From 0b6f0708c8932ed313cc9caa6bd316543ca94eb0 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 3 Jul 2013 10:39:02 -0400
Subject: [PATCH] Make BAM_to_SAM tool write temporary files to job working
 directory rather than generic temp space.

---
 tools/samtools/bam_to_sam.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/samtools/bam_to_sam.py b/tools/samtools/bam_to_sam.py
index 310d4b70a6e..17fb8688ef7 100644
--- a/tools/samtools/bam_to_sam.py
+++ b/tools/samtools/bam_to_sam.py
@@ -43,7 +43,7 @@ def __main__():
     except:
         sys.stdout.write( 'Could not determine Samtools version\n' )
 
-    tmp_dir = tempfile.mkdtemp()
+    tmp_dir = tempfile.mkdtemp( dir='.' )
 
     try:
         # exit if input file empty