How to use the ephemeris.get_tool_list_from_galaxy.GiToToolYaml function in ephemeris

To help you get started, we’ve selected a few ephemeris examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github galaxyproject / ephemeris / ephemeris / shed_tools_old.py View on Github external
if not gi:
        raise Exception('Could not get a galaxy connection')

    if repo_list_file:
        repository_list = load_yaml_file(repo_list_file)  # Input file contents
        repositories = repository_list['tools']  # The list of tools to install
        install_repository_dependencies = repository_list.get(
            'install_repository_dependencies', INSTALL_REPOSITORY_DEPENDENCIES)
        install_resolver_dependencies = repository_list.get(
            'install_resolver_dependencies', INSTALL_RESOLVER_DEPENDENCIES)
        install_tool_dependencies = repository_list.get(
            'install_tool_dependencies', INSTALL_TOOL_DEPENDENCIES)
    elif options.tool_yaml:
        repositories = [yaml.safe_load(options.tool_yaml)]
    elif options.action == "update":
        get_repository_list = GiToToolYaml(
            gi=gi,
            skip_tool_panel_section_name=False,
            get_data_managers=True
        )
        repository_list = get_repository_list.tool_list
        repositories = repository_list['tools']
    else:
        # An individual tool was specified on the command line
        repositories = [{
            "owner": options.owner,
            "name": options.name,
            "tool_panel_section_id": options.tool_panel_section_id,
            "tool_panel_section_label": options.tool_panel_section_label,
            "tool_shed_url": options.tool_shed_url or MTS,
            "revisions": options.revisions
        }]