def run(
cwl_document: str,
input_params: str,
exec_profile=LocalToolExec, # please note here class not
# the path to the module is required
outdir=os.path.abspath('.'),
tmp_outdir_prefix=cwltool.utils.DEFAULT_TMP_PREFIX,
cachedir="",
move_outputs="move", # one of "move", "copy", or "leave"
debug=False):
"""
Main API entry point. Executes c2wl_rocket.__main__.main"
"""
args = argparse.Namespace(debug=debug,
exec_profile=exec_profile,
cwl_document=cwl_document,
input_params=[input_params],
outdir=outdir,
tmp_outdir_prefix=tmp_outdir_prefix,
cachedir=cachedir,
move_outputs=move_outputs)
main(args)
else:
logger.error("Workflow cannot make any more progress.")
break
while self.jobs:
try:
self.cond.acquire()
self.cond.wait()
finally:
self.cond.release()
if self.final_output is None:
raise cwltool.workflow.WorkflowException("Workflow did not return a result.")
return self.final_output
def main(args, stdout, stderr):
runner = GGPCwlRunner()
args.insert(0, "--leave-outputs")
parser = cwltool.main.arg_parser()
parser.add_argument("--project", default=None)
parser.add_argument("--bucket", default=None)
return cwltool.main.main(args, executor=runner.ggp_executor, makeTool=runner.ggp_maketool, parser=parser)
if __name__ == "__main__":
main(sys.argv[1:], sys.stdout, sys.stderr)
if not options.basedir:
options.basedir = os.path.dirname(os.path.abspath(options.cwljob))
outdir = options.outdir
print "> the cwl file is for a ", t.tool["class"]
if t.tool["class"] == "Workflow":
print generateScriptForWorkflow(t, job, outdir)
elif t.tool["class"] == "CommandLineTool":
print generateScriptForTool(t, job, outdir)
return 0
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
# ---------------- some notes and tests for interactive debugging ----------- #
def test():
# cwltool and cwljob the two .cwl and .json files
print "i am in ", pwd
mycwltool = "src/cwl2script/test/revsort.cwl"
cwljob = ""
# help("cwltool.main")
# help("cwltool.main.load_tool")
help("cwltool.workflow")
# create a tool
worker.start(web_server_host=args.web_server_host,
web_server_port=int(args.web_server_port))
def run(
cwl_document: str,
input_params: str,
exec_profile=LocalToolExec, # please note here class not
# the path to the module is required
outdir=os.path.abspath('.'),
tmp_outdir_prefix=cwltool.utils.DEFAULT_TMP_PREFIX,
cachedir="",
move_outputs="move", # one of "move", "copy", or "leave"
debug=False):
"""
Main API entry point. Executes c2wl_rocket.__main__.main"
"""
args = argparse.Namespace(debug=debug,
exec_profile=exec_profile,
cwl_document=cwl_document,
input_params=[input_params],
outdir=outdir,
tmp_outdir_prefix=tmp_outdir_prefix,
cachedir=cachedir,
move_outputs=move_outputs)
main(args)
if __name__ == "__main__":
main()
default=True,
help="Run jobs in parallel (the default)")
exgroup.add_argument("--serial",
action="store_false",
dest="parallel",
help="Run jobs in parallel (the default)")
parser.add_argument(
"workflow",
type=Text,
nargs="?",
default=None,
metavar='cwl_document',
help="path or URL to a CWL Workflow, "
"CommandLineTool, or ExpressionTool. If the `inputs_object` has a "
"`cwl:tool` field indicating the path or URL to the cwl_document, "
" then the `workflow` argument is optional.")
parser.add_argument(
"job_order",
nargs=argparse.REMAINDER,
metavar='inputs_object',
help="path or URL to a YAML or JSON "
"formatted description of the required input values for the given "
"`cwl_document`.")
return parser
if __name__ == "__main__":
sys.exit(main())
action="store_true",
help="Print command line help for tool")
parser.add_argument(
"--project-uuid",
type=str,
help=
"Project that will own the workflow jobs, if not provided, will go to home project."
)
parser.add_argument(
"--ignore-docker-for-reuse",
action="store_true",
help=
"Ignore Docker image version when deciding whether to reuse past jobs.",
default=False)
parser.add_argument("workflow",
type=str,
nargs="?",
default=None,
help="The workflow to execute")
parser.add_argument("job_order",
nargs=argparse.REMAINDER,
help="The input object to the workflow.")
return parser
if __name__ == '__main__':
sys.exit(main(sys.argv[1:]))
