--- a/trinityrnaseq.xml	Tue Sep 01 16:15:38 2015 -0400
+++ b/trinityrnaseq.xml	Fri Sep 23 10:01:55 2016 -0400
@@ -2,19 +2,28 @@
 
     <!-- Written by Jeremy Goecks, now maintained here by bhaas and additional
          modifications by Nate Coraor -->
-    <description>(Beta) De novo assembly of RNA-Seq data Using Trinity on PSC's Greenfield</description>
+    <description>(Beta) De novo assembly of RNA-Seq data Using Trinity on PSC's Bridges</description>
     <requirements>
-        <!-- These are versions available as modules on Greenfield -->
-        <requirement type="package" version="1.1.1">bowtie</requirement>
-        <requirement type="package" version="1.1">samtools</requirement>
+        <!-- These are versions available as modules on Bridges -->
+        <requirement type="package" version="1.1.2">bowtie</requirement>
+        <requirement type="package" version="1.3">samtools</requirement>
         <requirement type="package" version="jre7">java</requirement>
-        <requirement type="package" version="2.0.6">trinity</requirement>
+        <requirement type="package" version="5.18.4">perl</requirement>
+        <requirement type="package" version="2.2.0">trinity</requirement>
     </requirements>
     <command>
-        MEM=`expr "\${GALAXY_SLOTS:-15}" \* 50 - 16` ;
+        MEM=`expr "\${GALAXY_SLOTS:-16}" \* 48 - 16` ;
+
+	workdir=`pwd`;
+        echo "workdir is \$workdir";
+	cd \$LOCAL;
+	echo "Running Trinity from `pwd`";
+
         Trinity --max_memory "\${MEM}G"
                 --CPU "\${GALAXY_SLOTS:-16}"
-                --bflyHeapSpaceMax "\${MEM}G"
+                --bflyHeapSpaceMax "32G"
+                --bflyHeapSpaceInit "2G"
+                --bflyGCThreads "6"
         
         ## Inputs.
         #if str($inputs.paired_or_single) == "paired":
@@ -52,7 +61,10 @@
         > $trinity_log 2>&amp;1
  
         ## if Trinity fails, output the end of the log to stderr for Galaxy, and touch the output file for Pulsar
-        || (ec=\$? ; cat $trinity_log >&amp;2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec)
+        || (ec=\$? ; cp -pr . \$workdir; cd \$workdir; cat $trinity_log >&amp;2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec);
+
+        cp -pr . \$workdir;
+	cd \$workdir;
 
     </command>
     <stdio>
@@ -109,12 +121,12 @@
     <tests>
     </tests>
     <help>
-.. warning:: This version of Trinity, which runs on Greenfield_ at the `Pittsburgh Supercomputing Center`_, is a **beta** version. It may not be possible to rerun the same version of this tool, Trinity itself, or its other dependencies (Bowtie, SAMtools) in the future. **When rerunning this tool on the same data, it should, but cannot be guaranteed to reproduce the exact same results to the level of certainty as other Galaxy tools.**
+.. warning:: This version of Trinity, which runs on Bridges_ at the `Pittsburgh Supercomputing Center`_, is a **beta** version. It may not be possible to rerun the same version of this tool, Trinity itself, or its other dependencies (Bowtie, SAMtools) in the future. **When rerunning this tool on the same data, it should, but cannot be guaranteed to reproduce the exact same results to the level of certainty as other Galaxy tools.**
 
 Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass.
         
 .. _Trinity: http://trinityrnaseq.github.io
 .. _Pittsburgh Supercomputing Center: http://www.psc.edu
-.. _Greenfield: http://www.psc.edu/index.php/resources-for-users/computing-resources/greenfield
+.. _Bridges: http://www.psc.edu/bridges 
     </help>
 </tool>