Merge c9e4714 into 4fc0649

apollo

@@ -7,13 +7,13 @@ function usage(){
     echo "Production Commands:";
     echo "";
     echo "deploy:           Builds war file (no processing of javascript) into the target directory.";
-    echo "install-tools:    Installs JBrowse tools in the ./bin directory if not preset."
+    echo "jbrowse-tools:    Installs JBrowse tools in the ./bin directory if not preset."
     echo "run-local <port>: Runs from current directory, but not in dev-mode. ";
     echo "help:             This message.";
     echo "";
     echo "Development Commands:";
     echo "devmode:          Runs from current directory debug mode (non-minimized javascript).";
-    echo "jbrowse:          Installs updated client/apollo files and JBrowse.";
+    echo "jbrowse:          Installs updated client/apollo files and JBrowse for the web.";
     echo "run-app   <port>: Runs from current directory, but does not compile annotator panel (you have to run run-local once first).";
     echo "test:             Runs test-suite.";
     echo "debug:            Runs from cuurent directory in debug mode (non-minimized javascript).";
@@ -207,10 +207,11 @@ if [[ $1 == "devmode" ]];then
     check_configs
     $gradle_executable installJBrowseWebOnly devmode &
     $grails_executable -reloading run-app
-elif [[ $1 == "install-tools" ]];then
+elif [[ $1 == "jbrowse-tools" ]];then
     check_configs
-    check_perldependencies
-    $gradle_executable installJBrowseLocal
+	$gradle_executable installJBrowseWebOnly
+	rm -rf bin
+	ln -s jbrowse/bin bin
 elif [[ $1 == "run-local" ]];then
     check_configs
     if [[ $# == 2 ]]; then

build.gradle

@@ -128,13 +128,6 @@ task cloneRepo3(dependsOn: evaluateJBrowseConfigs) {
     }
 }
 
-task installJBrowseLocal(type: Exec) {
-    doLast{
-        workingDir = '.'
-        commandLine './install_jbrowse.sh'
-    }
-}
-
 //task copyResourcesDev(dependsOn: installJBrowse) {
 task copyResourcesDev() {
     doLast {

client/apollo/js/TrackConfigTransformer.js

@@ -13,12 +13,19 @@ constructor: function( args )  {
     this.transformers=[];
     var browser=args.browser;
     this.overridePlugins=browser.config.overridePlugins;
+    this.transformers["NeatHTMLFeatures/View/Track/NeatFeatures"] = function(trackConfig) {
+        trackConfig.type = "WebApollo/View/Track/DraggableNeatHTMLFeatures";
+    };
+    // have to set this explicitly if you want undecorated features
+    // trackConfig.type = "WebApollo/View/Track/DraggableHTMLFeatures";
+    // and configure the jbrowse plugin off
     this.transformers["JBrowse/View/Track/HTMLFeatures"] = function(trackConfig) {
-        trackConfig.type = "WebApollo/View/Track/DraggableHTMLFeatures";
+        trackConfig.type = "WebApollo/View/Track/DraggableNeatHTMLFeatures";
     };
 
+    // trackConfig.type = "WebApollo/View/Track/WebApolloCanvasFeatures";
     this.transformers["JBrowse/View/Track/CanvasFeatures"] = function(trackConfig) {
-        trackConfig.type = "WebApollo/View/Track/WebApolloCanvasFeatures";
+        trackConfig.type = "WebApollo/View/Track/WebApolloNeatCanvasFeatures";
     };
 
     this.transformers["JBrowse/View/Track/HTMLVariants"] = function(trackConfig) {

client/apollo/js/View/Track/AnnotTrack.js

@@ -25,7 +25,7 @@ define([
         'dojox/grid/DataGrid',
         'dojox/grid/cells/dijit',
         'dojo/data/ItemFileWriteStore',
-        'WebApollo/View/Track/DraggableHTMLFeatures',
+        'WebApollo/View/Track/DraggableNeatHTMLFeatures',
         'WebApollo/FeatureSelectionManager',
         'WebApollo/JSONUtils',
         'WebApollo/BioFeatureUtils',

client/apollo/js/View/Track/DraggableNeatHTMLFeatures.js

@@ -0,0 +1,22 @@
+
+define( [
+            'dojo/_base/declare',
+            'dojo/_base/array',
+            'NeatHTMLFeatures/View/Track/NeatFeatures',
+            'WebApollo/View/Track/DraggableHTMLFeatures'
+        ],
+    function( declare,
+        array,
+        NeatFeatureTrack,
+        HTMLFeatureTrack
+        ) {
+
+
+var draggableTrack = declare( [NeatFeatureTrack,HTMLFeatureTrack],{
+    constructor: function(args)  {  }
+
+});
+
+    return draggableTrack;
+});
+

client/apollo/js/View/Track/WebApolloNeatCanvasFeatures.js

@@ -0,0 +1,24 @@
+define( [
+            'dojo/_base/declare',
+            'dojo/_base/array',
+            'NeatCanvasFeatures/View/Track/NeatFeatures',
+            'WebApollo/View/Track/WebApolloCanvasFeatures'
+        ],
+        function( declare,
+            array,
+            NeatFeatureTrack,
+            CanvasFeaturesTrack
+        )
+{
+
+return declare( [NeatFeatureTrack,CanvasFeaturesTrack], {
+    constructor: function() {
+        this.browser.getPlugin( 'WebApollo', dojo.hitch( this, function(p) {
+            this.webapollo = p;
+        }));
+    }
+});
+
+
+});
+

grails-app/conf/Config.groovy

@@ -418,13 +418,13 @@ jbrowse {
         WebApollo {
             included = true
         }
-//        NeatHTMLFeatures{
-//            included = true
-//            linearGradient = 0
-//        }
-//        NeatCanvasFeatures{
-//            included = true
-//        }
+        NeatHTMLFeatures{
+            included = true
+            linearGradient = 0
+        }
+        NeatCanvasFeatures{
+            included = true
+        }
         RegexSequenceSearch {
             included = true
         }

grails-app/controllers/org/bbop/apollo/JbrowseController.groovy

@@ -460,6 +460,9 @@ class JbrowseController {
             // add core plugin: https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Browser.js#L244
 //            pluginKeys.add("RegexSequenceSearch")
             pluginKeys.add("WebApollo")
+            // see https://github.com/GMOD/jbrowse/issues/897
+            // https://github.com/GMOD/Apollo/issues/2014
+            jsonObject.plugins.add("stub")
             for (plugin in plugins) {
                 if (!pluginKeys.contains(plugin.key)) {
                     pluginKeys.add(plugin.key)