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Merge pull request #4208 from jmchilton/singularity_volume_fix_2
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Add missing lines for fixing Singularity volumes.
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dannon committed Jun 22, 2017
2 parents c18479b + 67b798f commit a910763
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),
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