[ARVADOS] updated: 57c47bce1a0bcd4410c5261aaaa81b7a7cbaae75

[git at public.curoverse.com]

Summary of changes:
 crunch_scripts/arvados-bcbio-nextgen.py | 3 +++
 1 file changed, 3 insertions(+)

       via  57c47bce1a0bcd4410c5261aaaa81b7a7cbaae75 (commit)
      from  7d2a76ff4fd06d9bdb3fa5d30474e1294eedaa1d (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 57c47bce1a0bcd4410c5261aaaa81b7a7cbaae75
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Jul 7 22:46:36 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",

-----------------------------------------------------------------------


hooks/post-receive
--