From f71f0ff9d2db1a527a7769c76ee19604c6eeef12 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <ross.lazarus@gmail.com>
Date: Wed, 4 Apr 2012 06:11:54 +1000
Subject: [PATCH] Patch for picard_AddOrReplaceReadGroups.xml to add --tmpdir
 "${__new_file_path__}" to the command line generated. That will over-ride the
 default value "/tmp" for opts.tmpdir in picard_wrapper.py and solve the
 problem with /tmp filling reported by Matt Shirley.

---
 tools/picard/picard_AddOrReplaceReadGroups.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/picard/picard_AddOrReplaceReadGroups.xml b/tools/picard/picard_AddOrReplaceReadGroups.xml
index cc670abb9f0..89c4b50334e 100644
--- a/tools/picard/picard_AddOrReplaceReadGroups.xml
+++ b/tools/picard/picard_AddOrReplaceReadGroups.xml
@@ -16,6 +16,7 @@
       --output-format=$outputFormat
       --output=$outFile
       -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/AddOrReplaceReadGroups.jar"
+      --tmpdir "${__new_file_path__}" 
   </command>
   <inputs>
     <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in"