From 1847f3a94d355eed42e0d6ba7b5f929b7af7d143 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 28 Dec 2016 10:54:37 -0500 Subject: [PATCH] Fix crunch script to construct toolpath before it is turned into a File object. refs #10497 --- sdk/cwl/arvados_cwl/crunch_script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py index 9804572344..225d5ec504 100644 --- a/sdk/cwl/arvados_cwl/crunch_script.py +++ b/sdk/cwl/arvados_cwl/crunch_script.py @@ -36,6 +36,7 @@ def run(): runner = None try: job_order_object = arvados.current_job()['script_parameters'] + toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool")) pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$') @@ -78,7 +79,6 @@ def run(): runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()), output_name=output_name, output_tags=output_tags) - toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool")) t = load_tool(toolpath, runner.arv_make_tool) args = argparse.Namespace() -- 2.39.5