From 8a461dfac2becd0335edd2b820f4cd5755824ae0 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 2 Jul 2013 09:25:55 -0400
Subject: [PATCH] Make SAM_to_BAM tool write temporary files to job working
 directory rather than generic temp space.

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

diff --git a/tools/samtools/sam_to_bam.py b/tools/samtools/sam_to_bam.py
index f209a7e41c0..4a6b8a19bda 100644
--- a/tools/samtools/sam_to_bam.py
+++ b/tools/samtools/sam_to_bam.py
@@ -42,7 +42,7 @@ def __main__():
     except:
         sys.stdout.write( 'Could not determine Samtools version\n' )
 
-    tmp_dir = tempfile.mkdtemp()
+    tmp_dir = tempfile.mkdtemp( dir='.' )
     if not options.ref_file or options.ref_file == 'None':
         # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
         # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in