Python args_to_cromwell_cl 예제들

예제 #1

파일: tool.py 프로젝트: dauss75/bcbio-nextgen

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)

예제 #2

파일: tool.py 프로젝트: chapmanb/bcbio-nextgen

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)

예제 #3

파일: tool.py 프로젝트: Jason-Brickner/bcbio-nextgen

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)