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[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 d53e0694e713a4112526eb3d4972a5bfefda7db1..c2962483999b04cad29d7e20ef06e508240cdb36 100755 (executable)
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -2,9 +2,10 @@
 
 import arvados
 import subprocess
-import subst
+import crunchutil.subst as subst
 import shutil
 import os
+import sys
 
 if len(arvados.current_task()['parameters']) > 0:
     p = arvados.current_task()['parameters']
@@ -93,6 +94,9 @@ details:
       # variant_regions: /path/to/your.bed
 ''')
 
+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.chdir(arvados.current_task().tmpdir)
 
 rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/freebayes-variant.yaml", "project1",