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3338: move code that sets the share_links to its own before_filter
[arvados.git]
/
crunch_scripts
/
arvados-bcbio-nextgen.py
diff --git
a/crunch_scripts/arvados-bcbio-nextgen.py
b/crunch_scripts/arvados-bcbio-nextgen.py
index df66cf66e0e9ae7ead91c1622e2411e0fc4c2b5b..9351b058530285b760f017ca1f95e5c20b442a08 100755
(executable)
--- a/
crunch_scripts/arvados-bcbio-nextgen.py
+++ b/
crunch_scripts/arvados-bcbio-nextgen.py
@@
-2,10
+2,11
@@
import arvados
import subprocess
import arvados
import subprocess
-import subst
+import
crunchutil.subst as
subst
import shutil
import os
import sys
import shutil
import os
import sys
+import time
if len(arvados.current_task()['parameters']) > 0:
p = arvados.current_task()['parameters']
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
print("arvados-bcbio-nextgen: start writing output to keep")
done = False
+ api = arvados.api('v1')
while not done:
try:
out = arvados.CollectionWriter()
while not done:
try:
out = arvados.CollectionWriter()