X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/10543be10e5db9721a638d46e40bacc17d7599fe..57e0202fcbec42bf9f9aabade183c66551be0a88:/crunch_scripts/arvados-bcbio-nextgen.py

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index d53e0694e7..df66cf66e0 100755
--- 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",