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comparison trinityrnaseq.xml @ 1:976e99dd3c2b draft

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New version for Bridges
author nate
date Fri, 23 Sep 2016 10:01:55 -0400
parents d0c258caafaf
children 53b890343b67
comparison
equal deleted inserted replaced
0:d0c258caafaf 1:976e99dd3c2b
1 <tool id="trinity_psc" name="Trinity" version="0.0.1"> 1 <tool id="trinity_psc" name="Trinity" version="0.0.1">
2 2
3 <!-- Written by Jeremy Goecks, now maintained here by bhaas and additional 3 <!-- Written by Jeremy Goecks, now maintained here by bhaas and additional
4 modifications by Nate Coraor --> 4 modifications by Nate Coraor -->
5 <description>(Beta) De novo assembly of RNA-Seq data Using Trinity on PSC's Greenfield</description> 5 <description>(Beta) De novo assembly of RNA-Seq data Using Trinity on PSC's Bridges</description>
6 <requirements> 6 <requirements>
7 <!-- These are versions available as modules on Greenfield --> 7 <!-- These are versions available as modules on Bridges -->
8 <requirement type="package" version="1.1.1">bowtie</requirement> 8 <requirement type="package" version="1.1.2">bowtie</requirement>
9 <requirement type="package" version="1.1">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="2.0.6">trinity</requirement> 11 <requirement type="package" version="5.18.4">perl</requirement>
12 <requirement type="package" version="2.2.0">trinity</requirement>
12 </requirements> 13 </requirements>
13 <command> 14 <command>
14 MEM=`expr "\${GALAXY_SLOTS:-15}" \* 50 - 16` ; 15 MEM=`expr "\${GALAXY_SLOTS:-16}" \* 48 - 16` ;
16
17 workdir=`pwd`;
18 echo "workdir is \$workdir";
19 cd \$LOCAL;
20 echo "Running Trinity from `pwd`";
21
15 Trinity --max_memory "\${MEM}G" 22 Trinity --max_memory "\${MEM}G"
16 --CPU "\${GALAXY_SLOTS:-16}" 23 --CPU "\${GALAXY_SLOTS:-16}"
17 --bflyHeapSpaceMax "\${MEM}G" 24 --bflyHeapSpaceMax "32G"
25 --bflyHeapSpaceInit "2G"
26 --bflyGCThreads "6"
18 27
19 ## Inputs. 28 ## Inputs.
20 #if str($inputs.paired_or_single) == "paired": 29 #if str($inputs.paired_or_single) == "paired":
21 --left $inputs.left_input --right $inputs.right_input 30 --left $inputs.left_input --right $inputs.right_input
22 #if $inputs.left_input.ext == 'fa': 31 #if $inputs.left_input.ext == 'fa':
50 59
51 ## direct to output 60 ## direct to output
52 > $trinity_log 2>&amp;1 61 > $trinity_log 2>&amp;1
53 62
54 ## if Trinity fails, output the end of the log to stderr for Galaxy, and touch the output file for Pulsar 63 ## if Trinity fails, output the end of the log to stderr for Galaxy, and touch the output file for Pulsar
55 || (ec=\$? ; cat $trinity_log >&amp;2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec) 64 || (ec=\$? ; cp -pr . \$workdir; cd \$workdir; cat $trinity_log >&amp;2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec);
65
66 cp -pr . \$workdir;
67 cd \$workdir;
56 68
57 </command> 69 </command>
58 <stdio> 70 <stdio>
59 <exit_code range="1:" level="fatal" description="Program failed" /> 71 <exit_code range="1:" level="fatal" description="Program failed" />
60 <exit_code range=":-1" level="fatal" description="DRM killed job" /> 72 <exit_code range=":-1" level="fatal" description="DRM killed job" />
107 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> 119 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
108 </outputs> 120 </outputs>
109 <tests> 121 <tests>
110 </tests> 122 </tests>
111 <help> 123 <help>
112 .. 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.** 124 .. 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.**
113 125
114 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. 126 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.
115 127
116 .. _Trinity: http://trinityrnaseq.github.io 128 .. _Trinity: http://trinityrnaseq.github.io
117 .. _Pittsburgh Supercomputing Center: http://www.psc.edu 129 .. _Pittsburgh Supercomputing Center: http://www.psc.edu
118 .. _Greenfield: http://www.psc.edu/index.php/resources-for-users/computing-resources/greenfield 130 .. _Bridges: http://www.psc.edu/bridges
119 </help> 131 </help>
120 </tool> 132 </tool>