Skip to content

Commit

Permalink
Add missing lines for fixing Singularity volumes.
Browse files Browse the repository at this point in the history
These should have been included in #4180.
  • Loading branch information
jmchilton committed Jun 20, 2017
1 parent 89851e4 commit 67b798f
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion lib/galaxy/tools/deps/containers.py
Expand Up @@ -536,7 +536,8 @@ def prop(name, default):
raise Exception("Cannot containerize command [%s] without defined working directory." % working_directory)

volumes_raw = self._expand_volume_str(self.destination_info.get("singularity_volumes", "$defaults"))
volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw)
preprocessed_volumes_str = preprocess_volumes(volumes_raw, self.container_type)
volumes = docker_util.DockerVolume.volumes_from_str(preprocessed_volumes_str)

singularity_target_kwds = dict(
singularity_cmd=prop("cmd", singularity_util.DEFAULT_SINGULARITY_COMMAND),
Expand Down

0 comments on commit 67b798f

Please sign in to comment.