Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_full_clustering.xml @ 22:9eee8a12fd8a draft

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author petr-novak
date Mon, 25 Mar 2024 13:04:49 +0000
parents 19a3d199db8f
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21:84106349d4b1 22:9eee8a12fd8a
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.10.1" > 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.10.2" >
2 <stdio> 2 <stdio>
3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" /> 3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" />
4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
5 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 5 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" /> 6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
37 cat stdout.log >> ${log} ; 37 cat stdout.log >> ${log} ;
38 echo "STDERR CONTENT:" >> ${log}; 38 echo "STDERR CONTENT:" >> ${log};
39 cat stderr.log >> ${log} &amp;&amp; 39 cat stderr.log >> ${log} &amp;&amp;
40 /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp; 40 /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp;
41 cd tarean_output &amp;&amp; 41 cd tarean_output &amp;&amp;
42 zip -r ${ReportArchive}.zip * &amp;&amp; 42 zip -fz -r ${ReportArchive}.zip * &amp;&amp;
43 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp; 43 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
44 cp index.html ${ReportFile} &amp;&amp; 44 cp index.html ${ReportFile} &amp;&amp;
45 mkdir -p ${ReportFile.extra_files_path} &amp;&amp; 45 mkdir -p ${ReportFile.extra_files_path} &amp;&amp;
46 cp -r --parents libdir ${ReportFile.extra_files_path} &amp;&amp; 46 cp -r --parents libdir ${ReportFile.extra_files_path} &amp;&amp;
47 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &amp;&amp; 47 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &amp;&amp;