# HG changeset patch
# User pjbriggs
# Date 1429709339 14400
# Node ID e7c8359dfa239bbb9cc7b5c3ab6048559725b6fc
# Parent  a2e6088d116591ee8aa0258d5333a20e1927ec7e
Uploaded version 0.32.2 (now uses GALAXY_SLOTS).

diff -r a2e6088d1165 -r e7c8359dfa23 README.rst
--- a/README.rst	Thu Mar 19 06:13:35 2015 -0400
+++ b/README.rst	Wed Apr 22 09:28:59 2015 -0400
@@ -15,8 +15,9 @@
 Automated installation
 ======================
 
-Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
-the trimmomatic program and data, and setting the appropriate environment variables.
+Installation via the Galaxy Tool Shed will take care of installing the tool wrapper
+and the trimmomatic program and data, and setting the appropriate environment
+variables.
 
 Manual Installation
 ===================
@@ -57,6 +58,8 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+0.32.2     - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use
+             at runtime (default is 6).
 0.32.1     - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files
              into the XML wrapper.
 0.32.0     - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and
diff -r a2e6088d1165 -r e7c8359dfa23 trimmomatic.xml
--- a/trimmomatic.xml	Thu Mar 19 06:13:35 2015 -0400
+++ b/trimmomatic.xml	Wed Apr 22 09:28:59 2015 -0400
@@ -1,12 +1,12 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.32.1">
+<tool id="trimmomatic" name="Trimmomatic" version="0.32.2">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <command interpreter="bash">trimmomatic.sh
   -mx8G
   -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
   #if $paired_end.is_paired_end
-    PE -threads 6 -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired 
+    PE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired 
   #else
-    SE -threads 6 -phred33 $fastq_in $fastq_out
+    SE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_in $fastq_out
   #end if
   ## ILLUMINACLIP option
   #if $illuminaclip.do_illuminaclip