# HG changeset patch
# User nate
# Date 1489160544 18000
# Node ID f98f80675d6011575cf22b1481005e580ed631a1
# Parent  3d072b99688e0269c4e03fa6b771b853ea7dcab9
Corrected perl module name and improved output handling for better performance from Phil Blood.

diff -r 3d072b99688e -r f98f80675d60 trinityrnaseq.xml
--- a/trinityrnaseq.xml	Mon Sep 26 16:10:07 2016 -0400
+++ b/trinityrnaseq.xml	Fri Mar 10 10:42:24 2017 -0500
@@ -8,7 +8,7 @@
         <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="5.18.4">perl</requirement>
+        <requirement type="package" version="5.18.4-threads">perl</requirement>
         <requirement type="package" version="2.2.0">trinity</requirement>
     </requirements>
     <command>
@@ -64,12 +64,12 @@
         ## direct to output
         > $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=\$? ; cp -pr . \$workdir; cd \$workdir; cat $trinity_log >&amp;2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec);
+        ## if Trinity fails, output the end of the log to stderr for Galaxy, and touch the output file for Pulsar                         
+        || (ec=\$? ; cp -p $trinity_log \$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;
-
+        mkdir -p \$workdir/trinity_out_dir;
+        cp -p trinity_out_dir/Trinity* \$workdir/trinity_out_dir; 
+        cd \$workdir;   
     </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="Program failed" />
@@ -126,9 +126,7 @@
     <tests>
     </tests>
     <help>
-.. 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 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.  This version of Trinity runs on Bridges_ at the `Pittsburgh Supercomputing Center`_ using a version of Trinity 2.2.0 optimized for the unique memory profile of that system.
         
 .. _Trinity: http://trinityrnaseq.github.io
 .. _Pittsburgh Supercomputing Center: http://www.psc.edu