mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-31 01:02:04 +08:00
Dannon Baker
45 lines
1.5 KiB
Python
45 lines
1.5 KiB
Python
import os.path
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import sys
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
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from galaxy.config import configure_logging
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from galaxy.tool_util.deps import build_dependency_manager
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from galaxy.util.properties import find_config_file
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from galaxy.util.script import main_factory
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DESCRIPTION = "Script to manage tool dependencies (with focus on a Conda environments)."
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def _init_if_needed(args, kwargs):
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# If conda_auto_init is set, simply building the Conda resolver will call handle installation.
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_build_dependency_manager_no_config(kwargs)
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def _build_dependency_manager_no_config(kwargs):
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"""Simplified variant of build_dependency_manager from galaxy.tool_util.deps.
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The canonical factory method requires a full Galaxy configuration object
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which we do not have available in this script (an optimization).
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"""
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configure_logging(kwargs)
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base, ext = os.path.splitext(kwargs.get("dependency_resolvers_config_file", "dependency_resolvers_conf.xml"))
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dependency_resolvers_config_file = find_config_file(base, exts=[ext.lstrip(".")])
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# FIXME: default is wrong for installed Galaxy
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dependency_manager = build_dependency_manager(
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app_config_dict=kwargs,
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conf_file=dependency_resolvers_config_file,
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default_tool_dependency_dir="database/dependencies",
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)
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return dependency_manager
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ACTIONS = {
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"init_if_needed": _init_if_needed,
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}
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if __name__ == "__main__":
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main = main_factory(description=DESCRIPTION, actions=ACTIONS)
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main()
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