Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/ephemeris/workflow_install.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/ephemeris/workflow_install.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,52 @@ +#!/usr/bin/env python +'''Tool to install workflows on a Galaxy instance.''' +import argparse +import json +import os + +from . import get_galaxy_connection +from .common_parser import get_common_args + + +def import_workflow(gi, path, publish_wf=False): + """ + Given a connection to a Galaxy Instance (gi) and a path to a Galaxy workflow file, + this function will import the worklfow into Galaxy. + """ + with open(path, 'r') as wf_file: + import_uuid = json.load(wf_file).get('uuid') + existing_uuids = [d.get('latest_workflow_uuid') for d in gi.workflows.get_workflows()] + if import_uuid not in existing_uuids: + gi.workflows.import_workflow_from_local_path(path, publish=publish_wf) + + +def _parser(): + parent = get_common_args() + parser = argparse.ArgumentParser(parents=[parent]) + parser.add_argument("-w", "--workflow_path", + required=True, + help='Path to a workflow file or a directory with multiple workflow files ending with ".ga"') + parser.add_argument("--publish_workflows", + required=False, + action='store_true', + help='Flag to publish all imported workflows, so that they are viewable by other users') + return parser + + +def main(): + """ + This script uses bioblend to import .ga workflow files into a running instance of Galaxy + """ + args = _parser().parse_args() + gi = get_galaxy_connection(args) + + if os.path.isdir(args.workflow_path): + for file_path in os.listdir(args.workflow_path): + if file_path.endswith('.ga'): + import_workflow(gi, os.path.join(args.workflow_path, file_path), args.publish_workflows) + else: + import_workflow(gi, args.workflow_path, args.publish_workflows) + + +if __name__ == '__main__': + main()