mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
69 lines
4.2 KiB
Python
69 lines
4.2 KiB
Python
#!/usr/bin/env python
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"""
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If a repository name, owner and revision are specified,install the revision from a specified tool shed into Galaxy.
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Specifying a revision is optional, if it is no specified, the latest installable revision will automatically be installed.
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However, the name and owner are required.
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This example demonstrates installation of a repository that contains valid tools, loading them into a section of the
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Galaxy tool panel or creating a new tool panel section. You can choose if tool dependencies or repository dependencies
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should be installed, use --repository-deps or --tool-deps.
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This example requires a tool panel config file (e.g., tool_conf.xml, shed_tool_conf.xml, etc) to contain a tool panel section like the following:
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<section id="from_test_tool_shed" name="From Test Tool Shed" version="">
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</section>
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Here is a working example of how to use this script to install a repository from the test tool shed.
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./install_tool_shed_repositories.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --tool-deps
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"""
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import argparse
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from common import submit
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def main(options):
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"""Collect all user data and install the tools via the Galaxy API."""
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data = {}
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data['tool_shed_url'] = options.tool_shed_url
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data['name'] = options.name
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data['owner'] = options.owner
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if options.changeset_revision:
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data['changeset_revision'] = options.changeset_revision
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else:
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# If the changeset_revision is not specified, default to the latest installable revision.
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revision_data = {}
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revision_data['tool_shed_url'] = options.tool_shed_url.rstrip('/')
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revision_data['name'] = options.name
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revision_data['owner'] = options.owner
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revision_url = '{}{}'.format(options.local_url.rstrip('/'), '/api/tool_shed_repositories/get_latest_installable_revision')
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latest_installable_revision = submit(options.api,
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revision_url,
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revision_data,
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return_formatted=False)
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data['changeset_revision'] = latest_installable_revision
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if options.tool_panel_section_id:
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data['tool_panel_section_id'] = options.tool_panel_section_id
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elif options.new_tool_panel_section_label:
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data['new_tool_panel_section_label'] = options.new_tool_panel_section_label
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if options.install_repository_dependencies:
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data['install_repository_dependencies'] = options.install_repository_dependencies
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if options.install_tool_dependencies:
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data['install_tool_dependencies'] = options.install_tool_dependencies
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submit(options.api, '{}{}'.format(options.local_url.rstrip('/'), '/api/tool_shed_repositories/new/install_repository_revision'), data)
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='Installation of tool shed repositories via the Galaxy API.')
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parser.add_argument("-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL")
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parser.add_argument("-a", "--api", dest="api", required=True, help="API Key")
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parser.add_argument("-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance.")
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parser.add_argument("-n", "--name", required=True, help="Repository name.")
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parser.add_argument("-o", "--owner", required=True, help="Repository owner.")
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parser.add_argument("-r", "--revision", dest="changeset_revision", help="Repository revision.")
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parser.add_argument("--panel-section-id", dest="tool_panel_section_id", help="Tool panel section id if you want to add your repository to an existing tool section.")
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parser.add_argument("--panel-section-name", dest="new_tool_panel_section_label", help="New tool panel section label. If specified a new tool section will be created.")
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parser.add_argument("--repository-deps", dest="install_repository_dependencies", action="store_true", default=False, help="Install repository dependencies. [False]")
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parser.add_argument("--tool-deps", dest="install_tool_dependencies", action="store_true", default=False, help="Install tool dependencies. [False]")
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options = parser.parse_args()
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main(options)
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