main.py 文件源码

def main():
    parser = argparse.ArgumentParser(description='Generates CWL files from the GATK documentation')
    parser.add_argument("--version", "-v", dest='gatkversion', default="3.5",
        help="Sets the version of GATK to parse documentation for. Default is 3.5")
    parser.add_argument('--out', "-o", dest='outputdir',
        help="Sets the output directory for generated files. Default is ./gatk_cmdline_tools/<VERSION>/")
    parser.add_argument('--include', dest='include_file',
        help="Only generate this file (note, CommandLinkGATK has to be generated for v3.x)")
    parser.add_argument("--dev", dest="dev", action="store_true",
        help="Enable network caching and overwriting of the generated files (for development purposes). " + 
        "Requires requests_cache to be installed")
    parser.add_argument("--docker_container_name", "-c", dest="docker_container_name",
        help="Docker container name for generated cwl files. Default is 'broadinstitute/gatk3:<VERSION>' " + 
        "for version 3.x and 'broadinstitute/gatk:<VERSION>' for 4.x")
    parser.add_argument("--gatk_location", "-l", dest="gatk_location",
        help="Location of the gatk jar file. Default is '/usr/GenomeAnalysisTK.jar' for gatk 3.x and '/gatk/gatk.jar' for gatk 4.x")
    cmd_line_options = parser.parse_args()


    if cmd_line_options.dev:
        import requests_cache
        requests_cache.install_cache() # Decreases the time to run dramatically

    if not cmd_line_options.outputdir:
        cmd_line_options.outputdir = os.getcwd() + '/gatk_cmdline_tools/' + cmd_line_options.gatkversion

    if not cmd_line_options.docker_container_name:
        if is_version_3(cmd_line_options.gatkversion):
            cmd_line_options.docker_container_name = "broadinstitute/gatk3:" + cmd_line_options.gatkversion
        else:
            cmd_line_options.docker_container_name = "broadinstitute/gatk:" + cmd_line_options.gatkversion

    if not cmd_line_options.gatk_location:
        if is_version_3(cmd_line_options.gatkversion):
            cmd_line_options.gatk_location = "/usr/GenomeAnalysisTK.jar"
        else:
            cmd_line_options.gatk_location = "/gatk/gatk.jar"

    print("Your chosen directory is: %s" % cmd_line_options.outputdir)
    grouped_urls = get_json_links(cmd_line_options.gatkversion)

    generate_cwl_and_json_files(cmd_line_options.outputdir, grouped_urls, cmd_line_options)