[galaxy-commits] commit/galaxy-central: 3 new changesets

30 Nov 2013

3 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/842d13d7925c/
Changeset:   842d13d7925c
User:        jgoecks
Date:        2013-11-29 17:41:26
Summary:     Trackster: move static CSS settings out of JavaScript and into CSS file.
Affected #:  3 files

diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/scripts/viz/trackster/tracks.js

--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -32,8 +32,7 @@
 var moveable = function(element, handle_class, container_selector, element_js_obj) {
     // HACK: set default value for container selector.
     container_selector = ".group";
-    var css_border_props = {};
-
+    
     // Register element with its object.
     html_elt_js_obj_dict[element.attr("id")] = element_js_obj;
     
@@ -130,14 +129,9 @@
             html_elt_js_obj_dict[parent.attr("id")].move_drawable(this_obj, (d.deltaY > 0 ? i-1 : i) );
         }
     }).bind("dragstart", function() {
-        css_border_props["border-top"] = element.css("border-top");
-        css_border_props["border-bottom"] = element.css("border-bottom");
-        $(this).css({
-            "border-top": "1px solid blue",
-            "border-bottom": "1px solid blue"
-        });
+        $(this).addClass('dragging');
     }).bind("dragend", function() {
-        $(this).css(css_border_props);
+        $(this).removeClass('dragging');
     });
 };
 
@@ -236,7 +230,7 @@
         this.container_div.append(this.header_div);
         
         // Icons container.
-        this.icons_div = $("<div/>").css("float", "left").hide().appendTo(this.header_div);
+        this.icons_div = $("<div/>").addClass('track-icons').hide().appendTo(this.header_div);
         this.build_action_icons(this.action_icons_def);
                 
         this.header_div.append( $("<div style='clear: both'/>") );
@@ -930,7 +924,7 @@
         // Top container for things that are fixed at the top
         this.top_container = $("<div/>").addClass("top-container").appendTo(parent_element);
         // Browser content, primary tracks are contained in here
-        this.browser_content_div = $("<div/>").addClass("content").css("position", "relative").appendTo(parent_element);
+        this.browser_content_div = $("<div/>").addClass("content").appendTo(parent_element);
         // Bottom container for things that are fixed at the bottom
         this.bottom_container = $("<div/>").addClass("bottom-container").appendTo(parent_element);
         // Label track fixed at top 
@@ -967,7 +961,7 @@
         this.default_overview_height = this.overview_box.height();
         
         this.nav_controls = $("<div/>").addClass("nav-controls").appendTo(this.nav);
-        this.chrom_select = $("<select/>").attr({ "name": "chrom"}).css("width", "15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);
+        this.chrom_select = $("<select/>").attr({ "name": "chrom"}).addClass('chrom-nav').append("<option value=''>Loading</option>").appendTo(this.nav_controls);
         var submit_nav = function(e) {
             if (e.type === "focusout" || (e.keyCode || e.which) === 13 || (e.keyCode || e.which) === 27 ) {
                 if ((e.keyCode || e.which) !== 27) { // Not escape key
@@ -1708,7 +1702,7 @@
         // Add buttons for running on dataset, region.
         var run_tool_row = $("<div>").addClass("param-row").appendTo(parent_div);
         var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_tool_row);
-        var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row);
+        var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").appendTo(run_tool_row);
         run_on_region_button.click( function() {
             // Run tool to create new track.
             self.run_on_region();
@@ -2027,7 +2021,10 @@
                 else if ( param.type === 'color' ) {
                     var 
                         container_div = $("<div/>").appendTo(row),
-                        input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left")                  
+                        input = $('<input/>').attr({
+                            id: id,
+                            name: id
+                        }).val( value ).addClass('color-input') 
                             .appendTo(container_div).click(function(e) {
                             // Hide other pickers.
                             $(".tooltip").removeClass( "in" );
@@ -2517,7 +2514,7 @@
     },
 
     build_container_div: function () {
-        return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative");
+        return $("<div/>").addClass('track').attr("id", "track_" + this.id);
     },
 
     build_header_div: function() {
@@ -3532,7 +3529,6 @@
         while ( position < view.high ) {
             var screenPosition = ( position - view.low ) / range * width;
             new_div.append( $("<div/>").addClass('label').text(commatize( position )).css( {
-                // Reduce by one to account for border
                 left: screenPosition
             }));
             position += tickDistance;

diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/style/blue/trackster.css
--- a/static/style/blue/trackster.css
+++ b/static/style/blue/trackster.css
@@ -1,14 +1,14 @@
 .viewport-container{overflow-x:hidden;overflow-y:auto;background:white}
 .trackster-nav-container{width:100%;height:0;text-align:center}
 .trackster-nav{padding:0 0;color:#333;font-weight:bold;background:#cccccc;position:relative;display:inline-block;top:-2em;background:transparent;border:none}
-.content{font:10px verdana}
+.chrom-nav{width:15em}
+.content{font:10px verdana;position:relative}
 .nav-controls{text-align:center;padding:1px 0}.nav-controls input{margin:0 5px}
 #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer}
 #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat}
 #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat}
 .nav-input{font-size:12px;width:30em;z-index:2}
 .location{display:inline-block;width:15em;margin:0 10px}
-.draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px}
 .intro{z-index:2;margin-left:auto;margin-right:auto;color:#555;text-align:center;font-size:16px}.intro .action-button{background-color:#CCC;margin-top:10px;padding:1em;text-decoration:underline}
 .overview{width:100%;margin:0px;color:white}
 .overview-viewport{position:relative;height:14px;background:white;margin:0}
@@ -28,7 +28,7 @@
 .overlay{position:absolute;left:0;top:0}
 .track-tile{position:absolute;background:white}.track-tile canvas{position:relative;z-index:1}
 .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white}
-.track{border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none}
+.track{position:relative;border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none}
 .track.nodata .track-content{background-color:white;background-image:none}
 .track.pending .track-content{background-color:white;background-image:none}
 .track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px}
@@ -40,7 +40,8 @@
 .right-float{float:right;margin-left:5px}
 .top-labeltrack{position:relative;border-bottom:solid #999 1px}
 .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px}
-input{font:10px verdana}input[type="submit"]{padding:0px;font-size:inherit}
+input{font:10px verdana}input[type="submit"]{padding:0px;margin-right:20px;font-size:inherit}
+input.color-input{float:left}
 .dynamic-tool,.filters{padding-top:18px;padding-bottom:0.5em;margin-left:0.25em}
 .dynamic-tool{width:410px}
 .filters{float:left;margin:1em;width:60%;position:relative}
@@ -53,6 +54,7 @@
 .param-label{float:left;font-weight:bold;padding-top:0.2em;width:50%}
 .menu-button{margin:0px 4px 0px 4px}
 .exclamation{background:transparent url(../images/fugue/exclamation.png) no-repeat;margin-left:5em}
+.track-icons{float:left}
 .icon-button.bookmarks{background:transparent url('../images/fugue/bookmarks-bw.png') no-repeat}.icon-button.bookmarks:hover{background:transparent url('../images/fugue/bookmarks.png') no-repeat}
 .icon-button.layers-stack{background:transparent url('../images/fugue/layers-stack-bw.png') no-repeat}.icon-button.layers-stack:hover{background:transparent url('../images/fugue/layers-stack.png') no-repeat}
 .icon-button.hammer{background:transparent url('../images/fugue/hammer-bw.png') no-repeat}.icon-button.hammer:hover{background:transparent url('../images/fugue/hammer.png') no-repeat}
@@ -77,3 +79,5 @@
 .feature-popup{position:absolute;z-index:2;padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);background-position:top center}
 .feature-popup-inner{padding:5px 8px 4px 8px;background-color:black;color:white}
 .zoom-area{position:absolute;top:0px;background-color:#ccf;opacity:0.5;z-index:2}
+.draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px}
+.dragging{border:1px solid blue}

diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/style/src/less/trackster.less
--- a/static/style/src/less/trackster.less
+++ b/static/style/src/less/trackster.less
@@ -31,8 +31,13 @@
     border: none;
 }
 
+.chrom-nav {
+    width: 15em;
+}
+
 .content {
     font: 10px verdana;
+    position: relative;
 }
 
 .nav-controls {
@@ -72,15 +77,6 @@
     margin: 0 10px;
 }
 
-.draghandle {
-    margin-top: 2px;
-    cursor: move;
-    float: left;
-    background: transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;
-    width: 10px;
-    height: 12px;
-}
-
 .intro {
     z-index: @overlay-index;
 /*    margin-top: 200px;*/
@@ -244,6 +240,8 @@
 }
 
 .track {
+    position: relative;
+
     // Separates tracks.
     border-bottom: 1px solid @separator-color;
 
@@ -340,8 +338,13 @@
     // Override Galaxy defaults to make a smaller button.
     &[type="submit"] {
         padding: 0px;
+        margin-right: 20px;
         font-size: inherit;
     }
+
+    &.color-input {
+        float: left;
+    }
 }
 
 .dynamic-tool, .filters {
@@ -415,6 +418,10 @@
     margin-left: 5em;
 }
 
+.track-icons {
+    float: left
+}
+
 // Defines icons that change from black/white to normal on hover. Note that the images
 // are required to exist in the location specified.
 // TODO: make images into spritemap.
@@ -523,4 +530,19 @@
     background-color: #ccf;
     opacity: 0.5;
     z-index: @overlay-index; 
+}
+
+.draghandle {
+    margin-top: 2px;
+    cursor: move;
+    float: left;
+    background: transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;
+    width: 10px;
+    height: 12px;
+}
+
+// Highlight for element(s) being dragged. This definition must be after definition of draggable 
+// elements (e.g. track, group) in order to take precedence.
+.dragging {
+    border: 1px solid blue;
 }
\ No newline at end of file


https://bitbucket.org/galaxy/galaxy-central/commits/c2d705f7b50a/
Changeset:   c2d705f7b50a
User:        jgoecks
Date:        2013-11-30 23:00:01
Summary:     Trackster: (a) use colors to denote track state and (b) add and use function to show messages.
Affected #:  3 files

diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -2667,23 +2667,35 @@
     },
 
     /**
+     * Remove visualization content and display message.
+     */
+    show_message: function(msg_html) {
+        this.tiles_div.remove();
+        return $('<span/>').addClass('message').html(msg_html).appendTo(this.content_div);
+    },
+
+    /**
      * Initialize and draw the track.
      */
     init: function(retry) {
+        // FIXME: track should have a 'state' attribute that is checked on load; this state attribute should be
+        // used in this function to determine what action(s) to take.
+
         var track = this;
         track.enabled = false;
         track.tile_cache.clear();    
         track.data_manager.clear();
-        track.tiles_div.css("height", "auto");
         /*
         if (!track.content_div.text()) {
             track.content_div.text(DATA_LOADING);
         }
         */
         // Remove old track content (e.g. tiles, messages).
-        track.tiles_div.text('').children().remove();
+        track.content_div.children().remove();
         track.container_div.removeClass("nodata error pending");
-        
+
+        track.tiles_div = $("<div/>").addClass("tiles").appendTo(track.content_div);
+
         //
         // Tracks with no dataset id are handled differently.
         // FIXME: is this really necessary?
@@ -2705,16 +2717,16 @@
             if (!result || result === "error" || result.kind === "error") {
                 // Dataset is in error state.
                 track.container_div.addClass("error");
-                track.content_div.text(DATA_ERROR);
+                var msg_elt = track.show_message(DATA_ERROR);
                 if (result.message) {
                     // Add links to (a) show error and (b) try again.
-                    track.content_div.append(
+                    msg_elt.append(
                         $("<a href='javascript:void(0);'></a>").text("View error").click(function() {
                             Galaxy.modal.show({title: "Trackster Error", body: "<pre>" + result.message + "</pre>", buttons : {'Close' : function() { Galaxy.modal.hide(); } } });
                         })
                     );
-                    track.content_div.append( $('<span/>').text(' ') );
-                    track.content_div.append(
+                    msg_elt.append( $('<span/>').text(' ') );
+                    msg_elt.append(
                         $("<a href='javascript:void(0);'></a>").text("Try again").click(function() {
                             track.init(true);
                         })
@@ -2723,15 +2735,15 @@
             } 
             else if (result === "no converter") {
                 track.container_div.addClass("error");
-                track.tiles_div.text(DATA_NOCONVERTER);
+                track.show_message(DATA_NOCONVERTER);
             } 
             else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) {
                 track.container_div.addClass("nodata");
-                track.tiles_div.text(DATA_NONE);
+                track.show_message(DATA_NONE);
             } 
             else if (result === "pending") {
                 track.container_div.addClass("pending");
-                track.tiles_div.html(DATA_PENDING);
+                track.show_message(DATA_PENDING);
                 //$("<img/>").attr("src", image_path + "/yui/rel_interstitial_loading.gif").appendTo(track.tiles_div);
                 setTimeout(function() { track.init(); }, track.data_query_wait);
             } 

diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/style/blue/trackster.css
--- a/static/style/blue/trackster.css
+++ b/static/style/blue/trackster.css
@@ -20,7 +20,7 @@
 .yaxislabel{z-index:2;position:absolute;right:20px}
 .yaxislabel.bottom{bottom:2px}
 .group-handle{cursor:move;float:left;background:#eee url('../images/tracks/block.png');width:12px;height:12px}
-.group{min-height:20px;border-top:1px solid #bbb;border-bottom:1px solid #bbb}.group>.track-header{position:relative;float:left}
+.group{min-height:20px;border-top:1px solid #888;border-bottom:1px solid #888}.group>.track-header{position:relative;float:left}
 .track-header{height:16px;position:absolute;z-index:2;background-color:rgba(1,1,1,0.1);border-radius:5px;padding:0px 2px;text-align:left;margin:2px;}.track-header:hover{background-color:#DDDDDD}
 .track-header .menubutton{margin-left:0px}
 .track-name{float:left;margin-top:2px}
@@ -28,10 +28,10 @@
 .overlay{position:absolute;left:0;top:0}
 .track-tile{position:absolute;background:white}.track-tile canvas{position:relative;z-index:1}
 .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white}
-.track{position:relative;border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none}
-.track.nodata .track-content{background-color:white;background-image:none}
-.track.pending .track-content{background-color:white;background-image:none}
-.track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px}
+.track{position:relative;border-bottom:1px solid #888}.track.error{background:#ECB4AF}
+.track.nodata{background:#EEEEEE}
+.track.pending{background:#FFFFCC}
+.track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px}.track-content .message{position:relative;top:4px}
 .loading{min-height:100px}
 .label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden}.label-track .label-container{position:relative;height:1.3em}
 .label-track .label{position:absolute;border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block}

diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/style/src/less/trackster.less
--- a/static/style/src/less/trackster.less
+++ b/static/style/src/less/trackster.less
@@ -3,7 +3,7 @@
 @overlay-index: @base-index + 1;
 @track-header-height: 16px;
 @min-track-height: (@track-header-height + 4);
-@separator-color: #BBB;
+@separator-color: #888;
 
 .viewport-container {
     overflow-x: hidden;
@@ -246,22 +246,15 @@
     border-bottom: 1px solid @separator-color;
 
     &.error {
-        background-color: #ECB4AF;
-        background-image: none;
+        background: #ECB4AF;
     }
 
     &.nodata {
-        .track-content {
-            background-color: white;
-            background-image: none;
-        }
+        background: #EEEEEE;
     }
 
     &.pending {
-        .track-content {
-            background-color: white;
-            background-image: none;
-        }
+        background: #FFFFCC;
     }
 }
 
@@ -270,6 +263,12 @@
     position: relative;
     min-height: @min-track-height;
     padding: 0px 0px 1px 0px;
+
+    .message {
+        position: relative;
+        // To vertically center message in track:
+        top: 4px;
+    }
 }
 
 .loading {


https://bitbucket.org/galaxy/galaxy-central/commits/9a5a8d18cd16/
Changeset:   9a5a8d18cd16
User:        jgoecks
Date:        2013-11-30 23:00:44
Summary:     Automated merge of local changesets with default branch.
Affected #:  14 files

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3471,6 +3471,29 @@
     def can_reinstall_or_activate( self ):
         return self.deleted
 
+    @property
+    def installing( self ):
+        """
+        Used to determine if tool dependencies can denote this repository as
+        installing.
+        """
+        return self.status not in [ self.installation_status.DEACTIVATED,
+                                    self.installation_status.UNINSTALLED,
+                                    self.installation_status.ERROR,
+                                    self.installation_status.INSTALLED,
+                                    self.installation_status.NEW,
+                                  ]
+
+    @property
+    def installation_complete( self ):
+        """
+        Used to determine if tool dependency installations can proceed.
+        Installed artifacts must be available on disk.
+        """
+        return self.status in [ self.installation_status.DEACTIVATED,
+                                self.installation_status.INSTALLED,
+                              ]
+
     def to_dict( self, view='collection', value_mapper=None ):
         if value_mapper is None:
             value_mapper = {}

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/webapps/galaxy/api/provenance.py
--- a/lib/galaxy/webapps/galaxy/api/provenance.py
+++ b/lib/galaxy/webapps/galaxy/api/provenance.py
@@ -58,6 +58,8 @@
         for p in job.parameters:
             out[p.name] = p.value
         for in_d in job.input_datasets:
+            if not in_d.dataset:
+                continue
             if follow:
                 out[in_d.name] = self._get_record(trans, in_d.dataset, follow)
             else:

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/webapps/tool_shed/api/repository_revisions.py
--- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
+++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
@@ -107,10 +107,9 @@
         skip_tool_test = kwd.get( 'skip_tool_test', None )
         if skip_tool_test is not None:
             skip_tool_test = util.string_as_bool( skip_tool_test )
+        if skip_tool_test:
             skipped_metadata_ids_subquery = select( [ trans.app.model.SkipToolTest.table.c.repository_metadata_id ] )
-            if skip_tool_test:
-                clause_list.append( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) )
-            else:
+            if skipped_metadata_ids_subquery:
                 clause_list.append( not_( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) )
         # Generate and execute the query.
         try:

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
@@ -390,7 +390,7 @@
                     with lcd( current_dir ):
                         with settings( warn_only=True ):
                             for tarball_name in tarball_names:
-                                cmd = '''export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR && 
+                                cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; &&
                                     Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % ( str( tarball_name ) )
                                 cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) )
                                 return_code = handle_command( app, tool_dependency, install_dir, cmd )
@@ -432,24 +432,24 @@
                                 gem, gem_version = ruby_package_tup
                                 if os.path.isfile( gem ):
                                     # we assume a local shipped gem file
-                                    cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && 
+                                    cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
                                             gem install --local %s''' % ( gem )
                                 elif gem.find( '://' ) != -1:
                                     # We assume a URL to a gem file.
                                     url = gem
                                     gem_name = url.split( '/' )[ -1 ]
                                     td_common_util.url_download( work_dir, gem_name, url, extract=False )
-                                    cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && 
+                                    cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
                                             gem install --local %s ''' % ( gem_name )
                                 else:
                                     # gem file from rubygems.org with or without version number
                                     if gem_version:
                                         # version number was specified
-                                        cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && 
+                                        cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
                                             gem install %s --version "=%s"''' % ( gem, gem_version)
                                     else:
                                         # no version number given
-                                        cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && 
+                                        cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME;
                                             gem install %s''' % ( gem )
                                 cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) )
                                 return_code = handle_command( app, tool_dependency, install_dir, cmd )
@@ -490,7 +490,7 @@
                             for perl_package in perl_packages:
                                 # If set to a true value then MakeMaker's prompt function will always
                                 # return the default without waiting for user input.
-                                cmd = '''export PERL_MM_USE_DEFAULT=1 && '''
+                                cmd = '''PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; '''
                                 if perl_package.find( '://' ) != -1:
                                     # We assume a URL to a gem file.
                                     url = perl_package

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -40,6 +40,70 @@
         raise Exception( message )
         return None
 
+
+def find_complex_dependency_package( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ):
+    """
+    """
+    tool_dependencies = []
+    if not os.path.exists( dependent_install_dir ):
+        os.makedirs( dependent_install_dir )
+    env_file = None
+    if tool_dependencies_config:
+        required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config )
+        if required_td_tree:
+            required_td_root = required_td_tree.getroot()
+            for required_td_elem in required_td_root:
+                # Find the appropriate package name and version.
+                if required_td_elem.tag == 'package':
+                    # <package name="bwa" version="0.5.9">
+                    required_td_package_name = required_td_elem.get( 'name', None )
+                    required_td_package_version = required_td_elem.get( 'version', None )
+                    if required_td_package_name == package_name and required_td_package_version == package_version:
+                        tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app,
+                                                                                                 tool_shed_repository=tool_shed_repository,
+                                                                                                 name=package_name,
+                                                                                                 version=package_version,
+                                                                                                 type='package',
+                                                                                                 status=app.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                                                                                 set_status=True )
+
+                        if required_repository.installing:
+                            tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+                                                                                                   tool_dependency=tool_dependency,
+                                                                                                   status=app.model.ToolDependency.installation_status.INSTALLING )
+                        # What happens if dependent repository fails or is
+                        # uninstalled during this process.
+                        env_file = required_repository_package_env( app, package_name, package_version, required_repository )
+                        if required_repository.installation_complete:
+                            if not os.path.exists( env_file ):
+                                error_message = 'env.sh file %s for package %s in dependendent repository could not be found. Required repository has status %s.' % ( package_name, env_file, required_repository.status )
+                                tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app,
+                                                                                                              tool_dependency,
+                                                                                                              error_message,
+                                                                                                              remove_installation_path=False )
+                            else:
+                                tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+                                                                                                       tool_dependency=tool_dependency,
+                                                                                                       status=app.model.ToolDependency.installation_status.INSTALLED )
+                        else:
+                            # Ekk - handling tool depednencies for a dependent
+                            # repository that is not installed.
+                            #
+                            # Go ahead a return the env.sh file - Galaxy will
+                            # proceed to create an invalid symbolic link.
+                            # This is subtle-ly different than the previous
+                            # behavior which would have recreated an env.sh
+                            # from the the required repository's
+                            # tool_dependencies.xml but since it was not
+                            # installed all of the values inside would be
+                            # invalid path modifications. Either way, this file
+                            # is junk until the required repository is
+                            # installed properly.
+                            pass
+                        tool_dependencies.append( tool_dependency )
+    return tool_dependencies, env_file
+
+
 def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ):
     """Return the absolute path to a specified disk file contained in a repository."""
     stripped_file_name = strip_path( file_name )
@@ -91,6 +155,7 @@
     text = common_util.tool_shed_get( app, tool_shed_url, url )
     return text
 
+
 def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository ):
     handled_tool_dependencies = []
     tool_shed = elem.attrib[ 'toolshed' ]
@@ -125,8 +190,7 @@
                                                                                       tool_dependency_version=package_version )
         # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package.
         # We can get everything we need from the discovered installed required_repository.
-        if required_repository.status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED,
-                                           app.model.ToolShedRepository.installation_status.INSTALLED ]:
+        if required_repository.installation_complete:
             if not os.path.exists( required_repository_package_install_dir ):
                 print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir )
             repo_files_dir = required_repository.repo_files_directory( app )
@@ -156,22 +220,26 @@
                                                                       required_repository_owner,
                                                                       required_repository_changeset_revision )
             config_to_use = tmp_filename
-        tool_dependencies, actions_dict = populate_actions_dict( app=app,
-                                                                 dependent_install_dir=dependent_install_dir,
-                                                                 required_install_dir=required_repository_package_install_dir,
-                                                                 tool_shed_repository=tool_shed_repository,
-                                                                 required_repository=required_repository,
-                                                                 package_name=package_name,
-                                                                 package_version=package_version,
-                                                                 tool_dependencies_config=config_to_use )
+
+        tool_dependencies, package_env_sh_file = find_complex_dependency_package(
+            app=app,
+            dependent_install_dir=dependent_install_dir,
+            required_install_dir=required_repository_package_install_dir,
+            tool_shed_repository=tool_shed_repository,
+            required_repository=required_repository,
+            package_name=package_name,
+            package_version=package_version,
+            tool_dependencies_config=config_to_use
+        )
+        if package_env_sh_file:
+            os.symlink( package_env_sh_file, os.path.join( dependent_install_dir, "env.sh" ) )
         if tmp_filename:
             try:
                 os.remove( tmp_filename )
             except:
                 pass
         for tool_dependency in tool_dependencies:
-            # Install and build the package via fabric and update the tool_dependency record accordingly..
-            tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict )
+            tool_dependency = __mark_tool_dependency_installed( app, tool_dependency)
             handled_tool_dependencies.append( tool_dependency )
     else:
         message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
@@ -179,113 +247,6 @@
         raise Exception( message )
     return handled_tool_dependencies
 
-def handle_set_environment_entry_for_package( app, install_dir, tool_shed_repository, package_name, package_version, elem, required_repository ):
-    """
-    Populate a list of actions for creating an env.sh file for a dependent repository.  The received elem is the <package> tag set associated
-    with the tool-dependencies.xml file for one of the received tool_shed_repository's repository dependency.
-    """
-    action_dict = {}
-    actions = []
-    tool_dependencies = []
-    for package_elem in elem:
-        if package_elem.tag == 'install':
-            # Create the new tool_dependency record in the database.
-            tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app,
-                                                                                     tool_shed_repository=tool_shed_repository,
-                                                                                     name=package_name,
-                                                                                     version=package_version,
-                                                                                     type='package',
-                                                                                     status=app.model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                                                                     set_status=True )
-            # Get the installation method version from a tag like: <install version="1.0">
-            package_install_version = package_elem.get( 'version', '1.0' )
-            if package_install_version == '1.0':
-                # Update the tool dependency's status.
-                tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
-                                                                                       tool_dependency=tool_dependency,
-                                                                                       status=app.model.ToolDependency.installation_status.INSTALLING )
-                # Since the required tool dependency is installed for a repository dependency, we first need to inspect the <actions> tag set to find
-                # the <action type="set_environment"> tag.
-                env_var_dicts = []
-                for actions_elem in package_elem:
-                    for action_elem in actions_elem:
-                        action_type = action_elem.get( 'type', 'shell_command' )
-                        if action_type == 'set_environment':
-                            # <action type="set_environment">
-                            #     <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
-                            #     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                            # </action>
-                            for env_elem in action_elem:
-                                if env_elem.tag == 'environment_variable':
-                                    env_var_dict = td_common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir )
-                                    if env_var_dict:
-                                        if env_var_dict not in env_var_dicts:
-                                            env_var_dicts.append( env_var_dict )
-                        elif action_type == 'setup_virtualenv':
-                            # Add the virtualenv's site-packages to PYTHONPATH and bin to PATH.  This is a bit hackish.
-                            site_packages_command = "%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( install_dir, "venv", "bin", "python" )
-                            output = fabric_util.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True )
-                            if output.return_code:
-                                log.error( 'Tool dependency %s includes a setup_virtualenv action but venv python is broken: ' % \
-                                           ( str( tool_dependency.name ), str( output.stderr ) ) )
-                            elif not os.path.exists( output.stdout ):
-                                log.error( "virtualenv's site-packages directory '%s' does not exist", str( output.stdout ) )
-                            else:
-                                env_var_dicts.append( dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) )
-                                env_var_dicts.append( dict( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'venv', 'bin' ) ) )
-                if env_var_dicts:
-                    if required_repository.status in [ app.model.ToolShedRepository.installation_status.INSTALLED,
-                                                       app.model.ToolShedRepository.installation_status.DEACTIVATED ]:
-                        # Handle the case where we have an installed required repository due to the prior_installation_required = True
-                        # setting in the received tool_shed_repository's tool_dependencies.xml file and the required repository's
-                        # tool_dependencies.xml file may include the use of the $ENV[] variable inheritance feature.  To handle this,
-                        # we will replace the current "value" entries in each env_var_dict with the actual path taken from the env.sh
-                        # file generated for the installed required repository.  Each env_var_dict currently looks something like this:
-                        # {'action': 'append_to', 'name': 'LD_LIBRARY_PATH', 'value': '$BOOST_ROOT_DIR/lib/'}
-                        # We'll read the contents of the received required_repository's env.sh file and replace the 'value' entry of
-                        # each env_var_dict with the associated value in the env.sh file.
-                        new_env_var_dicts = []
-                        env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app,
-                                                                                                repository_name=required_repository.name,
-                                                                                                repository_owner=required_repository.owner,
-                                                                                                repository_changeset_revision=required_repository.installed_changeset_revision,
-                                                                                                tool_dependency_type='package',
-                                                                                                tool_dependency_name=package_name,
-                                                                                                tool_dependency_version=package_version )
-                        env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' )
-                        if os.path.exists( env_sh_file_path ):
-                            for i, line in enumerate( open( env_sh_file_path, 'r' ) ):
-                                env_var_dict = env_var_dicts[ i ]
-                                action = env_var_dict.get( 'action', None )
-                                name = env_var_dict.get( 'name', None )
-                                value = env_var_dict.get( 'value', None )
-                                if action and name and value:
-                                    new_value = parse_env_shell_entry( action, name, value, line )
-                                    env_var_dict[ 'value' ] = new_value
-                                new_env_var_dicts.append( env_var_dict )
-                        else:
-                            error_message = 'Invalid file %s specified, ignoring set_environment_for_install action.' % str( env_sh_file_path )
-                            tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, 
-                                                                                                              tool_dependency, 
-                                                                                                              error_message, 
-                                                                                                              remove_installation_path=False )
-                        action_dict[ 'environment_variable' ] = new_env_var_dicts
-                    else:
-                        action_dict[ 'environment_variable' ] = env_var_dicts
-                    actions.append( ( 'set_environment', action_dict ) )
-                if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR,
-                                                   app.model.ToolDependency.installation_status.INSTALLED ]:
-                    # Update the tool dependency's status.
-                    tool_dependency = \
-                        tool_dependency_util.set_tool_dependency_attributes( app,
-                                                                             tool_dependency=tool_dependency,
-                                                                             status=app.model.ToolDependency.installation_status.INSTALLED )
-                # Accumulate processed tool dependencies to return to the caller.
-                tool_dependencies.append( tool_dependency )
-            else:
-                raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' )
-            return tool_dependencies, actions
-    return tool_dependencies, actions
 
 def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ):
     sa_session = app.model.context.current
@@ -301,17 +262,10 @@
                                                                                           tool_dependency, 
                                                                                           error_message, 
                                                                                           remove_installation_path=False )
-    if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR,
-                                       app.model.ToolDependency.installation_status.INSTALLED ]:
-        log.debug( 'Changing status for tool dependency %s from %s to %s.' % \
-            ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) )        
-        tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
-                                                                               tool_dependency=tool_dependency,
-                                                                               status=app.model.ToolDependency.installation_status.INSTALLED,
-                                                                               error_message=None,
-                                                                               remove_from_disk=False )
+    tool_dependency = __mark_tool_dependency_installed( app, tool_dependency)
     return tool_dependency
 
+
 def install_package( app, elem, tool_shed_repository, tool_dependencies=None ):
     # The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository.
     sa_session = app.model.context.current
@@ -821,60 +775,22 @@
         tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict )
     return tool_dependency
 
-def parse_env_shell_entry( action, name, value, line ):
-    new_value = value
-    var_name = '$%s' % name
-    tmp_value = line.split( '=' )[ 1 ]
-    if action == 'prepend_to':
-        # PATH=/test/package_rdkit_2012_12/62ebd7bb637a/rdkit/bin:$PATH; export PATH
-        new_value = tmp_value.split( ':%s' % var_name )[ 0 ]
-    elif action == 'set_to':
-        # RDBASE=test/package_rdkit_2012_12/62ebd7bb637a/rdkit; export RDBASE
-        new_value = tmp_value.split( ';' )[ 0 ]
-    elif action == 'append_to':
-        # LD_LIBRARY_PATH=$LD_LIBRARY_PATH:test/package_rdkit_2012_12/62ebd7bb637a/rdkit/lib/; export LD_LIBRARY_PATH
-        new_value = tmp_value.split( ':' )[ 1 ]
-        new_value = new_value.split( ';' )[ 0 ]
-    return new_value
 
-def populate_actions_dict( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ):
+# TODO: Move to tool_dependency_util?
+def required_repository_package_env( app, package_name, package_version, required_repository ):
     """
-    Populate an actions dictionary that can be sent to fabric_util.install_and_build_package.  This method handles the scenario where a tool_dependencies.xml
-    file defines a complex repository dependency.  In this case, the tool dependency package will be installed in a separate repository and the tool dependency
-    defined for the dependent repository will use an environment_variable setting defined in it's env.sh file to locate the required package.  This method
-    basically does what the install_via_fabric method does, but restricts it's activity to the <action type="set_environment"> tag set within the required
-    repository's tool_dependencies.xml file.
+    Return path to env.sh file in required repository if the required repository has been installed.
     """
-    sa_session = app.model.context.current
-    if not os.path.exists( dependent_install_dir ):
-        os.makedirs( dependent_install_dir )
-    actions_dict = dict( install_dir=dependent_install_dir )
-    if package_name:
-        actions_dict[ 'package_name' ] = package_name
-    tool_dependencies = []
-    action_dict = {}
-    if tool_dependencies_config:
-        required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config )
-        if required_td_tree:
-            required_td_root = required_td_tree.getroot()
-            for required_td_elem in required_td_root:
-                # Find the appropriate package name and version.
-                if required_td_elem.tag == 'package':
-                    # <package name="bwa" version="0.5.9">
-                    required_td_package_name = required_td_elem.get( 'name', None )
-                    required_td_package_version = required_td_elem.get( 'version', None )
-                    if required_td_package_name==package_name and required_td_package_version==package_version:
-                        tool_dependencies, actions = handle_set_environment_entry_for_package( app=app,
-                                                                                               install_dir=required_install_dir,
-                                                                                               tool_shed_repository=tool_shed_repository,
-                                                                                               package_name=package_name,
-                                                                                               package_version=package_version,
-                                                                                               elem=required_td_elem,
-                                                                                               required_repository=required_repository )
-                        if actions:
-                            actions_dict[ 'actions' ] = actions
-                        break
-    return tool_dependencies, actions_dict
+    env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app,
+                                                                            repository_name=required_repository.name,
+                                                                            repository_owner=required_repository.owner,
+                                                                            repository_changeset_revision=required_repository.installed_changeset_revision,
+                                                                            tool_dependency_type='package',
+                                                                            tool_dependency_name=package_name,
+                                                                            tool_dependency_version=package_version )
+    env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' )
+    return env_sh_file_path
+
 
 def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ):
     """
@@ -1019,3 +935,17 @@
     for arg in args:
         parts.append( arg.strip( '/' ) )
     return '/'.join( parts )
+
+
+# TODO: Move to tool_dependency_util?
+def __mark_tool_dependency_installed( app, tool_dependency ):
+    if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR,
+                                       app.model.ToolDependency.installation_status.INSTALLED ]:
+        log.debug( 'Changing status for tool dependency %s from %s to %s.' % \
+            ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) )
+        tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+                                                                               tool_dependency=tool_dependency,
+                                                                               status=app.model.ToolDependency.installation_status.INSTALLED,
+                                                                               error_message=None,
+                                                                               remove_from_disk=False )
+    return tool_dependency

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/scripts/check_repositories_for_functional_tests.py
--- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py
+++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py
@@ -95,18 +95,25 @@
     invalid_revisions = 0
     records_checked = 0
     # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway.
-    skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] )
+    print '# -------------------------------------------------------------------------------------------'
+    print '# The skip_tool_test setting has been set for the following repository revision, so they will not be tested.'
+    skip_metadata_ids = []
+    for skip_tool_test in app.sa_session.query( app.model.SkipToolTest ):
+        print '# repository_metadata_id: %s, changeset_revision: %s' % \
+            ( str( skip_tool_test.repository_metadata_id ), str( skip_tool_test.initial_changeset_revision ) )
+        print 'reason: %s' % str( skip_tool_test.comment )
+        skip_metadata_ids.append( skip_tool_test.repository_metadata_id )
     # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test,
     # since there's no need to check them again if they won't be tested anyway. Also filter out changeset revisions that are not downloadable,
     # because it's redundant to test a revision that a user can't install.
     for repository_metadata in app.sa_session.query( app.model.RepositoryMetadata ) \
                                              .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True,
                                                             app.model.RepositoryMetadata.table.c.includes_tools == True,
-                                                            app.model.RepositoryMetadata.table.c.do_not_test == False,
-                                                            not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ):
-        # Clear any old invalid tests for this metadata revision, since this could lead to duplication of invalid test rows,
-        # or tests incorrectly labeled as invalid.
+                                                            app.model.RepositoryMetadata.table.c.do_not_test == False ) ):
+        # Initialize some items.
         missing_test_components = []
+        revision_has_test_data = False
+        testable_revision = False
         repository = repository_metadata.repository
         records_checked += 1
         # Check the next repository revision.
@@ -117,15 +124,14 @@
         repository = repository_metadata.repository
         if repository.id not in checked_repository_ids:
             checked_repository_ids.append( repository.id )
-        if verbosity >= 1:
-            print '# -------------------------------------------------------------------------------------------'
-            print '# Now checking revision %s of %s, owned by %s.' % ( changeset_revision,  name, owner )
+        print '# -------------------------------------------------------------------------------------------'
+        print '# Checking revision %s of %s owned by %s.' % ( changeset_revision,  name, owner )
+        if repository_metadata.id in skip_metadata_ids:
+            print'# Skipping revision %s of %s owned by %s because the skip_tool_test setting has been set.' % ( changeset_revision,  name, owner )
         # If this changeset revision has no tools, we don't need to do anything here, the install and test script has a filter for returning
         # only repositories that contain tools.
         tool_dicts = metadata.get( 'tools', None )
         if tool_dicts is not None:
-            has_test_data = False
-            testable_revision = False
             # Clone the repository up to the changeset revision we're checking.
             repo_dir = repository.repo_path( app )
             repo = hg.repository( suc.get_configured_ui(), repo_dir )
@@ -139,29 +145,30 @@
                     if '.hg' in dirs:
                         dirs.remove( '.hg' )
                     if 'test-data' in dirs:
-                        has_test_data = True
+                        revision_has_test_data = True
                         test_data_path = os.path.join( root, dirs[ dirs.index( 'test-data' ) ] )
                         break
-            if verbosity >= 1:
-                if has_test_data:
-                    print '# Test data directory found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner )
-                else:
-                    print '# Test data directory missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner )
-                print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \
-                    ( changeset_revision,  name, owner )
-            # Inspect each tool_dict for defined functional tests.
+            if revision_has_test_data:
+                print '# Test data directory found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner )
+            else:
+                print '# Test data directory missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner )
+            print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \
+                ( changeset_revision,  name, owner )
+            # Inspect each tool_dict for defined functional tests.  If there are no tests, this tool should not be tested, since the
+            # tool functional tests only report failure if the test itself fails, not if it's missing or undefined. Filtering out those
+            # repositories at this step will reduce the number of "false negatives" the automated functional test framework produces.
             for tool_dict in tool_dicts:
+                failure_reason = ''
+                problem_found = False
+                tool_has_defined_tests = False
+                tool_has_test_files = False
+                missing_test_files = []
                 tool_count += 1
                 tool_id = tool_dict[ 'id' ]
                 tool_version = tool_dict[ 'version' ]
                 tool_guid = tool_dict[ 'guid' ]
-                if verbosity >= 2:
-                    print "# Checking tool ID '%s' in changeset revision %s of %s." % \
-                        ( tool_id, changeset_revision, name )
-                # If there are no tests, this tool should not be tested, since the tool functional tests only report failure if the test itself fails,
-                # not if it's missing or undefined. Filtering out those repositories at this step will reduce the number of "false negatives" the
-                # automated functional test framework produces.
-                tool_has_tests = False
+                if verbosity >= 1:
+                    print "# Checking tool ID '%s' in changeset revision %s of %s." % ( tool_id, changeset_revision, name )
                 defined_test_dicts = tool_dict.get( 'tests', None )
                 if defined_test_dicts is not None:
                     # We need to inspect the <test> tags because the following tags...
@@ -182,33 +189,26 @@
                         outputs = defined_test_dict.get( 'outputs', [] )
                         if inputs and outputs:
                             # At least one tool within the repository has a valid <test> tag.
-                            tool_has_tests = True
+                            tool_has_defined_tests = True
                             break
-                if tool_has_tests:
-                    if verbosity >= 2:
-                        print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \
-                            ( tool_id, changeset_revision, name )
+                if tool_has_defined_tests:
+                    print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \
+                        ( tool_id, changeset_revision, name )
                     has_tests += 1
                 else:
-                    if verbosity >= 2:
-                        print '# No functional tests defined for %s.' % tool_id
+                    print '# No functional tests defined for %s.' % tool_id
                     no_tests += 1
-                failure_reason = ''
-                problem_found = False
-                missing_test_files = []
-                has_test_files = False
-                if tool_has_tests and has_test_data:
+                if tool_has_defined_tests and revision_has_test_data:
                     missing_test_files = check_for_missing_test_files( defined_test_dicts, test_data_path )
                     if missing_test_files:
-                        if verbosity >= 2:
-                            print "# Tool ID '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \
-                                ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) )
+                        print "# Tool id '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \
+                            ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) )
                     else:
-                        has_test_files = True
-                if not has_test_data:
+                        tool_has_test_files = True
+                if not revision_has_test_data:
                     failure_reason += 'Repository does not have a test-data directory. '
                     problem_found = True
-                if not tool_has_tests:
+                if not tool_has_defined_tests:
                     failure_reason += 'Functional test definitions missing for %s. ' % tool_id
                     problem_found = True
                 if missing_test_files:
@@ -219,23 +219,22 @@
                 if problem_found:
                     if test_errors not in missing_test_components:
                         missing_test_components.append( test_errors )
-                if tool_has_tests and has_test_files:
+                if tool_has_defined_tests and tool_has_test_files:
+                    print '# Revision %s of %s owned by %s is a testable revision.' % ( changeset_revision,  name, owner )
                     testable_revision = True
             # Remove the cloned repository path. This has to be done after the check for required test files, for obvious reasons.
             if os.path.exists( work_dir ):
                 shutil.rmtree( work_dir )
             if not missing_test_components:
                 valid_revisions += 1
-                if verbosity >= 1:
-                    print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner )
+                print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner )
             else:
                 invalid_revisions += 1
+                print '# Some tools have problematic functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner )
                 if verbosity >= 1:
-                    print '# Some tools have problematic functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner )
-                    if verbosity >= 2:
-                        for invalid_test in missing_test_components:
-                            if 'missing_components' in invalid_test:
-                                print '# %s' % invalid_test[ 'missing_components' ]
+                    for missing_test_component in missing_test_components:
+                        if 'missing_components' in missing_test_component:
+                            print '# %s' % missing_test_component[ 'missing_components' ]
             if not info_only:
                 # Get or create the list of tool_test_results dictionaries.
                 if repository_metadata.tool_test_results is not None:
@@ -249,8 +248,9 @@
                     # install_and_test_tool_sed_repositories.sh script which will further populate the tool_test_results_dict.
                     tool_test_results_dict = tool_test_results_dicts[ 0 ]
                     if len( tool_test_results_dict ) <= 1:
-                        # We can re-use the mostly empty tool_test_results_dict for this run, but we need to eliminate it from
-                        # the list of tool_test_results_dicts since it will be re-inserted later.
+                        # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only
+                        # a test_environment entry.  If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts
+                        # since it will be re-inserted later.
                         tool_test_results_dict = tool_test_results_dicts.pop( 0 )
                     else:
                         # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used.
@@ -259,6 +259,11 @@
                     # Create a new dictionary for the most recent test run.
                     tool_test_results_dict = {}
                 test_environment_dict = tool_test_results_dict.get( 'test_environment', {} )
+                # Add the current time as the approximate time that this test run occurs.  A similar value will also be
+                # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed
+                # may be configured to store multiple test run results, so each must be associated with a time stamp.
+                now = time.strftime( "%Y-%m-%d %H:%M:%S" )
+                test_environment_dict[ 'time_tested' ] = now
                 test_environment_dict[ 'tool_shed_database_version' ] = get_database_version( app )
                 test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version
                 test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() )
@@ -281,7 +286,13 @@
                         print "# and it is not the latest downloadable revision."
                         repository_metadata.do_not_test = True
                     repository_metadata.tools_functionally_correct = False
-                    repository_metadata.missing_test_components = True
+                    if not testable_revision:
+                        # Even though some tools may be missing test components, it may be possible to test other tools.  Since the
+                        # install and test framework filters out repositories marked as missing test components, we'll set it only if
+                        # no tools can be tested.
+                        print '# Setting missing_test_components to True for revision %s of %s owned by %s because all tools are missing test components.' % \
+                            ( changeset_revision,  name, owner )
+                        repository_metadata.missing_test_components = True
                     tool_test_results_dict[ 'missing_test_components' ] = missing_test_components
                 # Store only the configured number of test runs.
                 num_tool_test_results_saved = int( app.config.num_tool_test_results_saved )

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/util/container_util.py
--- a/lib/tool_shed/util/container_util.py
+++ b/lib/tool_shed/util/container_util.py
@@ -1052,45 +1052,51 @@
     """Return a folder hierarchy containing tool dependencies."""
     # This container is displayed only in the tool shed.
     if tool_test_results_dicts:
-        multiple_tool_test_results_dicts = len( tool_test_results_dicts ) > 1
         test_results_dict_id = 0
         folder_id += 1
         tool_test_results_root_folder = Folder( id=folder_id, key='root', label='root', parent=None )
+        multiple_tool_test_results_dicts = len( tool_test_results_dicts ) > 1
+        if multiple_tool_test_results_dicts:
+            folder_id += 1
+            test_runs_folder = Folder( id=folder_id, key='test_runs', label='Test runs', parent=tool_test_results_root_folder )
+            tool_test_results_root_folder.folders.append( test_runs_folder )
         for index, tool_test_results_dict in enumerate( tool_test_results_dicts ):
             test_environment_dict = tool_test_results_dict.get( 'test_environment', None )
-            if test_environment_dict is not None:
-                time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index )
-                if multiple_tool_test_results_dicts:
-                    folder_id += 1
-                    containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=tool_test_results_root_folder )
-                else:
-                    containing_folder = tool_test_results_root_folder
-                test_results_dict_id += 1
-                #folder_id += 1
-                #test_results_folder = Folder( id=folder_id, key='test_results', label='Automated test environment', parent=containing_folder )
-                #containing_folder.folders.append( test_results_folder )
+            if test_environment_dict is None:
+                # the test environment entry will exist only if the preparation script check_re;ositories_for_functional_tests.py
+                # was executed prior to the ~/install_and_test_repositories/functional_tests.py script.  If that did not occur,
+                # we'll display test result, but the test_environment entries will not be complete.
+                test_environment_dict = {}
+            time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index )
+            if multiple_tool_test_results_dicts:
                 folder_id += 1
-                folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder )
-                containing_folder.folders.append( folder )
-                architecture = test_environment_dict.get( 'architecture', '' )
-                galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' )
-                galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' )
-                python_version = test_environment_dict.get( 'python_version', '' )
-                system = test_environment_dict.get( 'system', '' )
-                tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' )
-                tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' )
-                tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' )
-                test_environment = TestEnvironment( id=1,
-                                                    architecture=architecture,
-                                                    galaxy_database_version=galaxy_database_version,
-                                                    galaxy_revision=galaxy_revision,
-                                                    python_version=python_version,
-                                                    system=system,
-                                                    time_tested=time_tested,
-                                                    tool_shed_database_version=tool_shed_database_version,
-                                                    tool_shed_mercurial_version=tool_shed_mercurial_version,
-                                                    tool_shed_revision=tool_shed_revision )
-                folder.test_environments.append( test_environment )
+                containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=test_runs_folder )
+                test_runs_folder.folders.append( containing_folder )
+            else:
+                containing_folder = tool_test_results_root_folder
+            test_results_dict_id += 1
+            folder_id += 1
+            folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder )
+            containing_folder.folders.append( folder )
+            architecture = test_environment_dict.get( 'architecture', '' )
+            galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' )
+            galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' )
+            python_version = test_environment_dict.get( 'python_version', '' )
+            system = test_environment_dict.get( 'system', '' )
+            tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' )
+            tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' )
+            tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' )
+            test_environment = TestEnvironment( id=1,
+                                                architecture=architecture,
+                                                galaxy_database_version=galaxy_database_version,
+                                                galaxy_revision=galaxy_revision,
+                                                python_version=python_version,
+                                                system=system,
+                                                time_tested=time_tested,
+                                                tool_shed_database_version=tool_shed_database_version,
+                                                tool_shed_mercurial_version=tool_shed_mercurial_version,
+                                                tool_shed_revision=tool_shed_revision )
+            folder.test_environments.append( test_environment )
             not_tested_dict = tool_test_results_dict.get( 'not_tested', {} )
             if not_tested_dict:
                 folder_id += 1
@@ -1120,6 +1126,9 @@
                 containing_folder.folders.append( folder )
                 failed_test_id = 0
                 for failed_tests_dict in failed_tests_dicts:
+                    # TODO: Remove this when invalid test data is eliminated.
+                    if isinstance( failed_tests_dict, list ):
+                        failed_tests_dict = failed_tests_dict[ 0 ]
                     failed_test_id += 1
                     failed_test = FailedTest( id=failed_test_id,
                                               stderr=failed_tests_dict.get( 'stderr', '' ),
@@ -1153,6 +1162,7 @@
                                                              key='installation_errors',
                                                              label='Installation errors',
                                                              parent=containing_folder )
+                    containing_folder.installation_errors.append( installation_error_base_folder )
                     if current_repository_errors:
                         folder_id += 1
                         subfolder = Folder( id=folder_id,
@@ -1203,10 +1213,6 @@
                                                                                                   error_message=tool_dependency_error_dict.get( 'error_message', '' ) )
                             subfolder.tool_dependency_installation_errors.append( tool_dependency_installation_error )
                         installation_error_base_folder.folders.append( subfolder )
-                    containing_folder.installation_errors.append( installation_error_base_folder )
-            #containing_folder.folders.append( containing_folder )
-            if multiple_tool_test_results_dicts:
-                tool_test_results_root_folder.folders.append( containing_folder )
     else:
         tool_test_results_root_folder = None
     return folder_id, tool_test_results_root_folder

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 test/install_and_test_tool_shed_repositories/functional_tests.py
--- a/test/install_and_test_tool_shed_repositories/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/functional_tests.py
@@ -363,6 +363,8 @@
     """
     error_message = ''
     latest_revision_only = '-check_all_revisions' not in sys.argv
+    if latest_revision_only:
+        log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' )
     repository_dicts = []
     params = urllib.urlencode( dict( do_not_test='false',
                                      downloadable='true',
@@ -374,13 +376,12 @@
     baseline_repository_dicts, error_message = json_from_url( api_url )
     if error_message:
         return None, error_message
-    log.debug( 'The Tool Shed API returned %d metadata revisions for installation and testing.' % len( baseline_repository_dicts ) )
     for baseline_repository_dict in baseline_repository_dicts:
         # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the
         # module that will generate the install methods.
         repository_dict, error_message = get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict )
         if error_message:
-            log.debug( 'Error getting additional details about repository %s from the API: %s' % ( str( name ), error_message ) )
+            log.debug( 'Error getting additional details from the API: %s' % str(  error_message ) )
         else:
             # Don't test empty repositories.
             changeset_revision = baseline_repository_dict[ 'changeset_revision' ]
@@ -393,10 +394,6 @@
                         repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) )
                 else:
                     repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) )
-    if latest_revision_only:
-        skipped_previous = ' and metadata revisions that are not the most recent'
-    else:
-        skipped_previous = ''
     if testing_single_repository:
         tsr_name = testing_single_repository[ 'name' ]
         tsr_owner = testing_single_repository[ 'owner' ]
@@ -414,14 +411,15 @@
                         return repository_dicts, error_message
         return repository_dicts, error_message
     # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable.
-    log.debug( "Retrieved %d repositories from the API url: %s." % ( len( repository_dicts ), str( galaxy_tool_shed_url ) ) )
-    if '-list_repositories' in sys.argv:
-        log.debug( "Repositories for testing:" )
-        for repository_dict in repository_dicts:
-            log.debug( "Revision %s of repository %s owned by %s" % \
-                ( str( repository_dict.get( 'changeset_revision', None ) ), \
-                  str( repository_dict.get( 'name', None ) ), \
-                  str( repository_dict.get( 'owner', None ) ) ) )
+    log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) )
+    log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) )
+    #if '-list_repositories' in sys.argv:
+    log.debug( "Repository revisions for testing:" )
+    for repository_dict in repository_dicts:
+        log.debug( "Revision %s of repository %s owned by %s" % \
+            ( str( repository_dict.get( 'changeset_revision', None ) ), \
+              str( repository_dict.get( 'name', None ) ), \
+              str( repository_dict.get( 'owner', None ) ) ) )
     return repository_dicts, error_message
 
 def get_static_settings():
@@ -503,7 +501,7 @@
     params = dict( tools_functionally_correct=False,
                    do_not_test=False,
                    test_install_error=True )
-    # TODO: do something usefule with response_dict
+    # TODO: do something useful with response_dict
     response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params )
     # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it.
     # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES
@@ -618,33 +616,39 @@
         name = str( repository_dict[ 'name' ] )
         owner = str( repository_dict[ 'owner' ] )
         changeset_revision = str( repository_dict[ 'changeset_revision' ] )
+        log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) )
         # Populate the tool_test_results_dict.
         tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id )
-        # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered
-        # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first
-        # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this
-        # information.
-        tool_test_results_dict = tool_test_results_dicts.pop( 0 )
-        # See if this repository should be skipped for any reason.
-        skip_this_repository = False
-        skip_reason = None
-        for exclude_dict in exclude_list:
-            reason = exclude_dict[ 'reason' ]
-            exclude_repositories = exclude_dict[ 'repositories' ]
-            if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories:
-                skip_this_repository = True
-                skip_reason = reason
-                break
-        if skip_this_repository:
-            tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason )
-            params = dict( tools_functionally_correct=False,
-                           do_not_test=False )
-            # TODO: do something usefule with response_dict
-            response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params )
-            log.debug( "Not testing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) )
+        if error_message:
+            log.debug( error_message )
         else:
-            if error_message:
-                log.debug( error_message )
+            # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered
+            # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first
+            # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this
+            # information.
+            try:
+                tool_test_results_dict = tool_test_results_dicts.pop( 0 )
+            except Exception, e:
+                log.exception( "Invalid list of tool_test_results_dicts %s: %s" % ( str( tool_test_results_dicts ), str( e ) ) )
+                continue
+            # See if this repository should be skipped for any reason.
+            this_repository_is_in_the_exclude_lost = False
+            skip_reason = None
+            for exclude_dict in exclude_list:
+                reason = exclude_dict[ 'reason' ]
+                exclude_repositories = exclude_dict[ 'repositories' ]
+                if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories:
+                    this_repository_is_in_the_exclude_lost = True
+                    skip_reason = reason
+                    break
+            if this_repository_is_in_the_exclude_lost:
+                tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason )
+                params = dict( tools_functionally_correct=False,
+                               do_not_test=False )
+                # TODO: do something useful with response_dict
+                response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params )
+                log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \
+                           ( changeset_revision, name, owner ) )
             else:
                 test_environment_dict = tool_test_results_dict.get( 'test_environment', None )
                 test_environment_dict = get_test_environment( test_environment_dict )
@@ -678,7 +682,7 @@
                     params = dict( tools_functionally_correct=False,
                                    test_install_error=True,
                                    do_not_test=False )
-                    # TODO: do something usefule with response_dict
+                    # TODO: do something useful with response_dict
                     response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params )
                     try:
                         if deactivate:
@@ -736,7 +740,7 @@
                             params = dict( tools_functionally_correct=False,
                                            do_not_test=False,
                                            test_install_error=False )
-                            # TODO: do something usefule with response_dict
+                            # TODO: do something useful with response_dict
                             response_dict =  register_test_result( galaxy_tool_shed_url,
                                                                    tool_test_results_dicts,
                                                                    tool_test_results_dict,
@@ -1066,13 +1070,14 @@
                 exclude_count += 1
                 exclude_dict[ 'repositories' ].append( repository_tuple )
         exclude_list.append( exclude_dict )
-    log.debug( '%s repositories will be excluded from testing...' % str( exclude_count ) )
-    if '-list_repositories' in sys.argv:
-        for name, owner, changeset_revision in exclude_verbose:
-            if changeset_revision:
-                log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) )
-            else:
-                log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) )
+    log.debug( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \
+        ( str( xml_filename ), str( exclude_count ) ) )
+    #if '-list_repositories' in sys.argv:
+    for name, owner, changeset_revision in exclude_verbose:
+        if changeset_revision:
+            log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) )
+        else:
+            log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) )
     return exclude_list
 
 def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ):
@@ -1202,17 +1207,18 @@
         params = dict( tools_functionally_correct=True,
                        do_not_test=False,
                        test_install_error=False )
-        # TODO: do something usefule with response_dict
+        # TODO: do something useful with response_dict
         response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params )
         log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) )
     else:
-        tool_test_results_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) )
+        # The extract_log_data() netod returns a list.
+        tool_test_results_dict[ 'failed_tests' ] = extract_log_data( result, from_tool_test=True )
         results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) )
         set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict )
         params = dict( tools_functionally_correct=False,
                        test_install_error=False,
                        do_not_test=str( set_do_not_test ) )
-        # TODO: do something usefule with response_dict
+        # TODO: do something useful with response_dict
         response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params )
         log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \
             ( str( changeset_revision ), str( name ) ) )

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tool_conf.xml.main
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -280,8 +280,6 @@
   <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" />
-   <tool file="genetrack/genetrack_indexer.xml" />
-   <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" />

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tool_conf.xml.sample
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -340,8 +340,6 @@
     <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" />
-    <tool file="genetrack/genetrack_indexer.xml" />
-    <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" />

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_indexer.py
--- a/tools/genetrack/genetrack_indexer.py
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy.
-
-usage: %prog input output shift
-"""
-
-import sys, shutil, os
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( "GeneTrack" )
-
-from genetrack.scripts import tabs2genetrack
-from genetrack import logger
-
-if __name__ == "__main__":
-    import os
-    os.environ[ 'LC_ALL' ] = 'C' 
-    #os.system( 'export' )
-    
-    parser = tabs2genetrack.option_parser()
-
-    options, args = parser.parse_args()
-
-    # uppercase the format
-    options.format = options.format.upper()
-
-    if options.format not in ('BED', 'GFF'):
-        sys.stdout = sys.stderr
-        parser.print_help()
-        sys.exit(-1)
-
-    logger.disable(options.verbosity)
-
-    # missing file names
-    if not (options.inpname and options.outname and options.format):
-        parser.print_help()
-        sys.exit(-1)
-    else:
-        tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\
-            format=options.format, shift=options.shift, index=options.index, options=options)

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_indexer.xml
--- a/tools/genetrack/genetrack_indexer.xml
+++ /dev/null
@@ -1,64 +0,0 @@
-<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1">
-  
-  <description>on a BED file</description>
-
-  <command interpreter="python">
-    genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x
-  </command>
-    
-  <inputs>
-    
-    <param format="bed6" name="input" type="data" help="Input data">
-      <label>Select input bed file</label>
-    </param>
-    
-    <param name="shift" size="4" type="integer" value="0" help="distance in basepairs">
-        <label>Shift at 5' end</label>
-    </param>
-
-    <!-- this parameter is currently not used, may not be feasible to use it
-    <param name="coverage" type="select" label="Full coverage">
-      <option value="no">NO</option>
-      <option value="yes">YES</option>
-    </param>
-    -->
-  
-  </inputs>
-
-  <outputs>  
-    <data format="genetrack" name="output" />
-  </outputs>
-   
-<help>
-**Help**
-
-This tool will create a visualization of the bed file that is selected. 
-
-**Parameters**
-
-- **Shift at 5' end** should be used when the location of interest is at a fixed distance from
-  the 5' end for **all sequenced fragments**! 
-  
-  For example if the sequenced sample consists
-  mono-nucleosomal DNA (146bp) we should expect that 
-  each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. 
-  Therefore we would enter 73 as the shift parameter. Once corrected the reads 
-  on each strand will coincide and indicate the actual midpoints 
-  of the nucleosomes.
-  
-  When shifting the averaging process in GeneTrack is able correct for longer or shorter
-  than expected fragment sizes as long as the errors are reasonably random.
-
-See http://genetrack.bx.psu.edu/ for more information on GeneTrack.
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-</help>
-
-</tool>

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_peak_prediction.py
--- a/tools/genetrack/genetrack_peak_prediction.py
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy.
-
-usage: %prog input output level sigma mode exclusion strand
-"""
-
-import sys
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( "GeneTrack" )
-
-from genetrack.scripts import peakpred
-from genetrack import logger
-
-if __name__ == "__main__":
-
-    parser = peakpred.option_parser()
-
-    options, args = parser.parse_args()
-
-    logger.disable(options.verbosity)
-
-    from genetrack import conf
-
-    # trigger test mode
-    if options.test:
-        options.inpname = conf.testdata('test-hdflib-input.gtrack')
-        options.outname = conf.testdata('predictions.bed')
-
-    # missing input file name
-    if not options.inpname and not options.outname:
-        parser.print_help()
-    else:
-        print 'Sigma = %s' % options.sigma
-        print 'Minimum peak = %s' % options.level
-        print 'Peak-to-peak = %s' % options.exclude
-
-        peakpred.predict(options.inpname, options.outname, options)

diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_peak_prediction.xml
--- a/tools/genetrack/genetrack_peak_prediction.xml
+++ /dev/null
@@ -1,69 +0,0 @@
-<tool id="predict2genetrack" name="Peak predictor">
-  
-  <description>on GeneTrack index</description>
-
-  <command interpreter="python">
-      genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x
-  </command>
-    
-  <inputs>
-    
-    <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/>
- 
-    <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values">
-      <option value="gauss">Gaussian kernel</option>
-      <!-- <option value="yes">Moving averages</option> -->
-    </param>
-  
-    <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" />
-        
-
-    <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> 
-      <option value="nolap">Maximal non-overlapping</option>
-      <!-- <option value="above">Above a threshold</option> -->
-      <option value="all">All peaks</option>
-    </param>
-  
-    <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks"  label="Peak-to-peak distance">
-    </param>
-
-    <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" />
-    
-    <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately">
-      <option value="all">Merge strands</option>
-      <!-- <option value="yes1">Above a threshold</option> -->
-      <option value="two">Separate strands</option>
-    </param>
-
-  </inputs>
-
-  <outputs>  
-    <data format="bed" name="output" />
-  </outputs>
-   
-<help>
-**Help**
-
-This tool will generate genome wide peak prediction from an index file.
-
-**Parameters**
-
-- **Smoothing method** the function used to average nearby values
-
-- **Smoothing value** the factor used in the method
-
-- **Prediction method** the function used to average nearby values
-
-See http://genetrack.bx.psu.edu/ for more information on GeneTrack.
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-</help>
-
-</tool>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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