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comparison trinityrnaseq.xml @ 4:f98f80675d60 draft

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Corrected perl module name and improved output handling for better performance from Phil Blood.
author nate
date Fri, 10 Mar 2017 10:42:24 -0500
parents 3d072b99688e
children 1de64ac61b4e
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3:3d072b99688e 4:f98f80675d60
6 <requirements> 6 <requirements>
7 <!-- These are versions available as modules on Bridges --> 7 <!-- These are versions available as modules on Bridges -->
8 <requirement type="package" version="1.1.2">bowtie</requirement> 8 <requirement type="package" version="1.1.2">bowtie</requirement>
9 <requirement type="package" version="1.3">samtools</requirement> 9 <requirement type="package" version="1.3">samtools</requirement>
10 <requirement type="package" version="jre7">java</requirement> 10 <requirement type="package" version="jre7">java</requirement>
11 <requirement type="package" version="5.18.4">perl</requirement> 11 <requirement type="package" version="5.18.4-threads">perl</requirement>
12 <requirement type="package" version="2.2.0">trinity</requirement> 12 <requirement type="package" version="2.2.0">trinity</requirement>
13 </requirements> 13 </requirements>
14 <command> 14 <command>
15 MEM=`expr "\${GALAXY_SLOTS:-16}" \* 48 - 16` ; 15 MEM=`expr "\${GALAXY_SLOTS:-16}" \* 48 - 16` ;
16 16
62 #end if 62 #end if
63 63
64 ## direct to output 64 ## direct to output
65 > $trinity_log 2>&amp;1 65 > $trinity_log 2>&amp;1
66 66
67 ## if Trinity fails, output the end of the log to stderr for Galaxy, and touch the output file for Pulsar 67 ## if Trinity fails, output the end of the log to stderr for Galaxy, and touch the output file for Pulsar
68 || (ec=\$? ; cp -pr . \$workdir; cd \$workdir; cat $trinity_log >&amp;2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec); 68 || (ec=\$? ; cp -p $trinity_log \$workdir; cd \$workdir; cat $trinity_log >&amp;2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec);
69 69
70 cp -pr . \$workdir; 70 mkdir -p \$workdir/trinity_out_dir;
71 cd \$workdir; 71 cp -p trinity_out_dir/Trinity* \$workdir/trinity_out_dir;
72 72 cd \$workdir;
73 </command> 73 </command>
74 <stdio> 74 <stdio>
75 <exit_code range="1:" level="fatal" description="Program failed" /> 75 <exit_code range="1:" level="fatal" description="Program failed" />
76 <exit_code range=":-1" level="fatal" description="DRM killed job" /> 76 <exit_code range=":-1" level="fatal" description="DRM killed job" />
77 </stdio> 77 </stdio>
124 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> 124 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
125 </outputs> 125 </outputs>
126 <tests> 126 <tests>
127 </tests> 127 </tests>
128 <help> 128 <help>
129 .. 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.** 129 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.
130
131 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.
132 130
133 .. _Trinity: http://trinityrnaseq.github.io 131 .. _Trinity: http://trinityrnaseq.github.io
134 .. _Pittsburgh Supercomputing Center: http://www.psc.edu 132 .. _Pittsburgh Supercomputing Center: http://www.psc.edu
135 .. _Bridges: http://www.psc.edu/bridges 133 .. _Bridges: http://www.psc.edu/bridges
136 </help> 134 </help>