open for writing

[arvados.git] / crunch_scripts / arvados-bcbio-nextgen.py

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index b8fb76fc99a285eb3ec29f84de6052bfd9dfef55..feb8ce0ac88b82296b703c389239ab3a84f58423 100755 (executable)
--- 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="#">