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Merge branch 'release_21.01' into dev

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This commit is contained in:
mvdbeek
2021-04-08 15:44:44 +02:00
parent 135b13548b c767adbed1
commit dec78b7204
1 changed files with 9 additions and 7 deletions
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lib/galaxy/tool_util/deps/container_classes.py
+9 -7
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@@ -200,6 +200,7 @@ class HasDockerLikeVolumes:
add_var("library_import_dir", self.app_info.library_import_dir)
add_var('tool_data_path', self.app_info.tool_data_path)
add_var('shed_tool_data_path', self.app_info.shed_tool_data_path)
if self.job_info.job_directory and self.job_info.job_directory_type == "pulsar":
# We have a Pulsar job directory, so everything needed (excluding index
# files) should be available in job_directory...
@@ -217,6 +218,12 @@ class HasDockerLikeVolumes:
defaults += ",$job_directory/configs:rw"
if self.job_info.tmp_directory is not None:
defaults += ",$tmp_directory:rw"
# If a tool definitely has a temp directory available set it to /tmp in container for compat.
# with CWL. This is part of that spec and should make it easier to share containers between CWL
# and Galaxy.
defaults += ",$tmp_directory:/tmp:rw"
else:
defaults += ",$_GALAXY_JOB_TMP_DIR:rw"
if self.job_info.home_directory is not None:
defaults += ",$home_directory:rw"
if self.app_info.outputs_to_working_directory:
@@ -247,6 +254,7 @@ class HasDockerLikeVolumes:
if end_index < 0:
end_index = len(volumes_str)
volumes_str = volumes_str[0:tool_directory_index] + volumes_str[end_index:len(volumes_str)]
return volumes_str
@@ -292,14 +300,8 @@ class DockerContainer(Container, HasDockerLikeVolumes):
preprocessed_volumes_list = preprocess_volumes(volumes_raw, self.container_type)
# TODO: Remove redundant volumes...
volumes = [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
# If a tool definitely has a temp directory available set it to /tmp in container for compat.
# with CWL. This is part of that spec and should make it easier to share containers between CWL
# and Galaxy.
if self.job_info.tmp_directory is not None:
volumes.append(DockerVolume.from_str("%s:/tmp:rw" % self.job_info.tmp_directory))
else:
volumes.append(DockerVolume.from_str("$_GALAXY_JOB_TMP_DIR:$_GALAXY_JOB_TMP_DIR:rw"))
volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM)
docker_host_props = self.docker_host_props
cached_image_file = self.__get_cached_image_file()