Mercurial > repos > petr-novak > repeatexplorer2_cerit

comparison repex_full_clustering.xml @ 7:919b0e127350 draft

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author petr-novak
date Wed, 22 May 2024 11:48:16 +0000
parents ed5a72d4693d
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6:ed5a72d4693d 7:919b0e127350
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.1" > 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.2" >
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" />
60 cat stdout.log >> ${log} ; 60 cat stdout.log >> ${log} ;
61 echo "STDERR CONTENT:" >> ${log}; 61 echo "STDERR CONTENT:" >> ${log};
62 cat stderr.log >> ${log} &amp;&amp; 62 cat stderr.log >> ${log} &amp;&amp;
63 \${REPEX}/stderr_filter.py stderr.log &amp;&amp; 63 \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
64 cd tarean_output &amp;&amp; 64 cd tarean_output &amp;&amp;
65 zip -r ${ReportArchive}.zip * &amp;&amp; 65 zip -fz -r ${ReportArchive}.zip * &amp;&amp;
66 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp; 66 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
67 cp index.html ${ReportFile} &amp;&amp; 67 cp index.html ${ReportFile} &amp;&amp;
68 mkdir ${ReportFile.files_path} &amp;&amp; 68 mkdir ${ReportFile.files_path} &amp;&amp;
69 cp -r --parents libdir ${ReportFile.files_path} &amp;&amp; 69 cp -r --parents libdir ${ReportFile.files_path} &amp;&amp;
70 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp; 70 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp;