[ARVADOS] created: 91761a833014c72f7d9dc839bd2c93aa91765c93

[git at public.curoverse.com]

        at  91761a833014c72f7d9dc839bd2c93aa91765c93 (commit)


commit 91761a833014c72f7d9dc839bd2c93aa91765c93
Author: Tim Pierce <twp at curoverse.com>
Date:   Mon Sep 8 15:47:54 2014 -0400

    3823: bug fixes for arvados-bcbio-nextgen.py

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index c296248..9351b05 100755
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -6,6 +6,7 @@ import crunchutil.subst as subst
 import shutil
 import os
 import sys
+import time
 
 if len(arvados.current_task()['parameters']) > 0:
     p = arvados.current_task()['parameters']
@@ -121,6 +122,7 @@ if rcode == 0:
     print("arvados-bcbio-nextgen: start writing output to keep")
 
     done = False
+    api = arvados.api('v1')
     while not done:
         try:
             out = arvados.CollectionWriter()

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