diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py index c659097036e0..df9d75330343 100644 --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -312,6 +312,7 @@ def _configure_toolbox(self): galaxy_root_dir=galaxy_root_dir, default_file_path=file_path, tool_data_path=self.config.tool_data_path, + galaxy_data_manager_data_path=self.config.galaxy_data_manager_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, diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py index 880a3a5d4b59..769729f6bf9e 100644 --- a/lib/galaxy/tool_util/deps/container_classes.py +++ b/lib/galaxy/tool_util/deps/container_classes.py @@ -338,6 +338,7 @@ def add_var(name, value): 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("galaxy_data_manager_data_path", self.app_info.galaxy_data_manager_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": @@ -376,6 +377,8 @@ def add_var(name, value): defaults += ",$library_import_dir:default_ro" if self.app_info.tool_data_path: defaults += ",$tool_data_path:default_ro" + if self.app_info.galaxy_data_manager_data_path: + defaults += ",$galaxy_data_manager_data_path:default_ro" if self.app_info.shed_tool_data_path: defaults += ",$shed_tool_data_path:default_ro" diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py index cb5d571b44d5..4791c6d9506e 100644 --- a/lib/galaxy/tool_util/deps/dependencies.py +++ b/lib/galaxy/tool_util/deps/dependencies.py @@ -21,6 +21,7 @@ def __init__( galaxy_root_dir: Optional[str] = None, default_file_path: Optional[str] = None, tool_data_path: Optional[str] = None, + galaxy_data_manager_data_path: Optional[str] = None, shed_tool_data_path: Optional[str] = None, outputs_to_working_directory: bool = False, container_image_cache_path: Optional[str] = None, @@ -35,6 +36,7 @@ def __init__( self.galaxy_root_dir = galaxy_root_dir self.default_file_path = default_file_path self.tool_data_path = tool_data_path + self.galaxy_data_manager_data_path = galaxy_data_manager_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