Mercurial > repos > shellac > sam_consensus_v3
view 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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#!/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()