[ARVADOS] updated: 4a040b5eb8e506a51376582093ad4e4c223450db

[git at public.curoverse.com]

Summary of changes:
 crunch_scripts/arvados-bcbio-nextgen.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

       via  4a040b5eb8e506a51376582093ad4e4c223450db (commit)
      from  42acc196ca8f5908f3cc214d5f715eb1db82c7a8 (commit)

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commit 4a040b5eb8e506a51376582093ad4e4c223450db
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 2 20:34:20 2014 -0400

    fix bwa_index

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index 8781087..fe3c6eb 100755
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -55,19 +55,19 @@ with open("/usr/local/share/bcbio-nextgen/galaxy/tool_data_table_conf.xml", "w")
 os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/tool-data")
 
 with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bowtie2_indices.loc", "w") as f:
-    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(dir $(bowtie2_indices))"))
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(dir $(bowtie2_indices))\n"))
 
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bwa_indices.loc", "w") as f:
-    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(bwa_indices))"))
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bwa_index.loc", "w") as f:
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(bwa_index))\n"))
 
 with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/gatk_sorted_picard_index.loc", "w") as f:
-    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(gatk_sorted_picard_index))"))
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(gatk_sorted_picard_index))\n"))
 
 with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/picard_index.loc", "w") as f:
-    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(picard_index))"))
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(picard_index))\n"))
 
 with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc", "w") as f:
-    f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))"))
+    f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))\n"))
 
 with open("/tmp/crunch-job/gatk-variant.yaml", "w") as f:
     f.write('''

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