def start(args):
"""Start and bootstrap a cluster."""
ec_args = ["elasticluster", "start", args.cluster]
ec_args = common.bcbio_args_to_ec(ec_args, args)
status = common.wrap_elasticluster(ec_args)
if status != 0:
sys.exit(status)
bootstrap_cluster(args)
def start(args):
"""Start and bootstrap a cluster."""
ec_args = ["elasticluster", "start", args.cluster]
ec_args = common.bcbio_args_to_ec(ec_args, args)
status = common.wrap_elasticluster(ec_args)
if status != 0:
sys.exit(status)
bootstrap_cluster(args)
parser = argparse.ArgumentParser(
description=
"Automatic installation for bcbio-nextgen pipelines, with docker.")
parser.add_argument(
"--datadir",
help="Directory with genome data and associated files.",
type=lambda x: (os.path.abspath(os.path.expanduser(x))))
subparsers = parser.add_subparsers(title="[sub-commands]")
_run_cmd(subparsers)
_install_cmd(subparsers, name="install")
_install_cmd(subparsers, name="upgrade")
_run_ipython_cmd(subparsers)
_run_ipythonprep_cmd(subparsers)
_template_cmd(subparsers)
_aws_cmd(subparsers)
_elasticluster_cmd(subparsers)
_graph_cmd(subparsers)
_run_clusterk_cmd(subparsers)
# _server_cmd(subparsers)
_runfn_cmd(subparsers)
devel.setup_cmd(subparsers)
_config_cmd(subparsers)
if len(sys.argv) == 1:
parser.print_help()
else:
if len(sys.argv) > 1 and sys.argv[1] == "elasticluster":
sys.exit(common.wrap_elasticluster(sys.argv[1:]))
else:
args = parser.parse_args()
args.func(args)
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="Automatic installation for bcbio-nextgen pipelines, with docker.")
parser.add_argument("--datadir", help="Directory with genome data and associated files.",
type=lambda x: (os.path.abspath(os.path.expanduser(x))))
subparsers = parser.add_subparsers(title="[sub-commands]")
_template_cmd(subparsers)
_cwl_cmd(subparsers)
_cwlrun_cmd(subparsers)
_install_cmd(subparsers, name="install")
_install_cmd(subparsers, name="upgrade")
_run_cmd(subparsers)
_run_ipython_cmd(subparsers)
_run_ipythonprep_cmd(subparsers)
#_run_clusterk_cmd(subparsers)
# _server_cmd(subparsers)
_runfn_cmd(subparsers)
devel.setup_cmd(subparsers)
_aws_cmd(subparsers)
_elasticluster_cmd(subparsers)
#_graph_cmd(subparsers)
_config_cmd(subparsers)
if len(sys.argv) == 1:
parser.print_help()
else:
if len(sys.argv) > 1 and sys.argv[1] == "elasticluster":
sys.exit(common.wrap_elasticluster(sys.argv[1:]))
else:
args = parser.parse_args()
args.func(args)
def stop(args):
"""Stop a cluster."""
ec_args = ["elasticluster", "stop", args.cluster]
ec_args = common.bcbio_args_to_ec(ec_args, args)
sys.exit(common.wrap_elasticluster(ec_args))
def setup(args):
"""Rerun cluster configuration commands."""
ec_args = ["elasticluster", "setup", args.cluster]
ec_args = common.bcbio_args_to_ec(ec_args, args)
sys.exit(common.wrap_elasticluster(ec_args))
def ssh(args):
"""SSH to a cluster."""
ec_args = ["elasticluster", "ssh", args.cluster]
ec_args = common.bcbio_args_to_ec(ec_args, args)
sys.exit(common.wrap_elasticluster(ec_args))
def stop(args):
"""Stop a cluster."""
ec_args = ["elasticluster", "stop", args.cluster]
ec_args = common.bcbio_args_to_ec(ec_args, args)
sys.exit(common.wrap_elasticluster(ec_args))
def setup(args):
"""Rerun cluster configuration commands."""
ec_args = ["elasticluster", "setup", args.cluster]
ec_args = common.bcbio_args_to_ec(ec_args, args)
sys.exit(common.wrap_elasticluster(ec_args))
def ssh(args):
"""SSH to a cluster."""
ec_args = ["elasticluster", "ssh", args.cluster]
ec_args = common.bcbio_args_to_ec(ec_args, args)
sys.exit(common.wrap_elasticluster(ec_args))
