Mercurial > repos > nate > trinity_psc
comparison trinityrnaseq.xml @ 4:f98f80675d60 draft
Corrected perl module name and improved output handling for better performance from Phil Blood.
author | nate |
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date | Fri, 10 Mar 2017 10:42:24 -0500 |
parents | 3d072b99688e |
children | 1de64ac61b4e |
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3:3d072b99688e | 4:f98f80675d60 |
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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>&1 | 65 > $trinity_log 2>&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 >&2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec); | 68 || (ec=\$? ; cp -p $trinity_log \$workdir; cd \$workdir; cat $trinity_log >&2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec); |
69 | 69 |
70 cp -pr . \$workdir; | 70 mkdir -p \$workdir/trinity_out_dir; |
71 cd \$workdir; | 71 cp -p trinity_out_dir/Trinity* \$workdir/trinity_out_dir; |
72 | 72 cd \$workdir; |
73 </command> | 73 </command> |
74 <stdio> | 74 <stdio> |
75 <exit_code range="1:" level="fatal" description="Program failed" /> | 75 <exit_code range="1:" level="fatal" description="Program failed" /> |
76 <exit_code range=":-1" level="fatal" description="DRM killed job" /> | 76 <exit_code range=":-1" level="fatal" description="DRM killed job" /> |
77 </stdio> | 77 </stdio> |
124 <data format="fasta" name="assembled_transcripts" label="${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> |