| Previous changeset 3:3d072b99688e (2016-09-26) Next changeset 5:1de64ac61b4e (2017-05-04) |
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Commit message:
Corrected perl module name and improved output handling for better performance from Phil Blood. |
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modified:
trinityrnaseq.xml |
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| 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 |
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| @@ -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>&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 >&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 >&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 |