def main(argv):
parser = argparse.ArgumentParser(description="NGSpeasy pipelines")
parser.add_argument("playbook_path", metavar='/path/to/your_pipeline.yml', type=cmdargs.existed_file)
parser.add_argument("--play_index", dest="play_index", type=int, help="play index", required=True)
parser.add_argument("--run_index", dest="run_index", type=int, default=-1, help="run index")
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",
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("--log_dir", dest="log_dir", type=cmdargs.existed_directory)
args = parser.parse_args(argv)
play_index = args.play_index
run_index = args.run_index
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]
logger().debug("Command line arguments: %s" % args)
logger().debug("TSV config path: %s" % samples_tsv)
pb = playbook_yaml.parse(playbook_path, samples_tsv, var_files, args.log_dir)
(play_run_vars, play_run_yaml, play_run_name) = pb.play_run(play_index, run_index)
if args.log_dir is not None:
init_play_run_logger(args.log_dir, str(play_index) + "_" + play_run_name)
task = play_run_yaml
task["hosts"] = "all"
temp_dir = tempfile.mkdtemp()
print temp_dir
try:
roles_dir = os.path.join(os.path.dirname(playbook_path), "roles")
if os.path.exists(roles_dir):
shutil.copytree(roles_dir, os.path.join(temp_dir, "roles"))
library_dir = os.path.join(os.path.dirname(playbook_path), "library")
if os.path.exists(library_dir):
shutil.copytree(library_dir, os.path.join(temp_dir, "library"))
playbook = os.path.join(temp_dir, "playbook.yml")
with open(playbook, 'w') as outfile:
outfile.write(yaml.dump([task], default_flow_style=False))
run_playbook(temp_dir, play_run_vars)
finally:
shutil.rmtree(temp_dir)
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()