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))