Disable chunking

[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..df66cf66e0e9ae7ead91c1622e2411e0fc4c2b5b 100755 (executable)
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -5,6 +5,7 @@ import subprocess
 import 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",