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Merge pull request #9310 from AndreasSko/release_19.09

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Allow setting container path for docker_volumes
This commit is contained in:
Marius van den Beek
2020-04-20 16:58:12 +02:00
committed by GitHub
parent 4f2a0459b8 1b76294589
commit a7fcf91ae1
1 changed files with 7 additions and 1 deletions
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lib/galaxy/tool_util/deps/container_classes.py
+7 -1
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@@ -123,6 +123,8 @@ def preprocess_volumes(volumes_raw_str, container_type):
['/a/b:rw']
>>> preprocess_volumes("/a/b:ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
['/a/b:ro', '/a/b/c:rw']
>>> preprocess_volumes("/a/b:/a:ro,/a/b/c:/a/b:rw", DOCKER_CONTAINER_TYPE)
['/a/b:/a:ro', '/a/b/c:/a/b:rw']
>>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
['/a/b:ro', '/a/b/c:rw']
>>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", SINGULARITY_CONTAINER_TYPE)
@@ -135,8 +137,12 @@ def preprocess_volumes(volumes_raw_str, container_type):
for volume_raw_str in volumes_raw_strs:
volume_parts = volume_raw_str.split(":")
if len(volume_parts) > 2:
if len(volume_parts) > 3:
raise Exception("Unparsable volumes string in configuration [%s]" % volumes_raw_str)
if len(volume_parts) == 3:
volume_parts = ["%s:%s" % (volume_parts[0], volume_parts[1]), volume_parts[2]]
if len(volume_parts) == 2 and volume_parts[1] not in ("rw", "ro", "default_ro"):
volume_parts = ["%s:%s" % (volume_parts[0], volume_parts[1]), "rw"]
if len(volume_parts) == 1:
volume_parts.append("rw")
volumes.append(volume_parts)