How to use the ephemeris.load_yaml_file function in ephemeris

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github galaxyproject / ephemeris / ephemeris / shed_tools_old.py View on Github external
"""
    Parse the default input file and proceed to install listed tools.
    :type options: OptionParser object
    :param options: command line arguments parsed by OptionParser
    """
    install_tool_dependencies = INSTALL_TOOL_DEPENDENCIES
    install_repository_dependencies = INSTALL_REPOSITORY_DEPENDENCIES
    install_resolver_dependencies = INSTALL_RESOLVER_DEPENDENCIES

    repo_list_file = options.tool_list_file
    gi = get_galaxy_connection(options, file=repo_list_file, log=log)
    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