From 162e4de0e1a8e146a061ab15c770410007fe1b2e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 5 Nov 2013 13:46:06 -0600
Subject: [PATCH] Enhance bfast to utilize GALAXY_SLOTS configuration when
 available.

---
 tools/sr_mapping/bfast_wrapper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/sr_mapping/bfast_wrapper.xml b/tools/sr_mapping/bfast_wrapper.xml
index 65fa785c740..e05ab88bdba 100644
--- a/tools/sr_mapping/bfast_wrapper.xml
+++ b/tools/sr_mapping/bfast_wrapper.xml
@@ -1,7 +1,7 @@
 <tool id="bfast_wrapper" name="Map with BFAST" version="0.1.3">
   <description></description>
   <command interpreter="python">bfast_wrapper.py
-    --numThreads="4" ##HACK: hardcode numThreads for now, should come from a location file
+    --numThreads="\${GALAXY_SLOTS:-4}"
     --fastq="$input1"
     #if $input1.extension.startswith( "fastqcs" ):
         ##if extention starts with fastqcs, then we have a color space file