[ARVADOS] updated: ee4212cfcef60795c229602a4e585cf36ce71c99
git at public.curoverse.com
git at public.curoverse.com
Tue Jul 8 08:42:48 EDT 2014
Summary of changes:
crunch_scripts/arvados-bcbio-nextgen.py | 3 +++
1 file changed, 3 insertions(+)
via ee4212cfcef60795c229602a4e585cf36ce71c99 (commit)
from ef34e7256fe96d2ad4c3f27ca0ba4bef14a195ff (commit)
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commit ee4212cfcef60795c229602a4e585cf36ce71c99
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Jul 7 22:45:29 2014 -0400
bc-bio script links gemini reference data. refs #2991
diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index bcb2a2c..8b69626 100755
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -94,6 +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",
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