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4024: Add test for double-load bug.
[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 8b696268730553e6d5ad07b35c6795b8288145d0..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']
@@
-95,7
+96,7
@@
details:
''')
os.unlink("/usr/local/share/bcbio-nextgen/gemini_data")
''')
os.unlink("/usr/local/share/bcbio-nextgen/gemini_data")
-os.symlink(arvados.get_job_param_mount("gemini_data", "/usr/local/share/bcbio-nextgen/gemini_data")
+os.symlink(arvados.get_job_param_mount("gemini_data"
)
, "/usr/local/share/bcbio-nextgen/gemini_data")
os.chdir(arvados.current_task().tmpdir)
os.chdir(arvados.current_task().tmpdir)
@@
-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()