mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
John Chilton
939e7774a8
This is (so far a subset of) the tool utilities from galaxy-lib. galaxy-lib mocked out a fake galaxy.tools to allow these to all exist below the galaxy.tools - but this was a terrible hack - in order for the new packages to be true subsets of Galaxy they need to be refactored into a new package that doesn't depend on models, SA, galaxy.jobs, etc... [x] galaxy.tools.deps -> galaxy.tool_util.deps [x] galaxy.tools.loader -> galaxy.tool_util.loader [x] galaxy.tools.cwl -> galaxy.tool_util.cwl [x] galaxy.tools.loader -> galaxy.tool_util.loader [x] galaxy.tools.fetcher -> galaxy.tool_util.fetcher [x] galaxy.tools.locations -> galaxy.tool_util.locations [x] galaxy.tools.parser -> galaxy.tool_util.parser
61 lines
2.0 KiB
Python
61 lines
2.0 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 (
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configure_logging,
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find_path,
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find_root,
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parse_dependency_options,
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)
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from galaxy.tool_util.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
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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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root = find_root(kwargs)
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dependency_resolvers_config_file = find_path(kwargs, "dependency_resolvers_config_file", root)
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use_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies = \
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parse_dependency_options(kwargs, root, dependency_resolvers_config_file)
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if not use_dependencies:
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dependency_manager = NullDependencyManager()
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else:
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dependency_manager_kwds = {
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'default_base_path': tool_dependency_dir,
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'conf_file': dependency_resolvers_config_file,
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'app_config': kwargs,
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}
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if use_cached_dependency_manager:
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dependency_manager_kwds['tool_dependency_cache_dir'] = tool_dependency_cache_dir
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dependency_manager = CachedDependencyManager(**dependency_manager_kwds)
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else:
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dependency_manager = DependencyManager(**dependency_manager_kwds)
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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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