Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_tarean.xml @ 23:5d6ff2684c5b draft

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Uploaded
author petr-novak
date Mon, 25 Mar 2024 13:05:26 +0000
parents 84106349d4b1
children a27646c27090
comparison
equal deleted inserted replaced
22:9eee8a12fd8a 23:5d6ff2684c5b
1 <tool id="tarean" name="Tandem Repeat Analyzer (TAREAN)" version="2.3.10.1" > 1 <tool id="tarean" name="Tandem Repeat Analyzer (TAREAN)" version="2.3.10.2" >
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" />
31 cat stdout.log >> ${log} ; 31 cat stdout.log >> ${log} ;
32 echo "STDERR CONTENT:" >> ${log} ; 32 echo "STDERR CONTENT:" >> ${log} ;
33 cat stderr.log >> ${log} &amp;&amp; 33 cat stderr.log >> ${log} &amp;&amp;
34 /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp; 34 /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp;
35 cd tarean_output &amp;&amp; 35 cd tarean_output &amp;&amp;
36 zip -r ${ReportArchive}.zip * &amp;&amp; 36 zip -fz -r ${ReportArchive}.zip * &amp;&amp;
37 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp; 37 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
38 cp index.html ${ReportFile} &amp;&amp; 38 cp index.html ${ReportFile} &amp;&amp;
39 mkdir -p ${ReportFile.extra_files_path} &amp;&amp; 39 mkdir -p ${ReportFile.extra_files_path} &amp;&amp;
40 cp -r --parents libdir ${ReportFile.extra_files_path} &amp;&amp; 40 cp -r --parents libdir ${ReportFile.extra_files_path} &amp;&amp;
41 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &amp;&amp; 41 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &amp;&amp;