diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index ca488a1d594..01fbc73e8e1 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/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 diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index ed0b64ff7ce..e314254c385 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/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. diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 62a72373b29..4a6bdf0756e 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/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 ): diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index d6f53557b69..8025c10873b 100644 --- a/lib/galaxy/workflow/run.py +++ b/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 ]