X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ee4212cfcef60795c229602a4e585cf36ce71c99..aca461985963f60c185a02c53377d75eebf26266:/crunch_scripts/arvados-bcbio-nextgen.py

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index 8b69626873..9351b05853 100755
--- 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()