From 9060fbf9984b5e05081931c4c30846fd304ebced Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Wed, 2 Jul 2014 16:24:44 -0400
Subject: [PATCH] open for writing

---
 crunch_scripts/arvados-bcbio-nextgen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index b8fb76fc99..feb8ce0ac8 100755
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -19,7 +19,7 @@ shutil.copy("/usr/local/share/bcbio-nextgen/config/bcbio_system.yaml", "/usr/loc
 
 os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/tool-data")
 
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/tool_data_table_conf.xml") as f:
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/tool_data_table_conf.xml", "w") as f:
     f.write('''<tables>
     <!-- Locations of indexes in the BWA mapper format -->
     <table name="bwa_indexes" comment_char="#">
-- 
2.30.2