github.com/galaxyproject/galaxy/pull/4903
+.. _Pull Request 4908: https://github.com/galaxyproject/galaxy/pull/4908
+.. _Pull Request 4909: https://github.com/galaxyproject/galaxy/pull/4909
+.. _Pull Request 4910: https://github.com/galaxyproject/galaxy/pull/4910
+.. _Pull Request 4912: https://github.com/galaxyproject/galaxy/pull/4912
+.. _Pull Request 4913: https://github.com/galaxyproject/galaxy/pull/4913
+.. _Pull Request 4914: https://github.com/galaxyproject/galaxy/pull/4914
+.. _Pull Request 4916: https://github.com/galaxyproject/galaxy/pull/4916
+.. _Pull Request 4917: https://github.com/galaxyproject/galaxy/pull/4917
+.. _Pull Request 4922: https://github.com/galaxyproject/galaxy/pull/4922
+.. _Pull Request 4925: https://github.com/galaxyproject/galaxy/pull/4925
+.. _Pull Request 4933: https://github.com/galaxyproject/galaxy/pull/4933
+.. _Pull Request 4934: https://github.com/galaxyproject/galaxy/pull/4934
+.. _Pull Request 4935: https://github.com/galaxyproject/galaxy/pull/4935
+.. _Pull Request 4939: https://github.com/galaxyproject/galaxy/pull/4939
+.. _Pull Request 4942: https://github.com/galaxyproject/galaxy/pull/4942
+.. _Pull Request 4944: https://github.com/galaxyproject/galaxy/pull/4944
+.. _Pull Request 4945: https://github.com/galaxyproject/galaxy/pull/4945
+.. _Pull Request 4948: https://github.com/galaxyproject/galaxy/pull/4948
+.. _Pull Request 4951: https://github.com/galaxyproject/galaxy/pull/4951
+.. _Pull Request 4952: https://github.com/galaxyproject/galaxy/pull/4952
+.. _Pull Request 4957: https://github.com/galaxyproject/galaxy/pull/4957
+.. _Pull Request 4958: https://github.com/galaxyproject/galaxy/pull/4958
+.. _Pull Request 4961: https://github.com/galaxyproject/galaxy/pull/4961
+.. _Pull Request 4962: https://github.com/galaxyproject/galaxy/pull/4962
+.. _Pull Request 4964: https://github.com/galaxyproject/galaxy/pull/4964
+.. _Pull Request 4965: https://github.com/galaxyproject/galaxy/pull/4965
+.. _Pull Request 4967: https://github.com/galaxyproject/galaxy/pull/4967
+.. _Pull Request 4968: https://github.com/galaxyproject/galaxy/pull/4968
+.. _Pull Request 4971: https://github.com/galaxyproject/galaxy/pull/4971
+.. _Pull Request 4972: https://github.com/galaxyproject/galaxy/pull/4972
+.. _Pull Request 4977: https://github.com/galaxyproject/galaxy/pull/4977
+.. _Pull Request 4978: https://github.com/galaxyproject/galaxy/pull/4978
+.. _Pull Request 4979: https://github.com/galaxyproject/galaxy/pull/4979
+.. _Pull Request 4981: https://github.com/galaxyproject/galaxy/pull/4981
+.. _Pull Request 4982: https://github.com/galaxyproject/galaxy/pull/4982
+.. _Pull Request 4984: https://github.com/galaxyproject/galaxy/pull/4984
+.. _Pull Request 4985: https://github.com/galaxyproject/galaxy/pull/4985
+.. _Pull Request 4986: https://github.com/galaxyproject/galaxy/pull/4986
+.. _Pull Request 4987: https://github.com/galaxyproject/galaxy/pull/4987
+.. _Pull Request 4988: https://github.com/galaxyproject/galaxy/pull/4988
+.. _Pull Request 4989: https://github.com/galaxyproject/galaxy/pull/4989
+.. _Pull Request 4990: https://github.com/galaxyproject/galaxy/pull/4990
+.. _Pull Request 4991: https://github.com/galaxyproject/galaxy/pull/4991
+.. _Pull Request 4992: https://github.com/galaxyproject/galaxy/pull/4992
+.. _Pull Request 4993: https://github.com/galaxyproject/galaxy/pull/4993
+.. _Pull Request 4994: https://github.com/galaxyproject/galaxy/pull/4994
+.. _Pull Request 4996: https://github.com/galaxyproject/galaxy/pull/4996
+.. _Pull Request 4997: https://github.com/galaxyproject/galaxy/pull/4997
+.. _Pull Request 4998: https://github.com/galaxyproject/galaxy/pull/4998
+.. _Pull Request 5000: https://github.com/galaxyproject/galaxy/pull/5000
+.. _Pull Request 5001: https://github.com/galaxyproject/galaxy/pull/5001
+.. _Pull Request 5002: https://github.com/galaxyproject/galaxy/pull/5002
+.. _Pull Request 5004: https://github.com/galaxyproject/galaxy/pull/5004
+.. _Pull Request 5005: https://github.com/galaxyproject/galaxy/pull/5005
+.. _Pull Request 5006: https://github.com/galaxyproject/galaxy/pull/5006
+.. _Pull Request 5007: https://github.com/galaxyproject/galaxy/pull/5007
+.. _Pull Request 5008: https://github.com/galaxyproject/galaxy/pull/5008
+.. _Pull Request 5010: https://github.com/galaxyproject/galaxy/pull/5010
+.. _Pull Request 5011: https://github.com/galaxyproject/galaxy/pull/5011
+.. _Pull Request 5013: https://github.com/galaxyproject/galaxy/pull/5013
+.. _Pull Request 5014: https://github.com/galaxyproject/galaxy/pull/5014
+.. _Pull Request 5015: https://github.com/galaxyproject/galaxy/pull/5015
+.. _Pull Request 5016: https://github.com/galaxyproject/galaxy/pull/5016
+.. _Pull Request 5017: https://github.com/galaxyproject/galaxy/pull/5017
+.. _Pull Request 5018: https://github.com/galaxyproject/galaxy/pull/5018
+.. _Pull Request 5020: https://github.com/galaxyproject/galaxy/pull/5020
+.. _Pull Request 5021: https://github.com/galaxyproject/galaxy/pull/5021
+.. _Pull Request 5022: https://github.com/galaxyproject/galaxy/pull/5022
+.. _Pull Request 5023: https://github.com/galaxyproject/galaxy/pull/5023
+.. _Pull Request 5027: https://github.com/galaxyproject/galaxy/pull/5027
+.. _Pull Request 5036: https://github.com/galaxyproject/galaxy/pull/5036
+.. _Pull Request 5037: https://github.com/galaxyproject/galaxy/pull/5037
+.. _Pull Request 5038: https://github.com/galaxyproject/galaxy/pull/5038
+.. _Pull Request 5042: https://github.com/galaxyproject/galaxy/pull/5042
+.. _Pull Request 5043: https://github.com/galaxyproject/galaxy/pull/5043
+.. _Pull Request 5045: https://github.com/galaxyproject/galaxy/pull/5045
+.. _Pull Request 5049: https://github.com/galaxyproject/galaxy/pull/5049
+.. _Pull Request 5050: https://github.com/galaxyproject/galaxy/pull/5050
+.. _Pull Request 5051: https://github.com/galaxyproject/galaxy/pull/5051
+.. _Pull Request 5054: https://github.com/galaxyproject/galaxy/pull/5054
+.. _Pull Request 5056: https://github.com/galaxyproject/galaxy/pull/5056
+.. _Pull Request 5058: https://github.com/galaxyproject/galaxy/pull/5058
+.. _Pull Request 5062: https://github.com/galaxyproject/galaxy/pull/5062
+.. _Pull Request 5063: https://github.com/galaxyproject/galaxy/pull/5063
+.. _Pull Request 5065: https://github.com/galaxyproject/galaxy/pull/5065
+.. _Pull Request 5066: https://github.com/galaxyproject/galaxy/pull/5066
+.. _Pull Request 5068: https://github.com/galaxyproject/galaxy/pull/5068
+.. _Pull Request 5070: https://github.com/galaxyproject/galaxy/pull/5070
+.. _Pull Request 5071: https://github.com/galaxyproject/galaxy/pull/5071
+.. _Pull Request 5072: https://github.com/galaxyproject/galaxy/pull/5072
+.. _Pull Request 5073: https://github.com/galaxyproject/galaxy/pull/5073
+.. _Pull Request 5074: https://github.com/galaxyproject/galaxy/pull/5074
+.. _Pull Request 5077: https://github.com/galaxyproject/galaxy/pull/5077
+.. _Pull Request 5078: https://github.com/galaxyproject/galaxy/pull/5078
+.. _Pull Request 5079: https://github.com/galaxyproject/galaxy/pull/5079
+.. _Pull Request 5080: https://github.com/galaxyproject/galaxy/pull/5080
+.. _Pull Request 5081: https://github.com/galaxyproject/galaxy/pull/5081
+.. _Pull Request 5086: https://github.com/galaxyproject/galaxy/pull/5086
+.. _Pull Request 5087: https://github.com/galaxyproject/galaxy/pull/5087
+.. _Pull Request 5088: https://github.com/galaxyproject/galaxy/pull/5088
+.. _Pull Request 5089: https://github.com/galaxyproject/galaxy/pull/5089
+.. _Pull Request 5091: https://github.com/galaxyproject/galaxy/pull/5091
+.. _Pull Request 5092: https://github.com/galaxyproject/galaxy/pull/5092
+.. _Pull Request 5093: https://github.com/galaxyproject/galaxy/pull/5093
+.. _Pull Request 5094: https://github.com/galaxyproject/galaxy/pull/5094
+.. _Pull Request 5095: https://github.com/galaxyproject/galaxy/pull/5095
+.. _Pull Request 5098: https://github.com/galaxyproject/galaxy/pull/5098
+.. _Pull Request 5099: https://github.com/galaxyproject/galaxy/pull/5099
+.. _Pull Request 5103: https://github.com/galaxyproject/galaxy/pull/5103
+.. _Pull Request 5104: https://github.com/galaxyproject/galaxy/pull/5104
+.. _Pull Request 5105: https://github.com/galaxyproject/galaxy/pull/5105
+.. _Pull Request 5106: https://github.com/galaxyproject/galaxy/pull/5106
+.. _Pull Request 5108: https://github.com/galaxyproject/galaxy/pull/5108
+.. _Pull Request 5109: https://github.com/galaxyproject/galaxy/pull/5109
+.. _Pull Request 5110: https://github.com/galaxyproject/galaxy/pull/5110
+.. _Pull Request 5114: https://github.com/galaxyproject/galaxy/pull/5114
+.. _Pull Request 5115: https://github.com/galaxyproject/galaxy/pull/5115
+.. _Pull Request 5116: https://github.com/galaxyproject/galaxy/pull/5116
+.. _Pull Request 5119: https://github.com/galaxyproject/galaxy/pull/5119
+.. _Pull Request 5121: https://github.com/galaxyproject/galaxy/pull/5121
+.. _Pull Request 5122: https://github.com/galaxyproject/galaxy/pull/5122
+.. _Pull Request 5124: https://github.com/galaxyproject/galaxy/pull/5124
+.. _Pull Request 5125: https://github.com/galaxyproject/galaxy/pull/5125
+.. _Pull Request 5128: https://github.com/galaxyproject/galaxy/pull/5128
+.. _Pull Request 5135: https://github.com/galaxyproject/galaxy/pull/5135
+.. _Pull Request 5137: https://github.com/galaxyproject/galaxy/pull/5137
+.. _Pull Request 5138: https://github.com/galaxyproject/galaxy/pull/5138
+.. _Pull Request 5139: https://github.com/galaxyproject/galaxy/pull/5139
+.. _Pull Request 5140: https://github.com/galaxyproject/galaxy/pull/5140
+.. _Pull Request 5143: https://github.com/galaxyproject/galaxy/pull/5143
+.. _Pull Request 5144: https://github.com/galaxyproject/galaxy/pull/5144
+.. _Pull Request 5145: https://github.com/galaxyproject/galaxy/pull/5145
+.. _Pull Request 5147: https://github.com/galaxyproject/galaxy/pull/5147
+.. _Pull Request 5154: https://github.com/galaxyproject/galaxy/pull/5154
+.. _Pull Request 5155: https://github.com/galaxyproject/galaxy/pull/5155
+.. _Pull Request 5156: https://github.com/galaxyproject/galaxy/pull/5156
+.. _Pull Request 5157: https://github.com/galaxyproject/galaxy/pull/5157
+.. _Pull Request 5161: https://github.com/galaxyproject/galaxy/pull/5161
+.. _Pull Request 5166: https://github.com/galaxyproject/galaxy/pull/5166
+.. _Pull Request 5170: https://github.com/galaxyproject/galaxy/pull/5170
+.. _Pull Request 5172: https://github.com/galaxyproject/galaxy/pull/5172
+.. _Pull Request 5173: https://github.com/galaxyproject/galaxy/pull/5173
+.. _Pull Request 5177: https://github.com/galaxyproject/galaxy/pull/5177
+.. _Pull Request 5180: https://github.com/galaxyproject/galaxy/pull/5180
+.. _Pull Request 5182: https://github.com/galaxyproject/galaxy/pull/5182
+.. _Pull Request 5185: https://github.com/galaxyproject/galaxy/pull/5185
+.. _Pull Request 5190: https://github.com/galaxyproject/galaxy/pull/5190
+.. _Pull Request 5191: https://github.com/galaxyproject/galaxy/pull/5191
+.. _Pull Request 5193: https://github.com/galaxyproject/galaxy/pull/5193
+.. _Pull Request 5196: https://github.com/galaxyproject/galaxy/pull/5196
+.. _Pull Request 5197: https://github.com/galaxyproject/galaxy/pull/5197
+.. _Pull Request 5198: https://github.com/galaxyproject/galaxy/pull/5198
+.. _Pull Request 5199: https://github.com/galaxyproject/galaxy/pull/5199
+.. _Pull Request 5200: https://github.com/galaxyproject/galaxy/pull/5200
+.. _Pull Request 5202: https://github.com/galaxyproject/galaxy/pull/5202
+.. _Pull Request 5204: https://github.com/galaxyproject/galaxy/pull/5204
+.. _Pull Request 5206: https://github.com/galaxyproject/galaxy/pull/5206
+.. _Pull Request 5208: https://github.com/galaxyproject/galaxy/pull/5208
+.. _Pull Request 5209: https://github.com/galaxyproject/galaxy/pull/5209
+.. _Pull Request 5210: https://github.com/galaxyproject/galaxy/pull/5210
+.. _Pull Request 5211: https://github.com/galaxyproject/galaxy/pull/5211
+.. _Pull Request 5212: https://github.com/galaxyproject/galaxy/pull/5212
+.. _Pull Request 5215: https://github.com/galaxyproject/galaxy/pull/5215
+.. _Pull Request 5217: https://github.com/galaxyproject/galaxy/pull/5217
+.. _Pull Request 5221: https://github.com/galaxyproject/galaxy/pull/5221
+.. _Pull Request 5223: https://github.com/galaxyproject/galaxy/pull/5223
+.. _Pull Request 5225: https://github.com/galaxyproject/galaxy/pull/5225
+.. _Pull Request 5226: https://github.com/galaxyproject/galaxy/pull/5226
+.. _Pull Request 5228: https://github.com/galaxyproject/galaxy/pull/5228
+.. _Pull Request 5229: https://github.com/galaxyproject/galaxy/pull/5229
+.. _Pull Request 5230: https://github.com/galaxyproject/galaxy/pull/5230
+.. _Pull Request 5232: https://github.com/galaxyproject/galaxy/pull/5232
+.. _Pull Request 5233: https://github.com/galaxyproject/galaxy/pull/5233
+.. _Pull Request 5234: https://github.com/galaxyproject/galaxy/pull/5234
+.. _Pull Request 5235: https://github.com/galaxyproject/galaxy/pull/5235
+.. _Pull Request 5237: https://github.com/galaxyproject/galaxy/pull/5237
+.. _Pull Request 5238: https://github.com/galaxyproject/galaxy/pull/5238
+.. _Pull Request 5240: https://github.com/galaxyproject/galaxy/pull/5240
+.. _Pull Request 5247: https://github.com/galaxyproject/galaxy/pull/5247
+.. _Pull Request 5249: https://github.com/galaxyproject/galaxy/pull/5249
+.. _Pull Request 5251: https://github.com/galaxyproject/galaxy/pull/5251
+.. _Pull Request 5253: https://github.com/galaxyproject/galaxy/pull/5253
+.. _Pull Request 5254: https://github.com/galaxyproject/galaxy/pull/5254
+.. _Pull Request 5258: https://github.com/galaxyproject/galaxy/pull/5258
+.. _Pull Request 5259: https://github.com/galaxyproject/galaxy/pull/5259
+.. _Pull Request 5260: https://github.com/galaxyproject/galaxy/pull/5260
+.. _Pull Request 5261: https://github.com/galaxyproject/galaxy/pull/5261
+.. _Pull Request 5262: https://github.com/galaxyproject/galaxy/pull/5262
+.. _Pull Request 5264: https://github.com/galaxyproject/galaxy/pull/5264
+.. _Pull Request 5266: https://github.com/galaxyproject/galaxy/pull/5266
+.. _Pull Request 5270: https://github.com/galaxyproject/galaxy/pull/5270
+.. _Pull Request 5272: https://github.com/galaxyproject/galaxy/pull/5272
+.. _Pull Request 5273: https://github.com/galaxyproject/galaxy/pull/5273
+.. _Pull Request 5276: https://github.com/galaxyproject/galaxy/pull/5276
+.. _Pull Request 5278: https://github.com/galaxyproject/galaxy/pull/5278
+.. _Pull Request 5279: https://github.com/galaxyproject/galaxy/pull/5279
+.. _Pull Request 5286: https://github.com/galaxyproject/galaxy/pull/5286
+.. _Pull Request 5288: https://github.com/galaxyproject/galaxy/pull/5288
+.. _Pull Request 5289: https://github.com/galaxyproject/galaxy/pull/5289
+.. _Pull Request 5293: https://github.com/galaxyproject/galaxy/pull/5293
+.. _Pull Request 5294: https://github.com/galaxyproject/galaxy/pull/5294
+.. _Pull Request 5295: https://github.com/galaxyproject/galaxy/pull/5295
+.. _Pull Request 5297: https://github.com/galaxyproject/galaxy/pull/5297
+.. _Pull Request 5299: https://github.com/galaxyproject/galaxy/pull/5299
+.. _Pull Request 5300: https://github.com/galaxyproject/galaxy/pull/5300
+.. _Pull Request 5301: https://github.com/galaxyproject/galaxy/pull/5301
+.. _Pull Request 5303: https://github.com/galaxyproject/galaxy/pull/5303
+.. _Pull Request 5304: https://github.com/galaxyproject/galaxy/pull/5304
+.. _Pull Request 5306: https://github.com/galaxyproject/galaxy/pull/5306
+.. _Pull Request 5311: https://github.com/galaxyproject/galaxy/pull/5311
+.. _Pull Request 5312: https://github.com/galaxyproject/galaxy/pull/5312
+.. _Pull Request 5321: https://github.com/galaxyproject/galaxy/pull/5321
+.. _Pull Request 5327: https://github.com/galaxyproject/galaxy/pull/5327
+.. _Pull Request 5331: https://github.com/galaxyproject/galaxy/pull/5331
+.. _Pull Request 5333: https://github.com/galaxyproject/galaxy/pull/5333
+.. _Pull Request 5335: https://github.com/galaxyproject/galaxy/pull/5335
+.. _Pull Request 5337: https://github.com/galaxyproject/galaxy/pull/5337
+.. _Pull Request 5340: https://github.com/galaxyproject/galaxy/pull/5340
+.. _Pull Request 5342: https://github.com/galaxyproject/galaxy/pull/5342
+.. _Pull Request 5343: https://github.com/galaxyproject/galaxy/pull/5343
+.. _Pull Request 5344: https://github.com/galaxyproject/galaxy/pull/5344
+.. _Pull Request 5346: https://github.com/galaxyproject/galaxy/pull/5346
+.. _Pull Request 5351: https://github.com/galaxyproject/galaxy/pull/5351
+.. _Pull Request 5353: https://github.com/galaxyproject/galaxy/pull/5353
+.. _Pull Request 5357: https://github.com/galaxyproject/galaxy/pull/5357
+.. _Pull Request 5358: https://github.com/galaxyproject/galaxy/pull/5358
+.. _Pull Request 5363: https://github.com/galaxyproject/galaxy/pull/5363
+.. _Pull Request 5364: https://github.com/galaxyproject/galaxy/pull/5364
+.. _Pull Request 5367: https://github.com/galaxyproject/galaxy/pull/5367
+.. _Pull Request 5368: https://github.com/galaxyproject/galaxy/pull/5368
+.. _Pull Request 5371: https://github.com/galaxyproject/galaxy/pull/5371
+.. _Pull Request 5373: https://github.com/galaxyproject/galaxy/pull/5373
+.. _Pull Request 5376: https://github.com/galaxyproject/galaxy/pull/5376
+.. _Pull Request 5377: https://github.com/galaxyproject/galaxy/pull/5377
+.. _Pull Request 5382: https://github.com/galaxyproject/galaxy/pull/5382
+.. _Pull Request 5383: https://github.com/galaxyproject/galaxy/pull/5383
+.. _Pull Request 5387: https://github.com/galaxyproject/galaxy/pull/5387
+.. _Pull Request 5390: https://github.com/galaxyproject/galaxy/pull/5390
+.. _Pull Request 5395: https://github.com/galaxyproject/galaxy/pull/5395
+.. _Pull Request 5397: https://github.com/galaxyproject/galaxy/pull/5397
+.. _Pull Request 5398: https://github.com/galaxyproject/galaxy/pull/5398
+.. _Pull Request 5403: https://github.com/galaxyproject/galaxy/pull/5403
+.. _Pull Request 5406: https://github.com/galaxyproject/galaxy/pull/5406
+.. _Pull Request 5413: https://github.com/galaxyproject/galaxy/pull/5413
+.. _Pull Request 5414: https://github.com/galaxyproject/galaxy/pull/5414
+.. _Pull Request 5416: https://github.com/galaxyproject/galaxy/pull/5416
+.. _Pull Request 5418: https://github.com/galaxyproject/galaxy/pull/5418
+.. _Pull Request 5426: https://github.com/galaxyproject/galaxy/pull/5426
+.. _Pull Request 5433: https://github.com/galaxyproject/galaxy/pull/5433
+.. _Pull Request 5440: https://github.com/galaxyproject/galaxy/pull/5440
+.. _Pull Request 5441: https://github.com/galaxyproject/galaxy/pull/5441
+.. _Pull Request 5442: https://github.com/galaxyproject/galaxy/pull/5442
+.. _Pull Request 5443: https://github.com/galaxyproject/galaxy/pull/5443
+.. _Pull Request 5444: https://github.com/galaxyproject/galaxy/pull/5444
+.. _Pull Request 5445: https://github.com/galaxyproject/galaxy/pull/5445
+.. _Pull Request 5447: https://github.com/galaxyproject/galaxy/pull/5447
+.. _Pull Request 5449: https://github.com/galaxyproject/galaxy/pull/5449
+.. _Pull Request 5455: https://github.com/galaxyproject/galaxy/pull/5455
+.. _Pull Request 5456: https://github.com/galaxyproject/galaxy/pull/5456
+.. _Pull Request 5460: https://github.com/galaxyproject/galaxy/pull/5460
+.. _Pull Request 5467: https://github.com/galaxyproject/galaxy/pull/5467
+.. _Pull Request 5470: https://github.com/galaxyproject/galaxy/pull/5470
+.. _Pull Request 5482: https://github.com/galaxyproject/galaxy/pull/5482
+.. _Pull Request 5485: https://github.com/galaxyproject/galaxy/pull/5485
+.. _Pull Request 5491: https://github.com/galaxyproject/galaxy/pull/5491
+.. _Pull Request 5506: https://github.com/galaxyproject/galaxy/pull/5506
+.. _Pull Request 5510: https://github.com/galaxyproject/galaxy/pull/5510
+.. _Pull Request 5512: https://github.com/galaxyproject/galaxy/pull/5512
+.. _Pull Request 5514: https://github.com/galaxyproject/galaxy/pull/5514
+.. _Pull Request 5515: https://github.com/galaxyproject/galaxy/pull/5515
+.. _Pull Request 5521: https://github.com/galaxyproject/galaxy/pull/5521
+.. _Pull Request 5526: https://github.com/galaxyproject/galaxy/pull/5526
+.. _Pull Request 5528: https://github.com/galaxyproject/galaxy/pull/5528
+.. _Pull Request 5531: https://github.com/galaxyproject/galaxy/pull/5531
+.. _Pull Request 5532: https://github.com/galaxyproject/galaxy/pull/5532
+.. _Pull Request 5533: https://github.com/galaxyproject/galaxy/pull/5533
+.. _Pull Request 5535: https://github.com/galaxyproject/galaxy/pull/5535
+.. _Pull Request 5542: https://github.com/galaxyproject/galaxy/pull/5542
+.. _Pull Request 5552: https://github.com/galaxyproject/galaxy/pull/5552
+.. _Pull Request 5556: https://github.com/galaxyproject/galaxy/pull/5556
+.. _Pull Request 5558: https://github.com/galaxyproject/galaxy/pull/5558
+.. _Pull Request 5561: https://github.com/galaxyproject/galaxy/pull/5561
+.. _Pull Request 5566: https://github.com/galaxyproject/galaxy/pull/5566
+.. _Pull Request 5569: https://github.com/galaxyproject/galaxy/pull/5569
+.. _Pull Request 5573: https://github.com/galaxyproject/galaxy/pull/5573
+.. _Pull Request 5574: https://github.com/galaxyproject/galaxy/pull/5574
+.. _Pull Request 5575: https://github.com/galaxyproject/galaxy/pull/5575
+.. _Pull Request 5576: https://github.com/galaxyproject/galaxy/pull/5576
+.. _Pull Request 5578: https://github.com/galaxyproject/galaxy/pull/5578
+.. _Pull Request 5579: https://github.com/galaxyproject/galaxy/pull/5579
+.. _Pull Request 5582: https://github.com/galaxyproject/galaxy/pull/5582
+.. _Pull Request 5583: https://github.com/galaxyproject/galaxy/pull/5583
+.. _Pull Request 5588: https://github.com/galaxyproject/galaxy/pull/5588
+.. _Pull Request 5589: https://github.com/galaxyproject/galaxy/pull/5589
+.. _Pull Request 5600: https://github.com/galaxyproject/galaxy/pull/5600
+.. _Pull Request 5605: https://github.com/galaxyproject/galaxy/pull/5605
+.. _Pull Request 5615: https://github.com/galaxyproject/galaxy/pull/5615
+.. _Pull Request 5616: https://github.com/galaxyproject/galaxy/pull/5616
+.. _Pull Request 5620: https://github.com/galaxyproject/galaxy/pull/5620
+.. _Pull Request 5626: https://github.com/galaxyproject/galaxy/pull/5626
+.. _Pull Request 5631: https://github.com/galaxyproject/galaxy/pull/5631
+.. _Pull Request 5634: https://github.com/galaxyproject/galaxy/pull/5634
+.. _Pull Request 5635: https://github.com/galaxyproject/galaxy/pull/5635
+.. _Pull Request 5643: https://github.com/galaxyproject/galaxy/pull/5643
+.. _Pull Request 5644: https://github.com/galaxyproject/galaxy/pull/5644
+.. _Pull Request 5650: https://github.com/galaxyproject/galaxy/pull/5650
+.. _Pull Request 5662: https://github.com/galaxyproject/galaxy/pull/5662
+.. _Pull Request 5663: https://github.com/galaxyproject/galaxy/pull/5663
+.. _Pull Request 5664: https://github.com/galaxyproject/galaxy/pull/5664
+.. _Pull Request 5665: https://github.com/galaxyproject/galaxy/pull/5665
+.. _Pull Request 5674: https://github.com/galaxyproject/galaxy/pull/5674
diff --git a/doc/source/releases/18.01_announce.rst b/doc/source/releases/18.01_announce.rst
index b62092b1e06..5cd42a4125d 100644
--- a/doc/source/releases/18.01_announce.rst
+++ b/doc/source/releases/18.01_announce.rst
@@ -3,8 +3,145 @@
 January 2018 Galaxy Release (v 18.01)
 ===========================================================
 
+.. include:: _header.rst
 
-Schedule
+Highlights
 ===========================================================
- * Planned Freeze Date: 2018-01-08
- * Planned Release Date: 2018-01-29
+
+**Performance and User Experience Improvements**
+  We made Galaxy more lively and responsive. Homepage, published workflows, published/saved histories, and data libraries should all load much faster now. Importing data from FTP will also take less of your time.
+  We achieved this by optimizing database queries, implementing cache, rethinking presentation, and adding progress bars and loading indicators where needed. See the `list of related performance pull requests`_.
+
+**Web Server and Configuration**
+  The default web server used by Galaxy has changed from Paste to `uWSGI <https://uwsgi-docs.readthedocs.io/>`__ and the default configuration file for Galaxy is now ``config/galaxy.yml`` instead of ``config/galaxy.ini``.
+  uWSGI is more production ready and allows Galaxy to scale better in its default
+  configuration. In the future uWSGI will allow Galaxy to setup GIE proxies without additional
+  configuration and use modern web technologies such as web sockets.
+  Read more about the server, configuration, and documentation changes in the `uWSGI details`_ section of this document.
+
+**Dataset Collection Usability**
+  This release has significantly improved the usability of Galaxy dataset collections. Dozens of improvements
+  to collections have been made, some of the key highlights include:
+
+  - Data library folders can now be sent to histories as a dataset collection. `Pull Request 4998`_, `Pull Request 5080`_
+  - Failed dataset collection elements can now be fixed using job re-running (thanks to `@mvdbeek <https://github.com/mvdbeek>`__). `Pull Request 5321`_, `Pull Request 5247`_, `Pull Request 5270`_
+  - Collections now appear with state and progress bars in the history panel and contained datasets
+    are hidden by default (with help from `@mvdbeek <https://github.com/mvdbeek>`__).
+    `Pull Request 5013`_, `Pull Request 5078`_
+  - We added intuitive workflow post job actions for dataset collections. `Pull Request 5416`_, `Pull Request 5418`_, `Pull Request 5414`_
+  - The web interface now supports collections with arbitrary nesting and size (with help
+    from `@mvdbeek <https://github.com/mvdbeek>`__). `Pull Request 4942`_, `Pull Request 4934`_, `Pull Request 5091`_
+  - More robust nametag discovery and propagation when using collections. `Pull Request 5403`_
+
+**Client Architecture**
+  The architecture for the client code that powers the Galaxy user interface has been significantly
+  overhauled. The code base has been converted to `ES6 <http://es6-features.org/>`__,
+  `Yarn <https://github.com/yarnpkg/yarn>`__ now powers the build and dependency management of the code,
+  `Prettier <https://prettier.io/>`__ is now used to ensure consistent code formatting,
+  and the `VueJS <https://vuejs.org/>`__ framework has been integrated. Taken together, these changes are
+  enabling Galaxy developers to write usable, responsive client code more quickly and concisely than
+  previously possible. A big thanks goes out to community contributions from
+  `@anuprulez <https://github.com/anuprulez>`__ and `@anatskiy <https://github.com/anatskiy>`__ that are
+  already converting existing Galaxy components to reactive VueJS ones. See the `list of related client pull requests`_.
+
+**New BAM datatypes**
+  Previously Galaxy only supported coordinate sorted BAM files by default (the ``bam`` datatype). In addition, this
+  release of Galaxy now supports three new types of BAM:
+
+  - ``qname_sorted.bam``, that ensures that the file is queryname sorted (e.g. ``SO:queryname``);
+  - ``qname_input_sorted.bam``, that can be used to describe the output of aligners which generally keep mate pairs adjacent
+  - ``unsorted.bam``, that makes no assumptions about the sort order of the file.
+
+  A huge thanks goes out to `@bgruening <https://github.com/bgruening>`__ and `@mvdbeek <https://github.com/mvdbeek>`__ who
+  implemented these datatypes.
+
+  `Pull Request 5180`_, `Pull Request 5589`_, `Pull Request 5532`_, `Pull Request 5644`_, `Pull Request 5674`_
+
+**Experimental Job Caching**
+  Galaxy can now be configured to allow users the option of skipping duplicated jobs if one with
+  identical parameters has been previously executed and simply reuse the previously generated outputs.
+  This contribution is thanks to `@mvdbeek <https://github.com/mvdbeek>`__.
+
+  `Pull Request 4690`_
+
+
+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_18.01 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git checkout release_18.01 && git pull --ff-only origin release_18.01
+
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
+
+
+Security
+========
+
+Breaking Changes
+================
+
+We have reworked the **Galaxy Webhook** interface so if you have custom webhooks at your instance
+you need to take the following steps in order to make them work:
+
+1. Rename the main config file: <name>.yml -> config.yml
+2. In the config file, rename the name attribute: name -> id
+3. Put all files into the plugin's root folder, which should contain only four files: ``config.yml`` (mandatory), ``__init__.py`` (optional), ``script.js`` (optional), ``styles.css`` (optional)
+
+Deprecation Notices
+===================
+
+* This is the last release we are shipping JavaScript source maps for Galaxy client.
+
+Removal Notices
+===============
+The following features that have been deprecated in the past releases are being removed in 18.01:
+
+* Sample tracking
+* Sample request and external services management
+* Legacy library interface for Administrators
+
+In addition to that, the PlantTribes datatypes have been commented out in the source code. Uncomment them if you want to re-enable it.
+
+uWSGI details
+=============
+
+To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a ``galaxy.ini``
+file configured, it will continue to use Paste by default unless additional steps are
+taken by the administrator (Galaxy can be forced to start under uWSGI even with an older configuration file
+by setting ``APP_WEBSERVER=uwsgi`` in the environment). As part of the transition to YAML-based
+configuration files, we have implemented a schema to validate Galaxy configuration files. Run
+``make config-validate`` from Galaxy's root directory to validate a schema and ``make config-lint`` to
+check for best practices. While there is no need to convert your configuration file (``galaxy.ini`` hasn't
+been deprecated), you can run ``make config-convert-dry-run`` and ``make config-convert``
+to respectively test and perform the conversion of an ``ini`` configuration file to a YAML one.
+
+These are big changes that affect many parts of Galaxy's administration documentation and makes
+this documentation very dependent on which Galaxy version they are targeting. To address this, we have
+moved a significant amount of administration documentation into Galaxy's code
+base and made it available on a per-release basis. The latest administration documentation for
+the previous release of Galaxy (17.09) which reference ``galaxy.ini`` files and Paste servers can
+be found `here <https://docs.galaxyproject.org/en/release_17.09/admin/index.html>`__, while documentation for this release can be found `here <https://docs.galaxyproject.org/en/release_18.01/admin/index.html>`__.
+
+`Pull Request 4475`_, `Pull Request 5135`_, `Pull Request 5390`_, `Pull Request 5373`_,
+`Pull Request 5105`_, `Pull Request 5441`_
+
+Release Notes
+=============
+
+.. include:: 18.01.rst
+   :start-after: announce_start
+
+Security patch details
+======================
+
+.. include:: _thanks.rst
+
diff --git a/doc/source/releases/18.05_announce.rst b/doc/source/releases/18.05_announce.rst
new file mode 100644
index 00000000000..15f289f613b
--- /dev/null
+++ b/doc/source/releases/18.05_announce.rst
@@ -0,0 +1,10 @@
+
+===========================================================
+May 2018 Galaxy Release (v 18.05)
+===========================================================
+
+
+Schedule
+===========================================================
+ * Planned Freeze Date: 2018-05-07
+ * Planned Release Date: 2018-05-28
diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst
index 448ab9bfbd0..c3a0f71450c 100644
--- a/doc/source/releases/index.rst
+++ b/doc/source/releases/index.rst
@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   18.01_announce
    17.09_announce
    17.05_announce
    17.01_announce
diff --git a/lib/galaxy/containers/docker_model.py b/lib/galaxy/containers/docker_model.py
index 302708d48df..9342d7cadd7 100644
--- a/lib/galaxy/containers/docker_model.py
+++ b/lib/galaxy/containers/docker_model.py
@@ -85,7 +85,12 @@ class DockerContainer(Container):
         #                 }
         #             ]
         rval = []
-        port_mappings = self.inspect[0]['NetworkSettings']['Ports']
+        try:
+            port_mappings = self.inspect[0]['NetworkSettings']['Ports']
+        except (IndexError, KeyError) as exc:
+            log.warning("Failed to get ports for container %s from `docker inspect` output at "
+                        "[0]['NetworkSettings']['Ports']: %s: %s", self.id, exc.__class__.__name__, str(exc))
+            return None
         for port_name in port_mappings:
             for binding in port_mappings[port_name]:
                 rval.append(ContainerPort(
@@ -165,7 +170,12 @@ class DockerService(Container):
         #             }
         #         ]
         rval = []
-        port_mappings = self.inspect[0]['Endpoint']['Ports']
+        try:
+            port_mappings = self.inspect[0]['Endpoint']['Ports']
+        except (IndexError, KeyError) as exc:
+            log.warning("Failed to get ports for container %s from `docker service inspect` output at "
+                        "[0]['Endpoint']['Ports']: %s: %s", self.id, exc.__class__.__name__, str(exc))
+            return None
         for binding in port_mappings:
             rval.append(ContainerPort(
                 binding['TargetPort'],
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 783f030177f..9d75f1232fb 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -192,7 +192,7 @@ class BamNative(Binary):
     """Class describing a BAM binary file that is not necessarily sorted"""
     edam_format = "format_2572"
     edam_data = "data_0863"
-    file_ext = "bam_native"
+    file_ext = "unsorted.bam"
     sort_flag = None
 
     MetadataElement(name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, no_value=None, visible=False, optional=True)
diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
index 50b8c1ca14c..43787ccc152 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -17,7 +17,7 @@
         > temp.bg && bedGraphToBigWig temp.bg '$chromInfo' '$output']]>
     </command>
     <inputs>
-        <param format="bam,bam_native" name="input" type="data" label="Choose BAM file"/>
+        <param format="bam,unsorted.bam" name="input" type="data" label="Choose BAM file"/>
     </inputs>
     <outputs>
         <data format="bigwig" name="output"/>
diff --git a/lib/galaxy/datatypes/converters/sam_to_bam_native.xml b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
similarity index 72%
rename from lib/galaxy/datatypes/converters/sam_to_bam_native.xml
rename to lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
index 1b0dfabe18b..2a99a793d27 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bam_native.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_sam_to_bam_native" name="Convert SAM to BAM native - without sorting" version="1.0.0" profile="18.01">
+<tool id="CONVERTER_sam_to_unsorted_bam" name="Convert SAM to BAM without sorting" version="1.0.0" profile="18.01">
     <requirements>
         <requirement type="package" version="1.6">samtools</requirement>
     </requirements>
@@ -15,7 +15,7 @@
         <param name="input" type="data" format="sam" label="SAM file"/>
     </inputs>
     <outputs>
-        <data name="output" format="bam_native"/>
+        <data name="output" format="unsorted.bam"/>
     </outputs>
     <help>
     </help>
diff --git a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
index 30847c6437b..1e2889a921c 100644
--- a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
@@ -12,7 +12,7 @@
     ]]>
     </command>
     <inputs>
-        <param format="sam,bam_native,qname_sorted.bam" name="input" type="data" label="Choose a BAM native or queryname sortedfile"/>
+        <param format="sam,unsorted.bam,qname_sorted.bam" name="input" type="data" label="Choose a BAM native or queryname sortedfile"/>
     </inputs>
     <outputs>
         <data format="bam" name="output"/>
diff --git a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
index ce606c5bf01..ced46c0cc31 100644
--- a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
@@ -13,7 +13,7 @@
     ]]>
     </command>
     <inputs>
-        <param format="sam,bam_native" name="input" type="data" label="Choose a BAM native or queryname sortedfile"/>
+        <param format="sam,unsorted.bam" name="input" type="data" label="Choose a BAM native or queryname sortedfile"/>
     </inputs>
     <outputs>
         <data format="qname_sorted.bam" name="output"/>
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index c69373b0669..221887ec82c 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -344,7 +344,7 @@ def guess_ext(fname, sniff_order):
     'bam'
     >>> fname = get_test_fname('3unsorted.bam')
     >>> guess_ext(fname, sniff_order)
-    'bam_native'
+    'unsorted.bam'
     >>> fname = get_test_fname('test.idpDB')
     >>> guess_ext(fname, sniff_order)
     'idpdb'
diff --git a/lib/galaxy/tools/toolbox/filters/__init__.py b/lib/galaxy/tools/toolbox/filters/__init__.py
index 8e9a1677f11..2184e37e846 100644
--- a/lib/galaxy/tools/toolbox/filters/__init__.py
+++ b/lib/galaxy/tools/toolbox/filters/__init__.py
@@ -34,7 +34,7 @@ class FilterFactory(object):
         filters = deepcopy(self.default_filters)
         if trans.user:
             for name, value in trans.user.preferences.items():
-                if value.strip():
+                if value and value.strip():
                     user_filters = listify(value, do_strip=True)
                     category = ''
                     if name == 'toolbox_tool_filters':
diff --git a/lib/galaxy/tools/verify/interactor.py b/lib/galaxy/tools/verify/interactor.py
index b1a28e27a3a..5623a7faa44 100644
--- a/lib/galaxy/tools/verify/interactor.py
+++ b/lib/galaxy/tools/verify/interactor.py
@@ -622,7 +622,7 @@ def _verify_extra_files_content(extra_files, hda_id, dataset_fetcher, test_data_
         _verify_composite_datatype_file_content(filepath, hda_id, base_name=filename, attributes=attributes, dataset_fetcher=dataset_fetcher, test_data_path_builder=test_data_path_builder, keep_outputs_dir=keep_outputs_dir)
 
 
-def verify_tool(tool_id, galaxy_interactor, resource_parameters={}, register_job_data=None, test_index=0, tool_version=None):
+def verify_tool(tool_id, galaxy_interactor, resource_parameters={}, register_job_data=None, test_index=0, tool_version=None, quiet=False):
     tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
     tool_test_dict = tool_test_dicts[test_index]
     testdef = ToolTestDescription(tool_test_dict)
@@ -642,6 +642,7 @@ def verify_tool(tool_id, galaxy_interactor, resource_parameters={}, register_job
     job_output_exceptions = None
     tool_execution_exception = None
     expected_failure_occurred = False
+    begin_time = time.time()
     try:
         try:
             tool_response = galaxy_interactor.run_tool(testdef, test_history, resource_parameters=resource_parameters)
@@ -662,7 +663,7 @@ def verify_tool(tool_id, galaxy_interactor, resource_parameters={}, register_job
             assert data_list or data_collection_list
 
             try:
-                job_stdio = _verify_outputs(testdef, test_history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor)
+                job_stdio = _verify_outputs(testdef, test_history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=quiet)
             except JobOutputsError as e:
                 job_stdio = e.job_stdio
                 job_output_exceptions = e.output_exceptions
@@ -671,16 +672,26 @@ def verify_tool(tool_id, galaxy_interactor, resource_parameters={}, register_job
                 job_output_exceptions = [e]
                 raise e
     finally:
-        job_data = {}
-        if tool_inputs is not None:
-            job_data["inputs"] = tool_inputs
-        if job_stdio is not None:
-            job_data["job"] = job_stdio
-        if job_output_exceptions:
-            job_data["output_problems"] = [str(_) for _ in job_output_exceptions]
-        if tool_execution_exception:
-            job_data["execution_problem"] = str(tool_execution_exception)
         if register_job_data is not None:
+            end_time = time.time()
+            job_data = {
+                "tool_id": tool_id,
+                "tool_version": tool_version,
+                "test_index": test_index,
+                "time_seconds": end_time - begin_time,
+            }
+            if tool_inputs is not None:
+                job_data["inputs"] = tool_inputs
+            if job_stdio is not None:
+                job_data["job"] = job_stdio
+            status = "success"
+            if job_output_exceptions:
+                job_data["output_problems"] = [str(_) for _ in job_output_exceptions]
+                status = "failure"
+            if tool_execution_exception:
+                job_data["execution_problem"] = str(tool_execution_exception)
+                status = "error"
+            job_data["status"] = status
             register_job_data(job_data)
 
     galaxy_interactor.delete_history(test_history)
@@ -698,7 +709,7 @@ def _handle_def_errors(testdef):
             raise Exception("Test parse failure")
 
 
-def _verify_outputs(testdef, history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor):
+def _verify_outputs(testdef, history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=False):
     assert len(jobs) == 1, "Test framework logic error, somehow tool test resulted in more than one job."
     job = jobs[0]
 
@@ -713,7 +724,7 @@ def _verify_outputs(testdef, history, jobs, tool_id, data_list, data_collection_
     found_exceptions = []
 
     def register_exception(e):
-        if not found_exceptions:
+        if not found_exceptions and not quiet:
             # Only print this stuff out once.
             for stream in ['stdout', 'stderr']:
                 if stream in job_stdio:
diff --git a/lib/galaxy/tools/verify/script.py b/lib/galaxy/tools/verify/script.py
index b9ca7b58c64..64873a368f4 100644
--- a/lib/galaxy/tools/verify/script.py
+++ b/lib/galaxy/tools/verify/script.py
@@ -1,11 +1,14 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import argparse
 import json
 import sys
 
 from galaxy.tools.verify.interactor import GalaxyInteractorApi, verify_tool
 
-DESCRIPTION = "Script to quickly run a tool test against a running Galaxy instance."
+DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
+ALL_TESTS = "*all_tests*"
 
 
 def main(argv=None):
@@ -20,35 +23,70 @@ def main(argv=None):
         "keep_outputs_dir": args.output,
     }
     tool_id = args.tool_id
-    test_index = int(args.test_index)
     tool_version = args.tool_version
 
     galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
+    raw_test_index = args.test_index
+    if raw_test_index == ALL_TESTS:
+        tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
+        test_indices = list(range(len(tool_test_dicts)))
+    else:
+        test_indices = [int(raw_test_index)]
 
     test_results = []
 
-    def _register_job_data(job_data):
-        test_results.append({
-            'id': tool_id + "-" + str(test_index),
-            'has_data': True,
-            'data': job_data,
-        })
+    if args.append:
+        with open(args.output_json, "r") as f:
+            previous_results = json.load(f)
+            test_results = previous_results["tests"]
 
-    try:
-        verify_tool(
-            tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version, register_job_data=_register_job_data
-        )
-    finally:
-        report_obj = {
-            'version': '0.1',
-            'tests': test_results,
-        }
-        output_json = args.output_json
-        if output_json:
+    exceptions = []
+    verbose = args.verbose
+    for test_index in test_indices:
+        if tool_version:
+            tool_id_and_version = "%s/%s" % (tool_id, tool_version)
+        else:
+            tool_id_and_version = tool_id
+
+        test_identifier = "tool %s test # %d" % (tool_id_and_version, test_index)
+
+        def register(job_data):
+            test_results.append({
+                'id': tool_id + "-" + str(test_index),
+                'has_data': True,
+                'data': job_data,
+            })
+
+        try:
+            verify_tool(
+                tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version,
+                register_job_data=register, quiet=not verbose
+            )
+
+            if verbose:
+                print("%s passed" % test_identifier)
+
+        except Exception as e:
+            if verbose:
+                print("%s failed, %s" % (test_identifier, e))
+            exceptions.append(e)
+
+    report_obj = {
+        'version': '0.1',
+        'tests': test_results,
+    }
+    output_json = args.output_json
+    if output_json:
+        if args.output_json == "-":
+            assert not args.append
+            print(json.dumps(report_obj))
+        else:
             with open(args.output_json, "w") as f:
-                print(report_obj)
                 json.dump(report_obj, f)
 
+    if exceptions:
+        raise exceptions[0]
+
 
 def _arg_parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION)
@@ -57,9 +95,11 @@ def _arg_parser():
     parser.add_argument('-a', '--admin-key', default=None, help='Galaxy Admin API Key')
     parser.add_argument('-t', '--tool-id', default=None, help='Tool ID')
     parser.add_argument('--tool-version', default=None, help='Tool Version')
-    parser.add_argument('-i', '--test-index', default=0, help='Tool Test Index (starting at 0)')
+    parser.add_argument('-i', '--test-index', default=ALL_TESTS, help='Tool Test Index (starting at 0) - by default all tests will run.')
     parser.add_argument('-o', '--output', default=None, help='directory to dump outputs to')
-    parser.add_argument('-j', '--output_json', default=None, help='output metadata json')
+    parser.add_argument('--append', default=False, action="store_true", help="Extend a test record json (created with --output-json) with additional tests.")
+    parser.add_argument('-j', '--output-json', default=None, help='output metadata json')
+    parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.")
     return parser
 
 
diff --git a/lib/galaxy/visualization/plugins/interactive_environments.py b/lib/galaxy/visualization/plugins/interactive_environments.py
index edb108eb864..10cb067282d 100644
--- a/lib/galaxy/visualization/plugins/interactive_environments.py
+++ b/lib/galaxy/visualization/plugins/interactive_environments.py
@@ -6,6 +6,7 @@ import shlex
 import stat
 import string
 import tempfile
+import time
 import uuid
 from itertools import product
 from subprocess import PIPE, Popen
@@ -442,7 +443,20 @@ class InteractiveEnvironmentRequest(object):
         """
         run_args = self.container_run_args(image, env_override, volumes)
         container = self.attr.container_interface.run_in_container(None, **run_args)
-        container_port = self._find_port_mapping(container.ports)
+        attempt = 0
+        container_ports = container.ports
+        while container_ports is None and attempt < 30:
+            # TODO: it would be better to do this in /interactive_environments/ready so the client doesn't block here,
+            # but _find_port_mapping needs certain non-persisted data (the port configured to be published) and the
+            # proxy manager doesn't have an update method, so that'd require bigger changes than I have the time for
+            # right now
+            attempt += 1
+            log.warning("Sleeping for 2 seconds while waiting for container %s ports", container.id)
+            time.sleep(2)
+            container_ports = container.ports
+        if container_ports is None:
+            raise Exception("Failed to determine ports for container '%s' after 30 attempts" % container.id)
+        container_port = self._find_port_mapping(container_ports)
         log.debug("Container '%s' accessible at: %s:%s", container.id, container_port.hostaddr, container_port.hostport)
         self.attr.proxy_request = self.trans.app.proxy_manager.setup_proxy(
             self.trans,
diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py
index b8508aebeef..5cae1668913 100644
--- a/lib/galaxy/visualization/plugins/plugin.py
+++ b/lib/galaxy/visualization/plugins/plugin.py
@@ -270,6 +270,14 @@ class InteractiveEnvironmentPlugin(VisualizationPlugin):
         context['base_url'] = 'interactive_environments'
         super(InteractiveEnvironmentPlugin, self).__init__(app, path, name, config, context=context, **kwargs)
 
+    def _error_template(self, trans):
+        return trans.fill_template('message.mako',
+            message='Loading the interactive environment failed, please contact the {admin_tag} for assistance'.format(
+                admin_tag='<a href="mailto:{admin_mail}">Galaxy administrator</a>'.format(
+                    admin_mail=trans.app.config.error_email_to)
+                if trans.app.config.error_email_to else 'Galaxy administrator'),
+            status='error')
+
     def _render(self, render_vars, trans=None, embedded=None, **kwargs):
         """
         Override to add interactive environment specific template vars.
@@ -295,16 +303,15 @@ class InteractiveEnvironmentPlugin(VisualizationPlugin):
                 request = self.INTENV_REQUEST_FACTORY(trans, self)
             except Exception:
                 log.exception("IE plugin request handling failed")
-                return trans.fill_template('message.mako',
-                    message='Loading the interactive environment failed, please contact the {admin_tag} for assistance'.format(
-                        admin_tag='<a href="mailto:{admin_mail}">Galaxy administrator</a>'.format(
-                            admin_mail=trans.app.config.error_email_to)
-                        if trans.app.config.error_email_to else 'Galaxy administrator'),
-                    status='error')
+                return self._error_template(trans)
             render_vars["ie_request"] = request
 
         template_filename = self.config['entry_point']['file']
-        return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars)
+        try:
+            return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars)
+        except Exception:
+            log.exception("IE plugin template fill failed")
+            return self._error_template(trans)
 
     def _get_url(self):
         return url_for('interactive_environment_plugin', visualization_name=self.name)
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index 2e2d1909af5..9d51b8a7618 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -494,11 +494,10 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         history = trans.sa_session.query(model.History).options(
             eagerload_all('active_datasets.creating_job_associations.job.workflow_invocation_step.workflow_invocation.workflow'),
         ).get(id)
-        assert history
-        # TODO: formalize to trans.show_error
-        assert (history.user and (history.user.id == trans.user.id) or
-                (history.id == trans.history.id) or
-                (trans.user_is_admin()))
+        if not (history and ((history.user and trans.user and history.user.id == trans.user.id) or
+                             (trans.history and history.id == trans.history.id) or
+                             trans.user_is_admin())):
+            return trans.show_error_message("Cannot display history structure.")
         # Resolve jobs and workflow invocations for the datasets in the history
         # items is filled with items (hdas, jobs, or workflows) that go at the
         # top level
@@ -1127,7 +1126,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
     @web.expose
     def purge_deleted_datasets(self, trans):
         count = 0
-        if trans.app.config.allow_user_dataset_purge:
+        if trans.app.config.allow_user_dataset_purge and trans.history:
             for hda in trans.history.datasets:
                 if not hda.deleted or hda.purged:
                     continue
@@ -1145,7 +1144,8 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                     except Exception:
                         log.exception('Unable to purge dataset (%s) on purge of hda (%s):' % (hda.dataset.id, hda.id))
                 count += 1
-        return trans.show_ok_message("%d datasets have been deleted permanently" % count, refresh_frames=['history'])
+            return trans.show_ok_message("%d datasets have been deleted permanently" % count, refresh_frames=['history'])
+        return trans.show_error_message("Cannot purge deleted datasets from this session.")
 
     @web.expose
     def delete(self, trans, id, purge=False):
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 638659cf031..96ba8b0a786 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -925,7 +925,9 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create
         Check whether token fits the user and then activate the user's account.
         """
         params = util.Params(kwd, sanitize=False)
-        email = unquote(params.get('email', None))
+        email = params.get('email', None)
+        if email is not None:
+            email = unquote(email)
         activation_token = params.get('activation_token', None)
 
         if email is None or activation_token is None:
@@ -934,6 +936,9 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create
         else:
             # Find the user
             user = trans.sa_session.query(trans.app.model.User).filter(trans.app.model.User.table.c.email == email).first()
+            if not user:
+                # Probably wrong email address
+                return trans.show_error_message("You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>") % web.url_for(controller="root", action="index")
             # If the user is active already don't try to activate
             if user.active is True:
                 return trans.show_ok_message("Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>") % web.url_for(controller='root', action='index')
diff --git a/lib/tool_shed/util/tool_util.py b/lib/tool_shed/util/tool_util.py
index 42dc7132d44..3a6ac2069cb 100644
--- a/lib/tool_shed/util/tool_util.py
+++ b/lib/tool_shed/util/tool_util.py
@@ -43,6 +43,7 @@ def copy_sample_file(app, filename, dest_path=None):
     """
     Copies a sample file at `filename` to `the dest_path`
     directory and strips the '.sample' extensions from `filename`.
+    Returns the path to the copied file (with the .sample extension).
     """
     if dest_path is None:
         dest_path = os.path.abspath(app.config.tool_data_path)
@@ -56,8 +57,10 @@ def copy_sample_file(app, filename, dest_path=None):
         shutil.copy(full_source_path, full_destination_path)
     # Only create the .loc file if it does not yet exist.  We don't overwrite it in case it
     # contains stuff proprietary to the local instance.
-    if not os.path.lexists(os.path.join(dest_path, copied_file)):
+    non_sample_path = os.path.join(dest_path, copied_file)
+    if not os.path.lexists(non_sample_path):
         shutil.copy(full_source_path, os.path.join(dest_path, copied_file))
+    return non_sample_path
 
 
 def copy_sample_files(app, sample_files, tool_path=None, sample_files_copied=None, dest_path=None):
@@ -159,10 +162,10 @@ def handle_missing_index_file(app, tool_path, sample_files, repository_tools_tup
                 for sample_file in sample_files:
                     sample_file_name = basic_util.strip_path(sample_file)
                     if sample_file_name == '%s.sample' % missing_file_name:
-                        copy_sample_file(app, os.path.join(tool_path, sample_file))
+                        target_path = copy_sample_file(app, os.path.join(tool_path, sample_file))
                         if options.tool_data_table and options.tool_data_table.missing_index_file:
-                            options.tool_data_table.handle_found_index_file(options.missing_index_file)
-                        sample_files_copied.append(options.missing_index_file)
+                            options.tool_data_table.handle_found_index_file(target_path)
+                        sample_files_copied.append(target_path)
                         break
     return repository_tools_tups, sample_files_copied
 
diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
index b503e1dc5b2..46b2cc941bf 100644
--- a/test/functional/test_toolbox.py
+++ b/test/functional/test_toolbox.py
@@ -10,6 +10,7 @@ except ImportError:
         return x
 
 from base.driver_util import setup_keep_outdir, target_url_parts
+from base.instrument import register_job_data
 from galaxy.tools import DataManagerTool  # noqa: I201
 from galaxy.tools.verify.interactor import GalaxyInteractorApi, verify_tool  # noqa: I201
 from .twilltestcase import TwillTestCase
@@ -37,7 +38,7 @@ class ToolTestCase(TwillTestCase):
             tool_id = self.tool_id
         assert tool_id
 
-        verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version)
+        verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)
 
 
 @nottest
diff --git a/test/functional/tools/sam_to_bam_native.xml b/test/functional/tools/sam_to_unsorted_bam.xml
similarity index 92%
rename from test/functional/tools/sam_to_bam_native.xml
rename to test/functional/tools/sam_to_unsorted_bam.xml
index b15fd0cbdde..3a0830e8838 100644
--- a/test/functional/tools/sam_to_bam_native.xml
+++ b/test/functional/tools/sam_to_unsorted_bam.xml
@@ -23,13 +23,13 @@
     </command>
     <inputs>
         <param name="input1" type="data" format="sam" label="SAM file" optional="true"/>
-        <param name="input2" type="data" format="bam_native" label="Unsorted BAM file" optional="true"/>
+        <param name="input2" type="data" format="unsorted.bam" label="Unsorted BAM file" optional="true"/>
         <param name="input3" type="data" format="bam" label="BAM file sorted by coordinate" optional="true"/>
         <param name="input4" type="data" format="qname_sorted.bam" label="BAM file sorted by queryname" optional="true"/>
         <param name="input5" type="data" format="qname_input_sorted.bam" label="BAM file with sort order determined by the aligner" optional="true"/>
     </inputs>
     <outputs>
-        <data name="bam_native_output" format="bam_native">
+        <data name="bam_native_output" format="unsorted.bam">
             <filter>input1 or input2</filter>
         </data>
         <data name="bam_output" format="bam">
@@ -46,12 +46,12 @@
         <!-- Test that bam native output won't be sorted-->
         <test>
             <param name="input1" value="sam_with_header.sam" ftype="sam"/>
-            <output name="bam_native_output" file="bam_native_from_sam.bam" ftype="bam_native"/>
+            <output name="bam_native_output" file="bam_native_from_sam.bam" ftype="unsorted.bam"/>
         </test>
         <!-- Test that sam input is properly converted to bam native -->
         <test>
             <param name="input2" value="sam_with_header.sam" ftype="sam"/>
-            <output name="bam_native_output" file="bam_native_from_sam.bam" ftype="bam_native"/>
+            <output name="bam_native_output" file="bam_native_from_sam.bam" ftype="unsorted.bam"/>
         </test>
         <!-- Test that sam input is properly converted to bam -->
         <test>
diff --git a/test/functional/tools/sample_datatypes_conf.xml b/test/functional/tools/sample_datatypes_conf.xml
index 29917074a99..3b8b0dc0d58 100644
--- a/test/functional/tools/sample_datatypes_conf.xml
+++ b/test/functional/tools/sample_datatypes_conf.xml
@@ -22,7 +22,7 @@
         <converter file="fastqsangerbz2_to_fastqsanger.xml" target_datatype="fastqsanger"/>
     </datatype>
     <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
-        <converter file="sam_to_bam_native.xml" target_datatype="bam_native"/>
+        <converter file="sam_to_unsorted_bam.xml" target_datatype="unsorted.bam"/>
         <converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
         <converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
         <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
@@ -30,7 +30,7 @@
     <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://galaxyproject.org/learn/datatypes/#bam" />
     <datatype extension="qname_input_sorted.bam" type="galaxy.datatypes.binary:BamInputSorted" mimetype="application/octet-stream" display_in_upload="false" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted based on the aligner output." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"/>
     <datatype extension="qname_sorted.bam" type="galaxy.datatypes.binary:BamQuerynameSorted" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted by queryname." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"/>
-    <datatype extension="bam_native" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
+    <datatype extension="unsorted.bam" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
         <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
         <converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
         <converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 788bab2d293..b1cf03ed24d 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -86,7 +86,7 @@
   <tool file="column_multi_param.xml" />
   <tool file="special_params.xml" />
   <tool file="section.xml" />
-  <tool file="sam_to_bam_native.xml" />
+  <tool file="sam_to_unsorted_bam.xml" />
   <tool file="top_level_data.xml" />
   <tool file="validation_default.xml" />
   <tool file="validation_sanitizer.xml" />