def main(argv):
parser = argparse.ArgumentParser(description="NGSpyeasy pipeline runner")
parser.add_argument("playbook_path", metavar='/path/to/your_pipeline.yml', type=cmdargs.existed_file)
parser.add_argument("--version", action="version", version="%(prog)s 3.0", help="print software version")
parser.add_argument("--samples", metavar="/path/to/config.tsv", dest="samples_tsv", required=False,
type=cmdargs.existed_file, help="List of samples in TSV format")
parser.add_argument("--vars", dest="var_files", metavar="/path/to/your/vars.yml", help="additional variables",
type=cmdargs.existed_file, action="append")
parser.add_argument("--provider", dest="provider", choices=["local", "lsf"], default="local",
help="job scheduler")
parser.add_argument("--log_dir", dest="log_dir", type=cmdargs.existed_directory)
args = parser.parse_args(argv)
if args.log_dir is not None:
init_main_logger(args.log_dir)
logger().debug("Command line arguments: %s" % args)
playbook_path = os.path.abspath(args.playbook_path)
samples_tsv = os.path.abspath(args.samples_tsv) if args.samples_tsv else None
var_files = [os.path.abspath(f) for f in args.var_files]
pb = playbook_yaml.parse(playbook_path, samples_tsv, var_files, args.log_dir)
logger().info("Starting job executor: provider=%s" % args.provider)
executor.start(provider=args.provider, log_dir=args.log_dir)
try:
for play in pb.plays():
logger().info("Starting play: %s" % play.name())
jobs = []
for name, cmd in play.commands():
logger().debug("cmd submit: name=%s\n %s\n" % (name, cmd))
executor.submit(name, cmd)
jobs.append(name)
if not wait_for_results(jobs):
break
except Exception as e:
logger().exception(e)
finally:
executor.stop()
def signal_handler(signum, frame):
logger().info("Got SIGINT(%s) signal" % str(signum))
executor.stop()