diff --git a/client/galaxy/scripts/galaxy.pages.js b/client/galaxy/scripts/galaxy.pages.js
index 2f3203f0d79..830a30e8e75 100644
--- a/client/galaxy/scripts/galaxy.pages.js
+++ b/client/galaxy/scripts/galaxy.pages.js
@@ -99,7 +99,7 @@ function get_item_info( dialog_type )
 // Make an item importable.
 function make_item_importable( item_controller, item_id, item_type )
 {
-    ajax_url = set_accessible_url.replace( "ITEM_CONTROLLER", item_controller );
+    var ajax_url = set_accessible_url.replace( "ITEM_CONTROLLER", item_controller );
     $.ajax({
       type: "POST",
       url: ajax_url,
@@ -273,9 +273,9 @@ WYMeditor.editor.prototype.dialog = function( dialogType, dialogFeatures, bodyHt
                               newCaption.innerHTML = sCaption;
 
                               //we create the rows and cells
-                              for(x=0; x<iRows; x++) {
+                              for(var x=0; x<iRows; x++) {
                                       newRow = table.insertRow(x);
-                                      for(y=0; y<iCols; y++) {newRow.insertCell(y);}
+                                      for(var y=0; y<iCols; y++) {newRow.insertCell(y);}
                               }
 
                       //set the summary attr
@@ -347,8 +347,8 @@ WYMeditor.editor.prototype.dialog = function( dialogType, dialogFeatures, bodyHt
                                 make_item_importable(item_info.controller, item_id, item_info.singular);
 
                             // Insert link(s) to item(s). This is done by getting item info and then manipulating wym.
-                            url_template = get_name_and_link_url + item_id;
-                            ajax_url = url_template.replace( "ITEM_CONTROLLER", item_info.controller);
+                            var url_template = get_name_and_link_url + item_id;
+                            var ajax_url = url_template.replace( "ITEM_CONTROLLER", item_info.controller);
                             $.getJSON( ajax_url, function( returned_item_info ) {
                                 // Get link text.
                                 wym._exec(WYMeditor.CREATE_LINK, sStamp);
diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
index 59560e1440e..92b385a44e1 100644
--- a/client/galaxy/scripts/mvc/collection/list-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
@@ -562,7 +562,7 @@ var ListCollectionCreator = Backbone.View.extend( BASE_MVC.LoggableMixin ).exten
     _errorHandler : function( data ){
         this.error( data );
 
-        var creator = this;
+        var creator = this,
             content = data.message || _l( 'An error occurred' );
         if( data.xhr ){
             var xhr = data.xhr,
diff --git a/client/galaxy/scripts/mvc/dataset/data.js b/client/galaxy/scripts/mvc/dataset/data.js
index f3bf46ac079..f8f6331b2e6 100644
--- a/client/galaxy/scripts/mvc/dataset/data.js
+++ b/client/galaxy/scripts/mvc/dataset/data.js
@@ -291,7 +291,7 @@ var TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({
         TabularDatasetChunkedView.prototype.initialize.call(this, options);
 
         // Scrolling happens in top-level elements.
-        scroll_elt = _.find(this.$el.parents(), function(p) {
+        var scroll_elt = _.find(this.$el.parents(), function(p) {
             return $(p).css('overflow') === 'auto';
         });
 
diff --git a/client/galaxy/scripts/mvc/grid/grid-template.js b/client/galaxy/scripts/mvc/grid/grid-template.js
index 31845c1aa96..ced04a6673b 100644
--- a/client/galaxy/scripts/mvc/grid/grid-template.js
+++ b/client/galaxy/scripts/mvc/grid/grid-template.js
@@ -60,7 +60,7 @@ return {
                 tmpl +=     '<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li>' +
                             '<div popupmenu="popup-global-actions">';
             }
-            for (i in options.global_actions) {
+            for (var i in options.global_actions) {
                 var action = options.global_actions[i];
                 tmpl +=         '<li>' +
                                     '<a class="action-button use-target" target="' + action.target + '" href="' + action.url_args + '" onclick="return false;" >' + action.label + '</a>' +
@@ -158,7 +158,7 @@ return {
             }
             
             // Data columns
-            for (j in options.columns) {
+            for (var j in options.columns) {
                 var column = options.columns[j];
                 if (column.visible) {
                     // Nowrap
@@ -242,6 +242,7 @@ return {
             // Set max page.
             var max_range = page_link_range + min_offset;
             var max_page = cur_page_num + max_range;
+            var max_offset;
             if (max_page <= num_pages) {
                 // Max page is fine.
                 max_offset = 0;
@@ -307,7 +308,7 @@ return {
                             'For <span class="grid-selected-count"></span> selected items: ';
             
             // configure buttons for operations
-            for (i in options.operations) {
+            for (var i in options.operations) {
                 var operation = options.operations[i];
                 if (operation.allow_multiple) {
                     tmpl += '<input type="button" value="' + operation.label + '" class="operation-button action-button">&nbsp;';
@@ -554,14 +555,14 @@ return {
             
             // add category filters
             var seperator = false;
-            for (cf_label in options.categorical_filters[column_key]) {
+            for (var cf_label in options.categorical_filters[column_key]) {
                 // get category filter
                 var cf = options.categorical_filters[column_key][cf_label];
                 
                 // each filter will have only a single argument, so get that single argument
                 var cf_key = '';
                 var cf_arg = '';
-                for (key in cf) {
+                for (var key in cf) {
                     cf_key = key;
                     cf_arg = cf[key];
                 }
diff --git a/client/galaxy/scripts/mvc/grid/grid-view.js b/client/galaxy/scripts/mvc/grid/grid-view.js
index 6fae6060e62..eb837f7942c 100644
--- a/client/galaxy/scripts/mvc/grid/grid-view.js
+++ b/client/galaxy/scripts/mvc/grid/grid-view.js
@@ -583,7 +583,7 @@ return Backbone.View.extend({
         this.grid.set('async', false);
 
         // get slide status
-        advanced_search = this.$el.find('#advanced-search').is(':visible');
+        var advanced_search = this.$el.find('#advanced-search').is(':visible');
         this.grid.set('advanced_search', advanced_search);
 
         // get default url
diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js
index 751f862c18f..ddc4f556493 100644
--- a/client/galaxy/scripts/mvc/library/library-dataset-view.js
+++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js
@@ -497,7 +497,7 @@ var LibraryDatasetView = Backbone.View.extend({
    * Extract the role ids from Select2 elements's 'data'
    */
   _extractIds: function(roles_list){
-    ids_list = [];
+    var ids_list = [];
     for (var i = roles_list.length - 1; i >= 0; i--) {
       ids_list.push(roles_list[i].id);
     };
@@ -531,7 +531,7 @@ var LibraryDatasetView = Backbone.View.extend({
     mod_utils.get({
         url      :  Galaxy.root + "api/datatypes?extension_only=False",
         success  :  function( datatypes ) {
-                        for (key in datatypes) {
+                        for (var key in datatypes) {
                             that.list_extensions.push({
                                 id              : datatypes[key].extension,
                                 text            : datatypes[key].extension,
@@ -548,7 +548,7 @@ var LibraryDatasetView = Backbone.View.extend({
     mod_utils.get({
         url     :    Galaxy.root + "api/genomes",
         success : function( genomes ) {
-                    for ( key in genomes ) {
+                    for (var key in genomes ) {
                         that.list_genomes.push({
                             id      : genomes[key][1],
                             text    : genomes[key][0]
diff --git a/client/galaxy/scripts/mvc/library/library-folder-view.js b/client/galaxy/scripts/mvc/library/library-folder-view.js
index ed3c30ed2b9..a66019ccbd7 100644
--- a/client/galaxy/scripts/mvc/library/library-folder-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folder-view.js
@@ -181,7 +181,7 @@ var FolderView = Backbone.View.extend({
    * Extract the role ids from Select2 elements's 'data'
    */
   _extractIds: function(roles_list){
-    ids_list = [];
+    var ids_list = [];
     for (var i = roles_list.length - 1; i >= 0; i--) {
       ids_list.push(roles_list[i].id);
     };
diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
index 644f9fdcd38..df4467b5e84 100644
--- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
@@ -112,7 +112,7 @@ var FolderListView = Backbone.View.extend({
 
         // when dataset_id is present render its details too
         if ( this.options.dataset_id ){
-            row = _.findWhere( that.rowViews, { id: this.options.dataset_id } );
+            var row = _.findWhere( that.rowViews, { id: this.options.dataset_id } );
             if ( row ) {
               row.showDatasetDetails();
             } else {
@@ -277,7 +277,7 @@ var FolderListView = Backbone.View.extend({
          // Iterate each checkbox
          $(':checkbox', '#folder_list_body').each(function() {
             this.checked = selected;
-            $row = $(this.parentElement.parentElement);
+            var $row = $(this.parentElement.parentElement);
             // Change color of selected/unselected
             if (selected) {
               that.makeDarkRow($row);
diff --git a/client/galaxy/scripts/mvc/library/library-folderrow-view.js b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
index ebb2d5e2822..138e487f180 100644
--- a/client/galaxy/scripts/mvc/library/library-folderrow-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
@@ -66,7 +66,7 @@ var FolderRowView = Backbone.View.extend({
    * the filling of the row template of a given folder.
    */
   prepareButtons: function(folder){
-    vis_config = this.options.visibility_config;
+    var vis_config = this.options.visibility_config;
     if (this.options.edit_mode === false){
       vis_config.save_folder_btn = false;
       vis_config.cancel_folder_btn = false;
diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
index ef8ee193f0c..0c301fa1c1b 100644
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -161,7 +161,8 @@ var FolderToolbarView = Backbone.View.extend({
       var folderDetails = this.serialize_new_folder();
       if (this.validate_new_folder(folderDetails)){
           var folder = new mod_library_model.FolderAsModel();
-          url_items = Backbone.history.fragment.split('/');
+          var url_items = Backbone.history.fragment.split('/'),
+              current_folder_id;
           if(url_items.indexOf('page') > -1){
             current_folder_id = url_items[url_items.length-3];
           }else {
@@ -317,7 +318,7 @@ var FolderToolbarView = Backbone.View.extend({
   updateProgress: function(){
       this.progress += this.progressStep;
       $( '.progress-bar-import' ).width( Math.round( this.progress ) + '%' );
-      txt_representation = Math.round( this.progress ) + '% Complete';
+      var txt_representation = Math.round( this.progress ) + '% Complete';
       $( '.completion_span' ).text( txt_representation );
   },
 
@@ -431,7 +432,7 @@ var FolderToolbarView = Backbone.View.extend({
         url      :  Galaxy.root + "api/datatypes?extension_only=False",
         success  :  function( datatypes ) {
                         that.list_extensions = [];
-                        for (key in datatypes) {
+                        for (var key in datatypes) {
                             that.list_extensions.push({
                                 id              : datatypes[key].extension,
                                 text            : datatypes[key].extension,
@@ -450,7 +451,7 @@ var FolderToolbarView = Backbone.View.extend({
         url     :    Galaxy.root + "api/genomes",
         success : function( genomes ) {
                     that.list_genomes = [];
-                    for ( key in genomes ) {
+                    for (var key in genomes ) {
                         that.list_genomes.push({
                             id      : genomes[key][1],
                             text    : genomes[key][0]
@@ -615,7 +616,7 @@ var FolderToolbarView = Backbone.View.extend({
       this.modal.disableButton('Import');
       paths = paths.split('\n');
       for (var i = paths.length - 1; i >= 0; i--) {
-        trimmed = paths[i].trim();
+        var trimmed = paths[i].trim();
         if (trimmed.length!==0){
           valid_paths.push(trimmed);
         }
@@ -674,7 +675,7 @@ var FolderToolbarView = Backbone.View.extend({
   importFromJstreePath: function ( that, options ){
     var all_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
     // remove the disabled elements that could have been trigerred with the 'select all'
-    selected_nodes = _.filter(all_nodes, function(node){ return node.state.disabled == false; })
+    var selected_nodes = _.filter(all_nodes, function(node){ return node.state.disabled == false; })
     var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
     var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
     var file_type = this.select_extension.value();
@@ -752,7 +753,7 @@ var FolderToolbarView = Backbone.View.extend({
         }
       });
       for ( var i = history_item_ids.length - 1; i >= 0; i-- ) {
-        history_item_id = history_item_ids[i];
+        var history_item_id = history_item_ids[i];
         var folder_item = new mod_library_model.Item();
         folder_item.url = Galaxy.root + 'api/folders/' + this.options.id + '/contents';
         if (history_item_types[i] === 'collection') {
diff --git a/client/galaxy/scripts/mvc/library/library-library-view.js b/client/galaxy/scripts/mvc/library/library-library-view.js
index 42650e04cab..9d6d6b82d19 100644
--- a/client/galaxy/scripts/mvc/library/library-library-view.js
+++ b/client/galaxy/scripts/mvc/library/library-library-view.js
@@ -212,7 +212,7 @@ var LibraryView = Backbone.View.extend({
   },
 
   _extractIds: function(roles_list){
-    ids_list = [];
+    var ids_list = [];
     for (var i = roles_list.length - 1; i >= 0; i--) {
       ids_list.push(roles_list[i].id);
     };
diff --git a/client/galaxy/scripts/mvc/library/library-libraryrow-view.js b/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
index e39cc2b0da5..757222170cb 100644
--- a/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
+++ b/client/galaxy/scripts/mvc/library/library-libraryrow-view.js
@@ -64,7 +64,7 @@ var LibraryRowView = Backbone.View.extend({
    * the filling of the row template of given library.
    */
   prepareButtons: function(library){
-    vis_config = this.element_visibility_config;
+    var vis_config = this.element_visibility_config;
 
     if (this.edit_mode === false){
       vis_config.save_library_btn = false;
diff --git a/client/galaxy/scripts/mvc/library/library-model.js b/client/galaxy/scripts/mvc/library/library-model.js
index 91f00cd92ba..be62bef4a13 100644
--- a/client/galaxy/scripts/mvc/library/library-model.js
+++ b/client/galaxy/scripts/mvc/library/library-model.js
@@ -41,7 +41,7 @@ define([], function() {
         if (search_term == "") return this;
         var lowercase_term = search_term.toLowerCase();
         return this.filter(function(data) {
-          lowercase_name = data.get("name").toLowerCase();
+          var lowercase_name = data.get("name").toLowerCase();
           return lowercase_name.indexOf(lowercase_term) !== -1;
         });
       },
diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
index 608109432c1..01144b1daa3 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
@@ -112,7 +112,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
             var wp_count = 0;
             this.wp_inputs = {};
             function _handleWorkflowParameter( value, callback ) {
-                var re = /\$\{(.+?)\}/g;
+                var re = /\$\{(.+?)\}/g, match;
                 while ( match = re.exec( String( value ) ) ) {
                     var wp_name = match[ 1 ];
                     callback( self.wp_inputs[ wp_name ] = self.wp_inputs[ wp_name ] || {
@@ -336,7 +336,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                                 new_value = { values: [] };
                                 _.each( input.step_linked, function( source_step ) {
                                     if ( self._isDataStep( source_step ) ) {
-                                        value = self.forms[ source_step.index ].data.create().input;
+                                        var value = self.forms[ source_step.index ].data.create().input;
                                         value && _.each( value.values, function( v ) { new_value.values.push( v ) } );
                                     }
                                 });
@@ -345,7 +345,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                                 }
                             } else if ( input.wp_linked ) {
                                 new_value = input.value;
-                                var re = /\$\{(.+?)\}/g;
+                                var re = /\$\{(.+?)\}/g, match;
                                 while ( match = re.exec( input.value ) ) {
                                     var wp_field = self.wp_form.field_list[ self.wp_form.data.match( match[ 1 ] ) ];
                                     var wp_value = wp_field && wp_field.value();
@@ -514,7 +514,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
 
         /** Is data input module/step */
         _isDataStep: function( steps ) {
-            lst = $.isArray( steps ) ? steps : [ steps ] ;
+            var lst = $.isArray( steps ) ? steps : [ steps ] ;
             for ( var i = 0; i < lst.length; i++ ) {
                 var step = lst[ i ];
                 if ( !step || !step.step_type || !step.step_type.startsWith( 'data' ) ) {
diff --git a/client/galaxy/scripts/mvc/toolshed/categories-view.js b/client/galaxy/scripts/mvc/toolshed/categories-view.js
index b914e55fe3a..b9226f8d5c4 100644
--- a/client/galaxy/scripts/mvc/toolshed/categories-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/categories-view.js
@@ -39,7 +39,7 @@ define(['mvc/toolshed/toolshed-model', 'mvc/toolshed/util'], function(toolshed_m
                         var params = {term: request.term, tool_shed_url: shed_url};
                         $.post(base_url, params, function(data) {
                             console.log(data);
-                            result_list = toolshed_util.shedParser(data);
+                            var result_list = toolshed_util.shedParser(data);
                             response(result_list);
                         });
                     },
diff --git a/client/galaxy/scripts/mvc/toolshed/repo-status-view.js b/client/galaxy/scripts/mvc/toolshed/repo-status-view.js
index 183de64a53d..0d8e381e87c 100644
--- a/client/galaxy/scripts/mvc/toolshed/repo-status-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/repo-status-view.js
@@ -16,7 +16,7 @@ define(['mvc/toolshed/toolshed-model', 'mvc/toolshed/util'], function(toolshed_m
                 var all_done = true;
                 _.some(self.model.models, function(repository) {
                     repo_id = repository.get('id');
-                    repo_status = repository.get('status').toLowerCase();
+                    var repo_status = repository.get('status').toLowerCase();
                     if (terminal_states.indexOf(repo_status) === -1) {
                         all_done = false;
                         return true;
diff --git a/client/galaxy/scripts/mvc/toolshed/repositories-view.js b/client/galaxy/scripts/mvc/toolshed/repositories-view.js
index 795adfa0471..acf7f2fa7f3 100644
--- a/client/galaxy/scripts/mvc/toolshed/repositories-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/repositories-view.js
@@ -32,7 +32,7 @@ define(['mvc/toolshed/toolshed-model', 'mvc/toolshed/util'], function(toolshed_m
                         var base_url = Galaxy.root + 'api/tool_shed/search';
                         var params = {term: request.term, tool_shed_url: shed_url};
                         $.post(base_url, params, function(data) {
-                            result_list = toolshed_util.shedParser(data);
+                            var result_list = toolshed_util.shedParser(data);
                             response(result_list);
                         });
                     },
diff --git a/client/galaxy/scripts/mvc/toolshed/repository-queue-view.js b/client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
index 24193a63d2b..509f0a869bb 100644
--- a/client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
@@ -63,7 +63,7 @@ define(['mvc/toolshed/toolshed-model', 'mvc/toolshed/util'], function(toolshed_m
                 if (queue_key === undefined) {
                     queue_key = toolshed_util.queueKey(repository_metadata);
                 }
-                repository_queue = JSON.parse(localStorage.repositories);
+                var repository_queue = JSON.parse(localStorage.repositories);
                 if (repository_queue.hasOwnProperty(queue_key)) {
                     delete repository_queue[queue_key];
                     localStorage.repositories = JSON.stringify(repository_queue);
@@ -82,7 +82,7 @@ define(['mvc/toolshed/toolshed-model', 'mvc/toolshed/util'], function(toolshed_m
         },
 
         loadFromQueue: function(queue_key) {
-            repository_queue = JSON.parse(localStorage.repositories);
+            var repository_queue = JSON.parse(localStorage.repositories);
             if (repository_queue.hasOwnProperty(queue_key)) {
                 return repository_queue[queue_key];
             }
diff --git a/client/galaxy/scripts/mvc/toolshed/repository-view.js b/client/galaxy/scripts/mvc/toolshed/repository-view.js
index 27403c54d02..9192988f16c 100644
--- a/client/galaxy/scripts/mvc/toolshed/repository-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/repository-view.js
@@ -19,7 +19,7 @@ define(['mvc/toolshed/toolshed-model',
             this.options = _.defaults(this.options || {}, this.defaults);
             this.model = new toolshed_model.RepositoryCollection();
             this.listenTo(this.model, 'sync', this.render);
-            shed = params.tool_shed.replace(/\//g, '%2f');
+            var shed = params.tool_shed.replace(/\//g, '%2f');
             this.model.url += '?tool_shed_url=' + shed + '&repository_id=' + params.repository_id;
             this.model.tool_shed_url = params.tool_shed.replace(/%2f/g, '/');
             this.model.tool_shed = shed;
@@ -81,7 +81,7 @@ define(['mvc/toolshed/toolshed-model',
                 params.tool_panel_section = JSON.stringify(that.panelSelect(params));
                 params.shed_tool_conf = $("select[name='shed_tool_conf']").find('option:selected').val()
                 params.changeset = $('#changeset').find("option:selected").val();
-                url = $('#repository_installation').attr('action');
+                var url = $('#repository_installation').attr('action');
                 that.prepareInstall(params, url);
             });
             $('#queue_install').on('click', function(ev) {
@@ -107,8 +107,8 @@ define(['mvc/toolshed/toolshed-model',
                 that.checkInstalled(repository_metadata);
             });
             $('.tool_panel_section_picker').on('change', function() {
-                new_value = $(this).find('option:selected').val();
-                default_tps = $('#tool_panel_section_select').find('option:selected').val();
+                var new_value = $(this).find('option:selected').val();
+                var default_tps = $('#tool_panel_section_select').find('option:selected').val();
                 if (new_value == default_tps) {
                     $(this).attr('default', 'active');
                 }
@@ -191,8 +191,8 @@ define(['mvc/toolshed/toolshed-model',
                 params.new_tool_panel_section = $("#new_tool_panel_section").val();
             }
             $('.tool_panel_section_picker').each(function() {
-                element_name = $(this).attr('name');
-                tool_guid = $(this).attr('data-toolguid');
+                var element_name = $(this).attr('name');
+                var tool_guid = $(this).attr('data-toolguid');
                 if (element_name === 'tool_panel_section_id') {
                     tool_panel_section[tool_guid] = { tool_panel_section: $(this).find("option:selected").val(), action: 'append' }
                 }
@@ -244,13 +244,13 @@ define(['mvc/toolshed/toolshed-model',
         prepareInstall: function(params, api_url) {
             var that = this;
             $.post(api_url, params, function(data) {
-                iri_parameters = JSON.parse(data);
+                var iri_parameters = JSON.parse(data);
                 that.doInstall(iri_parameters);
             });
         },
 
         doInstall: function(params) {
-            controller_url = Galaxy.root + 'admin_toolshed/manage_repositories';
+            var controller_url = Galaxy.root + 'admin_toolshed/manage_repositories';
             var repositories = params.repositories;
             var new_route = 'status/r/' + repositories.join('|');
             $.post(controller_url, params, function(data) {
diff --git a/client/galaxy/scripts/mvc/toolshed/util.js b/client/galaxy/scripts/mvc/toolshed/util.js
index ed052ecb8e8..143309f6df4 100644
--- a/client/galaxy/scripts/mvc/toolshed/util.js
+++ b/client/galaxy/scripts/mvc/toolshed/util.js
@@ -4,7 +4,7 @@ define([], function() {
         var shed_url = this.shed_url;
         var base_url = Galaxy.root + 'api/tool_shed/search';
         $.get(base_url, {term: request.term, tool_shed_url: shed_url}, function(data) {
-            result_list = that.shedParser(data);
+            var result_list = that.shedParser(data);
             response(result_list);
         });
 
@@ -16,7 +16,7 @@ define([], function() {
         $.each(hits, function(hit) {
             var record = hits[hit];
             var label = record.repository.name + ' by ' + record.repository.repo_owner_username + ': ' + record.repository.description;
-            result = {value: record.repository.id, label: label};
+            var result = {value: record.repository.id, label: label};
             results.push(result);
         });
         return results;
@@ -37,8 +37,8 @@ define([], function() {
 
     var queueLength = function() {
         if (localStorage.hasOwnProperty('repositories')) {
-            repo_queue = JSON.parse(localStorage.repositories);
-            queue_length = Object.keys(repo_queue).length;
+            var repo_queue = JSON.parse(localStorage.repositories);
+            var queue_length = Object.keys(repo_queue).length;
             return queue_length;
         }
         else {
diff --git a/client/galaxy/scripts/mvc/toolshed/workflows-view.js b/client/galaxy/scripts/mvc/toolshed/workflows-view.js
index bb47d9ba65a..45ea8faacb9 100644
--- a/client/galaxy/scripts/mvc/toolshed/workflows-view.js
+++ b/client/galaxy/scripts/mvc/toolshed/workflows-view.js
@@ -24,7 +24,7 @@ define(['mvc/toolshed/toolshed-model', 'mvc/toolshed/util'], function(toolshed_m
         },
 
         bindEvents: function() {
-            var that = this;
+            var that = this, repository_id;
             $('.show_wf_repo').on('click', function() {
                 var tool_ids = $(this).attr('data-toolids');
                 var toolshed = $(this).attr('data-shed');
diff --git a/client/galaxy/scripts/mvc/ui/ui-drilldown.js b/client/galaxy/scripts/mvc/ui/ui-drilldown.js
index 71627f2e651..88f56957b5b 100644
--- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js
+++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js
@@ -53,7 +53,7 @@ var View = Options.BaseIcons.extend({
         // recursive function which iterates through options
         function iterate ( $tmpl, options, header ) {
             header = header || [];
-            for ( i in options ) {
+            for (var i in options ) {
                 var level = options[ i ];
                 var has_options = level.options && level.options.length > 0;
                 var new_header = header.slice( 0 );
diff --git a/client/galaxy/scripts/mvc/ui/ui-popover.js b/client/galaxy/scripts/mvc/ui/ui-popover.js
index 3227a1c4408..7d8f013b419 100644
--- a/client/galaxy/scripts/mvc/ui/ui-popover.js
+++ b/client/galaxy/scripts/mvc/ui/ui-popover.js
@@ -116,7 +116,8 @@ var View = Backbone.View.extend({
         var container_position  = $container.position();
 
         // get position
-        var top  = left = 0;
+        var top, left;
+        top = left = 0;
         if ([ 'top', 'bottom' ].indexOf( placement ) != -1) {
             left = container_position.left - width + ( container_width + width ) / 2;
             switch ( placement ) {
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-default.js b/client/galaxy/scripts/mvc/ui/ui-select-default.js
index 4d0671344a5..20caebcd3d5 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-default.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js
@@ -315,7 +315,7 @@ var View = Backbone.View.extend({
         }
         if ( this.model.get( 'searchable' ) ) {
             if ( $.isArray( new_value ) ) {
-                val = [];
+                var val = [];
                 _.each( new_value, function( v ) {
                     var d = _.findWhere( self.data2, { id: v } );
                     d && val.push( d );
diff --git a/client/galaxy/scripts/mvc/upload/upload-ftp.js b/client/galaxy/scripts/mvc/upload/upload-ftp.js
index 4e36750f55f..b3547f82eee 100644
--- a/client/galaxy/scripts/mvc/upload/upload-ftp.js
+++ b/client/galaxy/scripts/mvc/upload/upload-ftp.js
@@ -27,7 +27,7 @@ define( [ 'utils/utils' ], function( Utils ) {
             if ( ftp_files && ftp_files.length > 0 ) {
                 this.$( '.upload-ftp-content' ).html( $( this._templateTable() ) );
                 var size = 0;
-                for ( index in ftp_files ) {
+                for (var index in ftp_files ) {
                     this.rows.push( this._add( ftp_files[ index ] ) );
                     size += ftp_files[ index ].size;
                 }
@@ -39,7 +39,7 @@ define( [ 'utils/utils' ], function( Utils ) {
                     this.$select_all = this.$( '.upload-selectall' ).addClass( this.options.class_add );
                     this.$select_all.on( 'click', function() {
                         var add = self.$select_all.hasClass( self.options.class_add );
-                        for ( index in ftp_files ) {
+                        for (var index in ftp_files ) {
                             var ftp_file = ftp_files[ index ];
                             var model_index = self._find( ftp_file );
                             if( !model_index && add || model_index && !add ) {
diff --git a/client/galaxy/scripts/mvc/upload/upload-view.js b/client/galaxy/scripts/mvc/upload/upload-view.js
index e6a8a2dc839..38e6b8329d1 100644
--- a/client/galaxy/scripts/mvc/upload/upload-view.js
+++ b/client/galaxy/scripts/mvc/upload/upload-view.js
@@ -48,7 +48,7 @@ function( Utils, Modal, Tabs, UploadButton, UploadViewDefault, UploadViewComposi
             Utils.get({
                 url     : Galaxy.root + 'api/datatypes?extension_only=False',
                 success : function( datatypes ) {
-                    for ( key in datatypes ) {
+                    for (var key in datatypes ) {
                         self.list_extensions.push({
                             id              : datatypes[ key ].extension,
                             text            : datatypes[ key ].extension,
@@ -72,7 +72,7 @@ function( Utils, Modal, Tabs, UploadButton, UploadViewDefault, UploadViewComposi
             Utils.get({
                 url     : Galaxy.root + 'api/genomes',
                 success : function( genomes ) {
-                    for ( key in genomes ) {
+                    for (var key in genomes ) {
                         self.list_genomes.push({
                             id      : genomes[ key ][ 1 ],
                             text    : genomes[ key ][ 0 ]
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index 0eb059caa73..1acc2a910f2 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -110,7 +110,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func
             var self = this;
             var extensions = [];
             var input_terminal_names = [];
-            for ( key in datatypes  ) {
+            for (var key in datatypes  ) {
                 extensions.push( { 0 : datatypes[ key ], 1 : datatypes[ key ] } );
             }
             for ( key in this.node.input_terminals ){
@@ -131,6 +131,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func
                 0 : 'Leave unchanged',
                 1 : '__empty__'
             });
+            var output;
             var input_config = {
                 title   : 'Configure Output: \'' + output_id + '\'',
                 type    : 'section',
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 299c792a200..2b098f14463 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -199,7 +199,7 @@ function( Connector, Toastr ) {
         },
         from_simple : function ( data, initialImport_ ) {
             var initialImport = (initialImport_ === undefined) ? true : initialImport_;
-            wf = this;
+            var wf = this;
             var offset = 0;
             if( initialImport ) {
                 wf.name = data.name;
@@ -264,7 +264,7 @@ function( Connector, Toastr ) {
                     $.each(node.output_terminals, function(ot_id, ot){
                         if(node.post_job_actions['HideDatasetAction'+ot.name] === undefined){
                             node.addWorkflowOutput(ot.name);
-                            callout = $(node.element).find('.callout.'+ot.name);
+                            var callout = $(node.element).find('.callout.'+ot.name);
                             callout.find('img').attr('src', Galaxy.root + 'static/images/fugue/asterisk-small.png');
                             wf.has_changes = true;
                         }
@@ -338,10 +338,10 @@ function( Connector, Toastr ) {
                 });
             });
             // Assemble order, tracking levels
-            node_ids_by_level = [];
+            var node_ids_by_level = [];
             while ( true ) {
                 // Everything without a predecessor
-                level_parents = [];
+                var level_parents = [];
                 for ( var pred_k in n_pred ) {
                     if ( n_pred[ pred_k ] == 0 ) {
                         level_parents.push( pred_k );
@@ -395,7 +395,7 @@ function( Connector, Toastr ) {
                 ymin = Infinity, ymax = -Infinity,
                 p;
             $.each( this.nodes, function( id, node ) {
-                e = $(node.element);
+                var e = $(node.element);
                 p = e.position();
                 xmin = Math.min( xmin, p.left );
                 xmax = Math.max( xmax, p.left + e.width() );
@@ -411,7 +411,7 @@ function( Connector, Toastr ) {
             }
             function fix_delta( x, n ) {
                 if ( x < n|| x > 3*n ) {
-                    new_pos = ( Math.ceil( ( ( x % n ) ) / n ) + 1 ) * n;
+                    var new_pos = ( Math.ceil( ( ( x % n ) ) / n ) + 1 ) * n;
                     return ( - ( x - new_pos ) );
                 }
                 return 0;
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index 159068cacb5..15cebc012f4 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -4,6 +4,9 @@ define(['mvc/workflow/workflow-globals'], function( Globals ) {
         this.isCollection = true;
         this.rank = collectionType.split(":").length;
     }
+
+    var ANY_COLLECTION_TYPE_DESCRIPTION, NULL_COLLECTION_TYPE_DESCRIPTION;
+
     $.extend( CollectionTypeDescription.prototype, {
         append: function( otherCollectionTypeDescription ) {
             if( otherCollectionTypeDescription === NULL_COLLECTION_TYPE_DESCRIPTION ) {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index 568fd357d2f..fa85f7841c5 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js
@@ -64,7 +64,7 @@ define([
             var close_editor = function() {
                 self.workflow.check_changes_in_active_form();
                 if ( workflow && self.workflow.has_changes ) {
-                    do_close = function() {
+                    var do_close = function() {
                         window.onbeforeunload = undefined;
                         window.document.location = self.urls.workflow_index;
                     };
@@ -227,7 +227,7 @@ define([
                      self.scroll_to_nodes();
                      self.canvas_manager.draw_overview();
                      // Determine if any parameters were 'upgraded' and provide message
-                     upgrade_message = "";
+                     var upgrade_message = "";
                      _.each( data.steps, function( step, step_id ) {
                         var details = "";
                         if ( step.errors ) {
@@ -335,7 +335,7 @@ define([
             }
 
             // On load, set the size to the pref stored in local storage if it exists
-            overview_size = $.jStorage.get("overview-size");
+            var overview_size = $.jStorage.get("overview-size");
             if (overview_size !== undefined) {
                 $("#overview-border").css( {
                     width: overview_size,
@@ -468,7 +468,7 @@ define([
                 success: function( data ) {
                     self.workflow.from_simple( data, false );
                     // Determine if any parameters were 'upgraded' and provide message
-                    upgrade_message = "";
+                    var upgrade_message = "";
                     $.each( data.upgrade_messages, function( k, v ) {
                        upgrade_message += ( "<li>Step " + ( parseInt(k, 10) + 1 ) + ": " + self.workflow.nodes[k].name + "<ul>");
                        $.each( v, function( i, vv ) {
@@ -538,18 +538,18 @@ define([
 
         // Add a new step to the workflow by tool id
         add_node_for_tool: function ( id, title ) {
-            node = this.workflow.create_node( 'tool', title, id );
+            var node = this.workflow.create_node( 'tool', title, id );
             this._moduleInitAjax(node, { type: "tool", tool_id: id, "_": "true" });
         },
 
         // Add a new step to the workflow by tool id
         add_node_for_subworkflow: function ( id, title ) {
-            node = this.workflow.create_node( 'subworkflow', title, id );
+            var node = this.workflow.create_node( 'subworkflow', title, id );
             this._moduleInitAjax(node, { type: "subworkflow", content_id: id, "_": "true" });
         },
 
         add_node_for_module: function ( type, title ) {
-            node = this.workflow.create_node( type, title );
+            var node = this.workflow.create_node( type, title );
             this._moduleInitAjax(node, { type: type, "_": "true" });
         },
 
@@ -559,7 +559,7 @@ define([
             var self = this;
             $("#pja_container").append( get_pja_form(pja, node) );
             $("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function (){
-                action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text();
+                var action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text();
                 $(this).closest(".toolForm").remove();
                 delete self.workflow.active_node.post_job_actions[action_to_rem];
                 self.workflow.active_form_has_changes = true;
@@ -571,7 +571,7 @@ define([
         },
 
         display_file_list: function (node){
-            addlist = "<select id='node_data_list' name='node_data_list'>";
+            var addlist = "<select id='node_data_list' name='node_data_list'>";
             for (var out_terminal in node.output_terminals){
                 addlist += "<option value='" + out_terminal + "'>"+ out_terminal +"</option>";
             }
diff --git a/client/galaxy/scripts/reports_webapp/run_stats.js b/client/galaxy/scripts/reports_webapp/run_stats.js
index 7542b63733b..e0138e08d5d 100644
--- a/client/galaxy/scripts/reports_webapp/run_stats.js
+++ b/client/galaxy/scripts/reports_webapp/run_stats.js
@@ -117,7 +117,7 @@ function create_chart( inp_data, name, time, title ) {
         .enter().append("g")
             .attr("transform", function(d, i) {
                 // Place the bar in the correct place
-                curr_margin = +margin.left;
+                var curr_margin = +margin.left;
                 curr_margin += +(i * barWidth);
                 return "translate(" + curr_margin + "," + margin.top + ")";
             })
@@ -503,8 +503,8 @@ function create_histogram( inp_data, name, title ) {
 
     // Formatter for x axis times (converting minutes to HH:MM).
     var formatMinutes = function(d) {
-            hours = Math.floor( d / 60 )
-            minutes = Math.floor(d - (hours * 60))
+            var hours = Math.floor( d / 60 ),
+                minutes = Math.floor(d - (hours * 60))
 
             if(hours < 10) {
                 hours = "0" + hours
@@ -542,8 +542,8 @@ function create_histogram( inp_data, name, title ) {
             return "translate(" + (+x(d.x) + +margin.left) + "," + (+y(d.y) + +margin.top) + ")"; })
         .on("mouseenter", function(d) {
             // Show tool tip
-            i = 0;
-            size = d.length;
+            var i = 0,
+                size = d.length;
 
             while( size >= 1) {
                 size = size / 10;
diff --git a/client/galaxy/scripts/ui/scroll-panel.js b/client/galaxy/scripts/ui/scroll-panel.js
index 3b9aafd0bf1..d8b496a2ebd 100644
--- a/client/galaxy/scripts/ui/scroll-panel.js
+++ b/client/galaxy/scripts/ui/scroll-panel.js
@@ -11,8 +11,8 @@ $.ui.plugin.add("draggable", "scrollPanel", {
             panel = o.panel,
             panel_pos = panel.position(),
             panel_w = panel.width(),
-            panel_h = panel.height()
-            viewport = panel.parent();
+            panel_h = panel.height(),
+            viewport = panel.parent(),
             viewport_w = viewport.width(),
             viewport_h = viewport.height(),
             element_w = element.width(),
diff --git a/client/galaxy/scripts/utils/graph.js b/client/galaxy/scripts/utils/graph.js
index b252354736e..fb1ac392154 100644
--- a/client/galaxy/scripts/utils/graph.js
+++ b/client/galaxy/scripts/utils/graph.js
@@ -387,8 +387,8 @@ Graph.prototype.createEdge = function( sourceName, targetName, directed, data ){
     var isReflexive = sourceName === targetName;
     if( !this.allowReflexiveEdges && isReflexive ){ return null; }
 
-    sourceVertex = this.vertices[ sourceName ];
-    targetVertex = this.vertices[ targetName ];
+    var sourceVertex = this.vertices[ sourceName ];
+    var targetVertex = this.vertices[ targetName ];
     //note: silently ignores edges from/to unknown vertices
     if( !( sourceVertex && targetVertex ) ){ return null; }
 
diff --git a/client/galaxy/scripts/utils/uploadbox.js b/client/galaxy/scripts/utils/uploadbox.js
index b75d855d3c5..1382c3179be 100755
--- a/client/galaxy/scripts/utils/uploadbox.js
+++ b/client/galaxy/scripts/utils/uploadbox.js
@@ -53,7 +53,7 @@
         }
 
         // prepare request
-        xhr = new XMLHttpRequest();
+        var xhr = new XMLHttpRequest();
         xhr.open('POST', cnf.url, true);
         xhr.setRequestHeader('Accept', 'application/json');
         xhr.setRequestHeader('Cache-Control', 'no-cache');
diff --git a/client/galaxy/scripts/viz/circster.js b/client/galaxy/scripts/viz/circster.js
index 7efe2ce6e1d..7f65d65f515 100644
--- a/client/galaxy/scripts/viz/circster.js
+++ b/client/galaxy/scripts/viz/circster.js
@@ -634,7 +634,7 @@ var CircsterTrackView = Backbone.View.extend({
             track.get('config').set_value('max_value', self.data_bounds[1], {silent: true});
 
             // Merge chroms layout with data.
-            layout_and_data = _.zip(chrom_arcs, genome_wide_data),
+            var layout_and_data = _.zip(chrom_arcs, genome_wide_data),
 
             // Render each chromosome's data.
             chroms_data_layout = _.map(layout_and_data, function(chrom_info) {
diff --git a/client/galaxy/scripts/viz/phyloviz.js b/client/galaxy/scripts/viz/phyloviz.js
index c2c6ded626d..6b6dfdd7269 100644
--- a/client/galaxy/scripts/viz/phyloviz.js
+++ b/client/galaxy/scripts/viz/phyloviz.js
@@ -726,7 +726,7 @@ var HeaderButtons = Backbone.View.extend({
     initRightHeaderBtns : function(){
         var self = this;
 
-        rightMenu = mod_icon_btn.create_icon_buttons_menu([
+        var rightMenu = mod_icon_btn.create_icon_buttons_menu([
             { icon_class: 'gear', title: 'PhyloViz Settings', on_click: function(){
                 $("#SettingsMenu").show();
                 self.settingsMenu.updateUI();
diff --git a/client/galaxy/scripts/viz/trackster/painters.js b/client/galaxy/scripts/viz/trackster/painters.js
index 5108d19737d..722fb1f91e3 100644
--- a/client/galaxy/scripts/viz/trackster/painters.js
+++ b/client/galaxy/scripts/viz/trackster/painters.js
@@ -516,7 +516,7 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             thickness, y_start, thick_start = null, thick_end = null,
             // TODO: is there any reason why block, label color cannot be set at the Painter level?
             // For now, assume '.' === '+'
-            block_color = (!feature_strand || feature_strand === "+" || feature_strand === "." ? this.prefs.block_color : this.prefs.reverse_strand_color);
+            block_color = (!feature_strand || feature_strand === "+" || feature_strand === "." ? this.prefs.block_color : this.prefs.reverse_strand_color),
             label_color = this.prefs.label_color;
 
         // Set global alpha.
@@ -1223,7 +1223,7 @@ Color.prototype = {
     },
 
     mix: function (color2, weight) {
-        color1 = this;
+        var color1 = this;
 
         var p = weight; // .value / 100.0;
         var w = p * 2 - 1;
@@ -1543,8 +1543,8 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
                     // Draw allele fractions onto summary.
                     for (j = 0; j < alt.length; j++) {
                         ctx.fillStyle = ( alt[j].type === 'deletion' ? 'black' : this.base_color_fn(alt[j].value) );
-                        allele_frac = allele_counts / sample_gts.length;
-                        draw_height = Math.ceil(this.prefs.summary_height * allele_frac);
+                        var allele_frac = allele_counts / sample_gts.length;
+                        var draw_height = Math.ceil(this.prefs.summary_height * allele_frac);
                         ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height);
                         draw_y_start -= draw_height;
                     }
diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js
index 5e0b520ce7a..a797c2afb24 100644
--- a/client/galaxy/scripts/viz/trackster/tracks.js
+++ b/client/galaxy/scripts/viz/trackster/tracks.js
@@ -791,7 +791,7 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
             // For all tracks, save current filter manager and set manager to shared (this object's) manager.
             this.saved_filters_managers = [];
             for (var i = 0; i < this.drawables.length; i++) {
-                drawable = this.drawables[i];
+                var drawable = this.drawables[i];
                 this.saved_filters_managers.push(drawable.filters_manager);
                 drawable.filters_manager = this.filters_manager;
             }
@@ -1699,7 +1699,7 @@ var TracksterToolView = Backbone.View.extend({
      * Render tool UI.
      */
     render: function() {
-        var self = this;
+        var self = this,
             tool = this.model,
             parent_div = this.$el.addClass("dynamic-tool").hide();
 
@@ -3959,6 +3959,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Returns appropriate display mode based on data.
      */
     get_mode: function(data) {
+        var mode;
         // HACK: use no_detail mode track is in overview to prevent overview from being too large.
         if (data.extra_info === "no_detail" || this.is_overview) {
             mode = "no_detail";
@@ -4030,7 +4031,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         // Preprocessing: filter features and determine whether all unfiltered features have been slotted.
         var
             filtered = [],
-            slots = this.slotters[w_scale].slots;
+            slots = this.slotters[w_scale].slots,
             all_slotted = true;
         if ( result.data ) {
             var filters = this.filters_manager.filters;
diff --git a/client/toolshed/scripts/mvc/groups/group-list-view.js b/client/toolshed/scripts/mvc/groups/group-list-view.js
index 75fffd3488a..973e6d76721 100644
--- a/client/toolshed/scripts/mvc/groups/group-list-view.js
+++ b/client/toolshed/scripts/mvc/groups/group-list-view.js
@@ -114,7 +114,7 @@ var GroupListView = Backbone.View.extend({
 // MMMMMMMMMMMMMMMMMM
 
     templateGroupsList: function(){
-        tmpl_array = [];
+        var tmpl_array = [];
 
         tmpl_array.push('<div id="groups">');
         tmpl_array.push('</div>');
diff --git a/config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js b/config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
index 77b3868abf9..68e51f6e036 100644
--- a/config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
+++ b/config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
@@ -30,7 +30,7 @@ function b64tohex(s) {
   var slop;
   for(i = 0; i < s.length; ++i) {
     if(s.charAt(i) == b64pad) break;
-    v = b64map.indexOf(s.charAt(i));
+    var v = b64map.indexOf(s.charAt(i));
     if(v < 0) continue;
     if(k == 0) {
       ret += int2char(v >> 2);
diff --git a/config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js b/config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
index 2389ea47282..db13dbbeec8 100644
--- a/config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
+++ b/config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
@@ -819,7 +819,7 @@ function b64tohex(s) {
   var slop;
   for(i = 0; i < s.length; ++i) {
     if(s.charAt(i) == b64pad) break;
-    v = b64map.indexOf(s.charAt(i));
+    var v = b64map.indexOf(s.charAt(i));
     if(v < 0) continue;
     if(k == 0) {
       ret += int2char(v >> 2);
diff --git a/config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js b/config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
index 77b3868abf9..68e51f6e036 100644
--- a/config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
+++ b/config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
@@ -30,7 +30,7 @@ function b64tohex(s) {
   var slop;
   for(i = 0; i < s.length; ++i) {
     if(s.charAt(i) == b64pad) break;
-    v = b64map.indexOf(s.charAt(i));
+    var v = b64map.indexOf(s.charAt(i));
     if(v < 0) continue;
     if(k == 0) {
       ret += int2char(v >> 2);
diff --git a/config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js b/config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
index ad53bb8ed06..1421d8772a4 100644
--- a/config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
+++ b/config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
@@ -29,7 +29,7 @@ function b64tohex(s) {
   var slop;
   for(i = 0; i < s.length; ++i) {
     if(s.charAt(i) == b64padchar) break;
-    v = b64map.indexOf(s.charAt(i));
+    var v = b64map.indexOf(s.charAt(i));
     if(v < 0) continue;
     if(k == 0) {
       ret += int2char(v >> 2);
diff --git a/config/plugins/visualizations/charts/static/client/components/screenshot.js b/config/plugins/visualizations/charts/static/client/components/screenshot.js
index dc4414c99e8..64f12f27e8c 100644
--- a/config/plugins/visualizations/charts/static/client/components/screenshot.js
+++ b/config/plugins/visualizations/charts/static/client/components/screenshot.js
@@ -37,7 +37,7 @@ define( [ 'libs/underscore' ], function( _ ) {
                     }
                 }
                 $canvas.children().each( function() { _toImage( $( this ), 0, 0 ) } );
-                imgData = newCanvas.toDataURL( 'image/png' );
+                var imgData = newCanvas.toDataURL( 'image/png' );
                 if ( imgData ) {
                     window.location.href = imgData.replace( 'image/png', 'image/octet-stream' );
                 }
@@ -97,7 +97,7 @@ define( [ 'libs/underscore' ], function( _ ) {
             $el.append( form );
         }
         form.empty();
-        for ( name in data ) {
+        for (var name in data ) {
             var input = $( '<input/>', {
                 type    : 'hidden',
                 name    : name,
diff --git a/config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js b/config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
index 2334d871911..33568d52f02 100644
--- a/config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
+++ b/config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
@@ -120,8 +120,8 @@ var Optspanel = Backbone.View.extend({
         .lasso()
         .on("lassoBegin", function(e, lassoPoints) {
             polygon = [];
-            canvas = self.vis.el.childNodes[1];
-            c2 = canvas.getContext('2d');
+            var canvas = self.vis.el.childNodes[1];
+            var c2 = canvas.getContext('2d');
             c2.fillStyle = "rgba(100, 100, 100, 0.02)";
             c2.beginPath();
 
diff --git a/config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js b/config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
index 779477afcae..e2c954b22d9 100644
--- a/config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
+++ b/config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
@@ -89,7 +89,7 @@ var Vispanel = Backbone.View.extend({
     setResidueNodes: function(cy){
         //index nodes
         for(var i=1; i<this.struct.get("seq").length/5; i++){
-            pos = this.getPos(this.struct, (i*5)-1);
+            var pos = this.getPos(this.struct, (i*5)-1);
             this.cy.add({
                 group: "nodes",
                 data: {
diff --git a/config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js b/config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
index cb11d9cd651..ff570f5a5a3 100644
--- a/config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
+++ b/config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
@@ -1,7 +1,7 @@
 define( [], function() {
     var axisLabel = function( name, options ) {
         options = options || {};
-        prefix  = name.substr( 0, 1 );
+        var prefix  = name.substr( 0, 1 );
         return {
             name        : name,
             label       : prefix.toUpperCase() + '-Axis label',
@@ -13,7 +13,7 @@ define( [], function() {
     }
     var axisType = function( name, options ) {
         options = options || {};
-        prefix  = name.substr( 0, 1 );
+        var prefix  = name.substr( 0, 1 );
         var axisPrecision = function() {
             return { name    : 'precision',
                      label   : 'Axis tick format',
diff --git a/config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js b/config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
index e097330e725..69fdd8c43bd 100644
--- a/config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
+++ b/config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
@@ -4,7 +4,7 @@ define( [ 'utilities/utils', 'visualizations/utilities/tabular-datasets' ], func
         var settings_string = '';
         var columns_string = '';
         var group_index = 0;
-        for ( key in chart.settings.attributes ) {
+        for (var key in chart.settings.attributes ) {
             var settings_value = chart.settings.get( key );
             _.each( [ [ ' ', '&#32;' ], [ ',', '&#44;' ], [ ':', '&#58;' ] ], function( pair ) {
                 settings_value = settings_value.replace( new RegExp( pair[ 0 ], 'g' ), pair[ 1 ] );
diff --git a/config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js b/config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
index 1108c67e7af..095a0b41971 100644
--- a/config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
+++ b/config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
@@ -1,8 +1,9 @@
 $(function() { // on dom ready
-
+	var showIn, showOut;
 
 	///// show/hide Labels
 	$('#nodeLabelCheck').change(function() {
+		var showNodeLabel;
 		if ($(this).is(":checked")) {
 
 			showNodeLabel = 'data(id)'; //.replace(/[^0-9\.]+/g, "")';  // change to label or name if needed
@@ -19,6 +20,7 @@ $(function() { // on dom ready
 	});
 
 	$('#linkLabelCheck').change(function() {
+		var showEdgeLabel;
 		if ($(this).is(":checked")) {
 			showEdgeLabel = "data(id)"; // change to label or name if needed
 		} else {
@@ -67,7 +69,6 @@ $(function() { // on dom ready
 	////////  highlighting incoming nodes
 
 	$('#showInNode').change(function() {
-
 		if ($('#showInNode').is(":checked")) {
 			showIn = true;
 			cy.nodes().on("tapend", highlightIn);
@@ -532,7 +533,7 @@ function expandNodes(selectedNode) {
 
 	var eles = allcy.nodes();
 
-	nodesToAdd = eles[selectedNodeId].outgoers();
+	var nodesToAdd = eles[selectedNodeId].outgoers();
 
 	showNodesToExpand(nodesToAdd);
 	cy.add(eles[selectedNodeId].outgoers());
@@ -570,7 +571,7 @@ function showNodesToExpand(toAdd) {
 // checkBox options
 
 function checkBoxes() {
-
+	var showIn;
 
 	if ($('#showInNode').is(":checked")) {
 		showIn = true;
diff --git a/config/plugins/webhooks/demo/search/static/script.js b/config/plugins/webhooks/demo/search/static/script.js
index 6a54efb0c51..8b1a5b5e0b4 100644
--- a/config/plugins/webhooks/demo/search/static/script.js
+++ b/config/plugins/webhooks/demo/search/static/script.js
@@ -673,7 +673,7 @@ $(document).ready(function() {
             $el_removed_result.html( "" );
             // Build the removed result from web storage
             removed_results_html = self.getStorageObject( self, window.Galaxy.user.id, 'removed_results' );
-            for( item in removed_results_html ) {
+            for(var item in removed_results_html ) {
                 html_text = html_text + removed_results_html[ item ];
             }
             // Build html if there is an item
diff --git a/lib/galaxy/web/proxy/js/lib/proxy.js b/lib/galaxy/web/proxy/js/lib/proxy.js
index 95ebd8ed9cc..1857e2632e1 100644
--- a/lib/galaxy/web/proxy/js/lib/proxy.js
+++ b/lib/galaxy/web/proxy/js/lib/proxy.js
@@ -70,7 +70,7 @@ DynamicProxy.prototype.targetForRequest = function(request) {
 };
 
 DynamicProxy.prototype.findSession = function(request) {
-    var sessionCookie = this.sessionCookie;
+    var sessionCookie = this.sessionCookie,
         rc = request.headers.cookie;
     if(!rc) {
         return null;
diff --git a/scripts/communication/template/communication.js b/scripts/communication/template/communication.js
index 4f23f7381f2..702157da801 100644
--- a/scripts/communication/template/communication.js
+++ b/scripts/communication/template/communication.js
@@ -70,7 +70,7 @@ var events_module = {
             }
             else { // normal message sharing when connected
                 var room = utils.check_room_by_roomname( click_events.connected_room, msg.chatroom );
-                $el_room_msg = $( '#all_messages_' + room.id );
+                var $el_room_msg = $( '#all_messages_' + room.id );
                 utils.append_message( $el_room_msg, utils.build_message( msg ) );
                 utils.vertical_center_align_gravatar( $( '#all_messages_' + room.id + ' .message' ) );
                 utils.fancyscroll_to_last( $( "#galaxy_tabroom_" + room.id ) );
@@ -192,8 +192,8 @@ var click_events = {
     },
     // makes disconnect and raises disconnect event at the server
     make_disconnect: function ( uid, $el_input_text, $el_online_status ) {
-        var send_data = {}
-        disconnected_message = 'You are now disconnected. To send/receive messages, please connect';
+        var send_data = {};
+        var disconnected_message = 'You are now disconnected. To send/receive messages, please connect';
         click_events.is_connected = false;
         socket.emit( 'event disconnect', send_data );
         sessionStorage.removeItem( uid );