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Merge pull request #10625 from bernt-matthias/topic/singularity-bind-spec

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Don't specify default bind type for singularity
This commit is contained in:
John Chilton
2020-11-05 09:24:03 -05:00
committed by GitHub
parent 2f5742c7c0 f35d06eef0
commit 97305501bd
1 changed files with 9 additions and 1 deletions
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lib/galaxy/tool_util/deps/container_classes.py
+9 -1
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@@ -125,8 +125,10 @@ def preprocess_volumes(volumes_raw_str, 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:ro", SINGULARITY_CONTAINER_TYPE)
['/a/b:ro', '/a/b/c:ro']
>>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", SINGULARITY_CONTAINER_TYPE)
['/a/b:rw', '/a/b/c:rw']
['/a/b', '/a/b/c']
"""
volumes_raw_strs = [v.strip() for v in volumes_raw_str.split(",")]
@@ -160,6 +162,12 @@ def preprocess_volumes(volumes_raw_str, container_type):
volume[1] = how
# for a while singularity did not allow to specify the bind type rw
# (which is the default). so we omit this default
# see https://github.com/hpcng/singularity/pull/5487
if container_type == SINGULARITY_CONTAINER_TYPE and volume[1] == 'rw':
del volume[1]
return [":".join(v) for v in volumes]