Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_tarean.xml @ 4:72c028e3e70e draft

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Uploaded
author petr-novak
date Thu, 08 Apr 2021 10:31:53 +0000
parents d1f67a13b70f
children 397394c00bf7
comparison
equal deleted inserted replaced
3:d1f67a13b70f 4:72c028e3e70e
1 <tool id="tarean_dev" name="Tandem Repeat Analyzer" version="2.3.8" > 1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8" >
2 <stdio> 2 <stdio>
3 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 3 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
4 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 4 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
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">imagemagick</requirement> 10 <container type="singularity">shub://repeatexplorer/repex_tarean:0.3.8.dbaa07f</container>
11 <requirement type="package">mafft</requirement> 11 </requirements>
12 <requirement type="package">blast</requirement>
13 <requirement type="package" version="0.9.29">diamond</requirement>
14 <requirement type="package">blast-legacy</requirement>
15 <requirement type="package">r-igraph</requirement>
16 <requirement type="package">r-data.tree</requirement>
17 <requirement type="package">r-stringr</requirement>
18 <requirement type="package">r-r2html</requirement>
19 <requirement type="package">r-hwriter</requirement>
20 <requirement type="package">r-dt</requirement>
21 <requirement type="package">r-scales</requirement>
22 <requirement type="package">r-plotrix</requirement>
23 <requirement type="package">r-png</requirement>
24 <requirement type="package">r-plyr</requirement>
25 <requirement type="package">r-dplyr</requirement>
26 <requirement type="package">r-optparse</requirement>
27 <requirement type="package">r-dbi</requirement>
28 <requirement type="package">r-rsqlite</requirement>
29 <requirement type="package">r-rserve</requirement>
30 <requirement type="package">bioconductor-biostrings</requirement>
31 <requirement type="package" version="2.3.8">repex_tarean_dev</requirement>
32 <requirement type="set_environment">REPEX</requirement>
33 <requirement type="set_environment">REPEX_VERSION</requirement>
34 <requirement type="package" version="0.9.1">pyrserve</requirement>
35 </requirements>
36 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
37 export PYTHONHASHSEED=0; 13 export PYTHONHASHSEED=0;
38 \${REPEX}/seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode 14 seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
39 #if $advanced_options.advanced: 15 #if $advanced_options.advanced:
40 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging 16 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging
41 #if $advanced_options.custom_library.options_custom_library : 17 #if $advanced_options.custom_library.options_custom_library :
42 -d $advanced_options.custom_library.library extra_database 18 -d $advanced_options.custom_library.library extra_database
43 #end if 19 #end if
51 ${FastaFile} >stdout.log 2> stderr.log ; 27 ${FastaFile} >stdout.log 2> stderr.log ;
52 echo "STDOUT CONTENT:" >> ${log} ; 28 echo "STDOUT CONTENT:" >> ${log} ;
53 cat stdout.log >> ${log} ; 29 cat stdout.log >> ${log} ;
54 echo "STDERR CONTENT:" >> ${log} ; 30 echo "STDERR CONTENT:" >> ${log} ;
55 cat stderr.log >> ${log} &amp;&amp; 31 cat stderr.log >> ${log} &amp;&amp;
56 \${REPEX}/stderr_filter.py stderr.log &amp;&amp; 32 /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp;
57 cd tarean_output &amp;&amp; 33 cd tarean_output &amp;&amp;
58 zip -r ${ReportArchive}.zip * &amp;&amp; 34 zip -r ${ReportArchive}.zip * &amp;&amp;
59 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp; 35 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
60 cp index.html ${ReportFile} &amp;&amp; 36 cp index.html ${ReportFile} &amp;&amp;
61 mkdir ${ReportFile.files_path} &amp;&amp; 37 mkdir ${ReportFile.files_path} &amp;&amp;