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diff trimmomatic.xml @ 2:a60283899c6d draft

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Version 0.32.2: use GALAXY_SLOTS to set number of threads.
author pjbriggs
date Wed, 22 Apr 2015 09:36:27 -0400
parents 2bd7cdbb6228
children f8a9a5eaca8a
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--- a/trimmomatic.xml	Tue Dec 09 09:41:33 2014 -0500
+++ b/trimmomatic.xml	Wed Apr 22 09:36:27 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