def _run_cromwell(args):
"""Run CWL with Cromwell.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "cromwell_work"))
final_dir = utils.safe_makedir(os.path.join(work_dir, "final"))
if args.no_container:
_remove_bcbiovm_path()
log_file = os.path.join(work_dir, "%s-cromwell.log" % project_name)
metadata_file = os.path.join(work_dir, "%s-metadata.json" % project_name)
option_file = os.path.join(work_dir, "%s-options.json" % project_name)
cromwell_opts = {"final_workflow_outputs_dir": final_dir,
"default_runtime_attributes": {"bootDiskSizeGb": 20}}
with open(option_file, "w") as out_handle:
json.dump(cromwell_opts, out_handle)
cmd = ["cromwell", "-Xms1g", "-Xmx3g", "run", "--type", "CWL",
"-Dconfig.file=%s" % hpc.create_cromwell_config(args, work_dir, json_file)]
cmd += hpc.args_to_cromwell_cl(args)
cmd += ["--metadata-output", metadata_file, "--options", option_file,
"--inputs", json_file, main_file]
with utils.chdir(work_dir):
_run_tool(cmd, not args.no_container, work_dir, log_file)
if metadata_file and utils.file_exists(metadata_file):
with open(metadata_file) as in_handle:
metadata = json.load(in_handle)
if metadata["status"] == "Failed":
_cromwell_debug(metadata)
sys.exit(1)
else:
_cromwell_move_outputs(metadata, final_dir)
def _run_cromwell(args):
"""Run CWL with Cromwell.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "cromwell_work"))
final_dir = utils.safe_makedir(os.path.join(work_dir, "final"))
if args.no_container:
_remove_bcbiovm_path()
log_file = os.path.join(work_dir, "%s-cromwell.log" % project_name)
metadata_file = os.path.join(work_dir, "%s-metadata.json" % project_name)
option_file = os.path.join(work_dir, "%s-options.json" % project_name)
cromwell_opts = {"final_workflow_outputs_dir": final_dir,
"default_runtime_attributes": {"bootDiskSizeGb": 20}}
with open(option_file, "w") as out_handle:
json.dump(cromwell_opts, out_handle)
cmd = ["cromwell", "-Xms1g", "-Xmx%s" % _estimate_runner_memory(json_file),
"run", "--type", "CWL",
"-Dconfig.file=%s" % hpc.create_cromwell_config(args, work_dir, json_file)]
cmd += hpc.args_to_cromwell_cl(args)
cmd += ["--metadata-output", metadata_file, "--options", option_file,
"--inputs", json_file, main_file]
with utils.chdir(work_dir):
_run_tool(cmd, not args.no_container, work_dir, log_file)
if metadata_file and utils.file_exists(metadata_file):
with open(metadata_file) as in_handle:
metadata = json.load(in_handle)
if metadata["status"] == "Failed":
_cromwell_debug(metadata)
sys.exit(1)
else:
_cromwell_move_outputs(metadata, final_dir)
def _run_cromwell(args):
"""Run CWL with Cromwell.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "cromwell_work"))
if args.no_container:
_remove_bcbiovm_path()
log_file = os.path.join(work_dir, "%s-cromwell.log" % project_name)
cmd = ["cromwell", "run", "--type", "CWL", "-Dconfig.file=%s" % hpc.create_cromwell_config(args, work_dir)]
cmd += hpc.args_to_cromwell_cl(args)
cmd += ["--inputs", json_file, main_file]
with utils.chdir(work_dir):
_run_tool(cmd, not args.no_container, work_dir, log_file)