Mercurial > repos > petr-novak > repeatexplorer2_testing
comparison repex_full_clustering.xml @ 22:9eee8a12fd8a draft
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author | petr-novak |
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date | Mon, 25 Mar 2024 13:04:49 +0000 |
parents | 19a3d199db8f |
children | adf6673735f7 |
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21:84106349d4b1 | 22:9eee8a12fd8a |
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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} && | 39 cat stderr.log >> ${log} && |
40 /opt/repex_tarean/stderr_filter.py stderr.log && | 40 /opt/repex_tarean/stderr_filter.py stderr.log && |
41 cd tarean_output && | 41 cd tarean_output && |
42 zip -r ${ReportArchive}.zip * && | 42 zip -fz -r ${ReportArchive}.zip * && |
43 mv ${ReportArchive}.zip ${ReportArchive} && | 43 mv ${ReportArchive}.zip ${ReportArchive} && |
44 cp index.html ${ReportFile} && | 44 cp index.html ${ReportFile} && |
45 mkdir -p ${ReportFile.extra_files_path} && | 45 mkdir -p ${ReportFile.extra_files_path} && |
46 cp -r --parents libdir ${ReportFile.extra_files_path} && | 46 cp -r --parents libdir ${ReportFile.extra_files_path} && |
47 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} && | 47 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} && |