[ARVADOS] updated: ec0278bcf9affbbe9f88c413116f6aaa2713e0f6

[git at public.curoverse.com]

Summary of changes:
 crunch_scripts/arvados-bcbio-nextgen.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

       via  ec0278bcf9affbbe9f88c413116f6aaa2713e0f6 (commit)
      from  004bbae6c7ddfb8c952270781974591407502279 (commit)

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commit ec0278bcf9affbbe9f88c413116f6aaa2713e0f6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 2 16:37:20 2014 -0400

    fix sub R1 R2

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index 692ace3..5281737 100755
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -95,8 +95,8 @@ with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc",
 os.chdir(arvados.current_task().tmpdir)
 
 rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/gatk-variant.yaml", "project1",
-                         subst.do_substitution(p, "$(R1)"),
-                         subst.do_substitution(p, "$(R2)")])
+                         subst.do_substitution(p, "$(file $(R1))"),
+                         subst.do_substitution(p, "$(file $(R2))")])
 
 os.chdir("project1/work")
 

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