Mercurial > repos > nate > trinity_psc
changeset 1:976e99dd3c2b draft
New version for Bridges
| author | nate |
|---|---|
| date | Fri, 23 Sep 2016 10:01:55 -0400 |
| parents | d0c258caafaf |
| children | 53b890343b67 |
| files | trinityrnaseq.xml |
| diffstat | 1 files changed, 22 insertions(+), 10 deletions(-) [+] |
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--- 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>&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 >&2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec) + || (ec=\$? ; cp -pr . \$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; </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>