[ARVADOS] updated: 004bbae6c7ddfb8c952270781974591407502279

[git at public.curoverse.com]

Summary of changes:
 crunch_scripts/arvados-bcbio-nextgen.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

       via  004bbae6c7ddfb8c952270781974591407502279 (commit)
      from  c0f1da371e57752ac48d314264fdd445a05192cb (commit)

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commit 004bbae6c7ddfb8c952270781974591407502279
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 2 16:35:35 2014 -0400

    refer template directly

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index 070e8cd..692ace3 100755
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -54,9 +54,7 @@ with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/tool_data_table_conf.
 </tables>
 ''')
 
-os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/templates")
-
-with open("/usr/local/share/bcbio-nextgen/galaxy/templates/gatk-variant.yaml", "w") as f:
+with open("/tmp/crunch-job/gatk-variant.yaml", "w") as f:
     f.write('''
 # Template for whole genome Illumina variant calling with GATK pipeline
 ---
@@ -96,7 +94,7 @@ 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", "gatk-variant", "project1",
+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)")])
 

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