Package build directories get same owner as $WORKSPACE.

[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 subst
+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']
@@ -95,7 +96,7 @@ details:
 ''')
 
 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)
 
@@ -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()