Merge branch 'release_16.07' into dev

client/galaxy/scripts/layout/scratchbook.js

@@ -175,7 +175,7 @@ return Backbone.View.extend({
             var $galaxy_main = $( window.parent.document ).find( '#galaxy_main' );
             if ( options.target == 'galaxy_main' || options.target == 'center' ) {
                 if ( $galaxy_main.length === 0 ) {
-                    window.location = options.url + ( href.indexOf( '?' ) == -1 ? '?' : '&' ) + 'use_panels=True';
+                    window.location = options.url + ( options.url.indexOf( '?' ) == -1 ? '?' : '&' ) + 'use_panels=True';
                 } else {
                     $galaxy_main.attr( 'src', options.url );
                 }

client/galaxy/scripts/mvc/tool/tool-form.js

@@ -77,7 +77,8 @@ define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-modal', 'mvc/tool/tool-form
                 data    : job_def,
                 success : function( response ) {
                     callback && callback();
-                    self.$el.empty().append( self._templateSuccess( response ) );
+                    self.$el.children().hide();
+                    self.$el.append( self._templateSuccess( response ) );
                     parent.Galaxy && parent.Galaxy.currHistoryPanel && parent.Galaxy.currHistoryPanel.refreshContents();
                 },
                 error   : function( response ) {

client/galaxy/scripts/mvc/ui/ui-buttons.js

@@ -111,7 +111,10 @@ define( [ 'utils/utils' ], function( Utils ) {
                              href       : options.href || 'javascript:void(0)',
                              title      : options.title,
                              target     : options.target || '_top',
-                             disabled   : options.disabled } );
+                             disabled   : options.disabled } )
+                    .off( 'click' ).on( 'click' , function() {
+                        options.onclick && !options.disabled && options.onclick();
+                    });
             this.$icon.removeClass().addClass( options.icon );
         }
     });

config/job_conf.xml.sample_advanced

@@ -263,7 +263,7 @@
           <!-- For a stock Galaxy instance and traditional job runner $defaults will
                expand out as:
 
-               $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw
+               $galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:rw,$default_file_path:rw
 
                This assumes most of what is needed is available under Galaxy's root directory,
                the tool directory, and the Galaxy's file_path (if using object store creatively
@@ -274,7 +274,7 @@
                galaxy.ini. This will cause $defaults to allow writing to much
                less. It will then expand as follows:
 
-               $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro
+               $galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:rw,$default_file_path:ro
 
                If using the Pulsar, defaults will be even further restricted because the
                Pulsar will (by default) stage all needed inputs into the job's job_directory

lib/galaxy/jobs/runners/__init__.py

@@ -328,18 +328,27 @@ def _find_container(
         job_wrapper,
         compute_working_directory=None,
         compute_tool_directory=None,
-        compute_job_directory=None
+        compute_job_directory=None,
     ):
+        job_directory_type = "galaxy" if compute_working_directory is None else "pulsar"
         if not compute_working_directory:
             compute_working_directory = job_wrapper.tool_working_directory
 
+        if not compute_job_directory:
+            compute_job_directory = job_wrapper.working_directory
+
         if not compute_tool_directory:
             compute_tool_directory = job_wrapper.tool.tool_dir
 
         tool = job_wrapper.tool
         from galaxy.tools.deps import containers
         tool_info = containers.ToolInfo(tool.containers, tool.requirements)
-        job_info = containers.JobInfo(compute_working_directory, compute_tool_directory, compute_job_directory)
+        job_info = containers.JobInfo(
+            compute_working_directory,
+            compute_tool_directory,
+            compute_job_directory,
+            job_directory_type,
+        )
 
         destination_info = job_wrapper.job_destination.params
         return self.app.container_finder.find_container(

lib/galaxy/tools/deps/containers.py

@@ -197,12 +197,13 @@ def __init__(self, container_descriptions=[], requirements=[]):
 
 class JobInfo(object):
 
-    def __init__(self, working_directory, tool_directory, job_directory):
+    def __init__(self, working_directory, tool_directory, job_directory, job_directory_type):
         self.working_directory = working_directory
         self.job_directory = job_directory
         # Tool files may be remote staged - so this is unintuitively a property
         # of the job not of the tool.
         self.tool_directory = tool_directory
+        self.job_directory_type = job_directory_type  # "galaxy" or "pulsar"
 
 
 class Container( object ):
@@ -321,16 +322,16 @@ def add_var(name, value):
         add_var("default_file_path", self.app_info.default_file_path)
         add_var("library_import_dir", self.app_info.library_import_dir)
 
-        if self.job_info.job_directory:
-            # We have a job directory, so everything needed (excluding index
+        if self.job_info.job_directory and self.job_info.job_directory_type == "pulsar":
+            # We have a Pulsar job directory, so everything needed (excluding index
             # files) should be available in job_directory...
             defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw"
         elif self.app_info.outputs_to_working_directory:
             # Should need default_file_path (which is a course estimate given
             # object stores anyway).
-            defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro"
+            defaults = "$galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:rw,$default_file_path:ro"
         else:
-            defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw"
+            defaults = "$galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:rw,$default_file_path:rw"
 
         if self.app_info.library_import_dir:
             defaults += ",$library_import_dir:ro"