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Merge pull request #9314 from mvdbeek/mount_tool_data_path_readonly

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[20.01] Mount tool_data_path (ro) when running containerized tools
This commit is contained in:
John Chilton
2020-02-05 11:36:11 -05:00
committed by GitHub
parent ec5f59b270 392753af54
commit 6019d52345
3 changed files with 12 additions and 0 deletions
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lib/galaxy/config/__init__.py
+2
View File
@@ -1029,6 +1029,8 @@ class ConfiguresGalaxyMixin(object):
app_info = AppInfo(
galaxy_root_dir=galaxy_root_dir,
default_file_path=file_path,
tool_data_path=self.config.tool_data_path,
shed_tool_data_path=self.config.shed_tool_data_path,
outputs_to_working_directory=self.config.outputs_to_working_directory,
container_image_cache_path=self.config.container_image_cache_path,
library_import_dir=self.config.library_import_dir,
lib/galaxy/tool_util/deps/container_classes.py
+6
View File
@@ -186,6 +186,8 @@ class HasDockerLikeVolumes(object):
add_var("galaxy_root", self.app_info.galaxy_root_dir)
add_var("default_file_path", self.app_info.default_file_path)
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
@@ -215,6 +217,10 @@ class HasDockerLikeVolumes(object):
if self.app_info.library_import_dir:
defaults += ",$library_import_dir:default_ro"
if self.app_info.tool_data_path:
defaults += ",$tool_data_path:default_ro"
if self.app_info.shed_tool_data_path:
defaults += ",$shed_tool_data_path:default_ro"
# Define $defaults that can easily be extended with external library and
# index data without deployer worrying about above details.
lib/galaxy/tool_util/deps/dependencies.py
+4
View File
@@ -9,6 +9,8 @@ class AppInfo(object):
self,
galaxy_root_dir=None,
default_file_path=None,
tool_data_path=None,
shed_tool_data_path=None,
outputs_to_working_directory=False,
container_image_cache_path=None,
library_import_dir=None,
@@ -20,6 +22,8 @@ class AppInfo(object):
):
self.galaxy_root_dir = galaxy_root_dir
self.default_file_path = default_file_path
self.tool_data_path = tool_data_path
self.shed_tool_data_path = shed_tool_data_path
# TODO: Vary default value for docker_volumes based on this...
self.outputs_to_working_directory = outputs_to_working_directory
self.container_image_cache_path = container_image_cache_path