[ARVADOS] updated: 1847f3a94d355eed42e0d6ba7b5f929b7af7d143

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Summary of changes:
 sdk/cwl/arvados_cwl/crunch_script.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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commit 1847f3a94d355eed42e0d6ba7b5f929b7af7d143
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Dec 28 10:54:37 2016 -0500

    Fix crunch script to construct toolpath before it is turned into a File object. refs #10497

diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index 9804572..225d5ec 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()

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