def main(): """ Main configuration method made to be called in order to prepare reference files. """ print blue("Welcome to NGS configurator\n") parser = argparse.ArgumentParser(description=blue('NGS configurator')) parser.add_argument('-download', default=joiner('downloads'), help='path to download directory') parser.add_argument('-hg', default=joiner('hg19'), help='path to hg19 reference files directory') args = parser.parse_args() prepare_input_files(args)
def download_file(name, url, destination): file_name = url.split('/')[-1] blue('\tDownloading: ' + file_name) command = 'wget ' + url + ' -O ' + os.path.join(destination, file_name) run_command(command, Exception, hide_stderr=True) return True