Merge branch 'release_15.07'

config/plugins/interactive_environments/ipython/config/ipython.ini.sample

@@ -12,7 +12,7 @@
 command = docker
 
 # The docker image name that should be started.
-image = bgruening/docker-ipython-notebook:dev
+image = bgruening/docker-ipython-notebook:15.07
 
 # Additional arguments that are passed to the `docker run` command.
 command_inject = --sig-proxy=true -e DEBUG=false

config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample

@@ -7,7 +7,7 @@ ssl = False
 
 [docker]
 command = docker
-image = erasche/docker-rstudio-notebook:dev
+image = erasche/docker-rstudio-notebook:15.07
 
 # Additional arguments that are passed to the `docker run` command. `-u`
 # settings are completely ignored.

lib/galaxy/datatypes/binary.py

@@ -41,11 +41,11 @@ class Binary( data.Data ):
 
     @staticmethod
     def register_sniffable_binary_format(data_type, ext, type_class):
-        Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext, "class": type_class})
+        Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext.lower(), "class": type_class})
 
     @staticmethod
     def register_unsniffable_binary_ext(ext):
-        Binary.unsniffable_binary_formats.append(ext)
+        Binary.unsniffable_binary_formats.append(ext.lower())
 
     @staticmethod
     def is_sniffable_binary( filename ):

lib/galaxy/workflow/run.py

@@ -285,7 +285,10 @@ class WorkflowProgress( object ):
                 raise modules.DelayedWorkflowEvaluation()
         return replacement
 
-    def set_outputs_for_input( self, step, outputs={} ):
+    def set_outputs_for_input( self, step, outputs=None ):
+        if outputs is None:
+            outputs = {}
+
         if self.inputs_by_step_id:
             outputs[ 'output' ] = self.inputs_by_step_id[ step.id ]