From a481327ab3f4a36fe5499575ea237e15f4478503 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <soranzo@crs4.it>
Date: Sat, 16 Nov 2013 00:52:36 +0100
Subject: [PATCH 1/3] Enhance trinity to utilize GALAXY_SLOTS configuration
 when available.

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

diff --git a/tools/ngs_rna/trinity_all.xml b/tools/ngs_rna/trinity_all.xml
index 8f5dae15022..ed5edc84c7a 100644
--- a/tools/ngs_rna/trinity_all.xml
+++ b/tools/ngs_rna/trinity_all.xml
@@ -36,7 +36,7 @@
         --JM 10G
 
         ## CPU and butterfly options.
-        --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&amp;1
+        --CPU \${GALAXY_SLOTS:-6} --bfly_opts "-V 10 --stderr" > $trinity_log 2>&amp;1
     </command>
     <inputs>
         <conditional name="inputs">

From c4e9999a3361bec3590296e32eb055caae53f5f5 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <soranzo@crs4.it>
Date: Sat, 16 Nov 2013 00:53:35 +0100
Subject: [PATCH 2/3] Enhance mosaik to utilize GALAXY_SLOTS configuration when
 available.

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

diff --git a/tools/sr_mapping/mosaik.xml b/tools/sr_mapping/mosaik.xml
index aa96a41e32b..473da9a2053 100644
--- a/tools/sr_mapping/mosaik.xml
+++ b/tools/sr_mapping/mosaik.xml
@@ -3,7 +3,7 @@
   <description/>
   <requirements><requirement type="package">mosaik</requirement></requirements>
   <command>
-    #set $processors = '-p 4'
+    #set $processors = '-p ${GALAXY_SLOTS:-4}'
     #set $lm = ''
     #if $paired.kind == 'single':
         #set $mfl = ''

From 3e528ae02b7a95c84fb4a0852567b19b59c6b588 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <soranzo@crs4.it>
Date: Sat, 16 Nov 2013 00:53:52 +0100
Subject: [PATCH 3/3] Enhance bowtie2 to utilize GALAXY_SLOTS configuration
 when available.

---
 tools/sr_mapping/bowtie2_wrapper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/sr_mapping/bowtie2_wrapper.xml b/tools/sr_mapping/bowtie2_wrapper.xml
index f67fb4899e4..62aac10956f 100644
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -21,7 +21,7 @@
         bowtie2
         
         ## number of threads
-        -p 4
+        -p \${GALAXY_SLOTS:-4}
 
         ## index file path
         -x $index_path