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comparison repex_tarean.xml @ 23:bb426ce3c12b draft default tip

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author petrn
date Tue, 07 Jan 2020 13:38:54 +0000
parents 0ab0aad9e106
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22:5da81c4ff67e 23:bb426ce3c12b
5 <regex match="warning" source="stderr" level="warning" description="Unknown warning" /> 5 <regex match="warning" source="stderr" level="warning" description="Unknown warning" />
6 <exit_code range="1:" level="fatal" description="Error" /> 6 <exit_code range="1:" level="fatal" description="Error" />
7 </stdio> 7 </stdio>
8 <description>Identification of genomic tandem repeats from NGS data</description> 8 <description>Identification of genomic tandem repeats from NGS data</description>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="0.9.1">pyrserve</requirement> 10 <requirement type="package">imagemagick</requirement>
11 <requirement type="package" version="3.7.4">python</requirement>
12 <requirement type="package">last</requirement>
13 <requirement type="package">mafft</requirement> 11 <requirement type="package">mafft</requirement>
14 <requirement type="package">imagemagick</requirement>
15 <requirement type="package">blast</requirement> 12 <requirement type="package">blast</requirement>
16 <requirement type="package">diamond</requirement> 13 <requirement type="package">diamond</requirement>
17 <requirement type="package">blast-legacy</requirement> 14 <requirement type="package">blast-legacy</requirement>
18 <requirement type="package">r-igraph</requirement> 15 <requirement type="package">r-igraph</requirement>
19 <requirement type="package">r-data.tree</requirement> 16 <requirement type="package">r-data.tree</requirement>
29 <requirement type="package">r-optparse</requirement> 26 <requirement type="package">r-optparse</requirement>
30 <requirement type="package">r-dbi</requirement> 27 <requirement type="package">r-dbi</requirement>
31 <requirement type="package">r-rsqlite</requirement> 28 <requirement type="package">r-rsqlite</requirement>
32 <requirement type="package">r-rserve</requirement> 29 <requirement type="package">r-rserve</requirement>
33 <requirement type="package">bioconductor-biostrings</requirement> 30 <requirement type="package">bioconductor-biostrings</requirement>
34 <requirement type="package" version="1.0">repex_tarean</requirement> 31 <requirement type="package" version="1.1">repex_tarean</requirement>
35 <requirement type="set_environment">REPEX</requirement> 32 <requirement type="set_environment">REPEX</requirement>
33 <requirement type="package" version="0.9.1">pyrserve</requirement>
36 </requirements> 34 </requirements>
37 <command detect_errors="exit_code"> 35 <command detect_errors="exit_code">
38 export PYTHONHASHSEED=0; 36 export PYTHONHASHSEED=0;
39 \${REPEX}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode 37 \${REPEX}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
40 #if $advanced_options.advanced: 38 #if $advanced_options.advanced:
52 ${FastaFile} >stdout.log 2> stderr.log ; 50 ${FastaFile} >stdout.log 2> stderr.log ;
53 echo "STDOUT CONTENT:" >> ${log} ; 51 echo "STDOUT CONTENT:" >> ${log} ;
54 cat stdout.log >> ${log} ; 52 cat stdout.log >> ${log} ;
55 echo "STDERR CONTENT:" >> ${log} ; 53 echo "STDERR CONTENT:" >> ${log} ;
56 cat stderr.log >> ${log} &amp;&amp; 54 cat stderr.log >> ${log} &amp;&amp;
57 ${__tool_directory__}/stderr_filter.py stderr.log &amp;&amp; 55 \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
58 cd tarean_output &amp;&amp; 56 cd tarean_output &amp;&amp;
59 zip -r ${ReportArchive}.zip * &amp;&amp; 57 zip -r ${ReportArchive}.zip * &amp;&amp;
60 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp; 58 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
61 cp index.html ${ReportFile} &amp;&amp; 59 cp index.html ${ReportFile} &amp;&amp;
62 mkdir ${ReportFile.files_path} &amp;&amp; 60 mkdir ${ReportFile.files_path} &amp;&amp;