Mercurial > repos > petr-novak > repeatexplorer2_testing
comparison repex_full_clustering.xml @ 6:4b3af335dca8 draft
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author | petr-novak |
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date | Wed, 14 Apr 2021 06:20:12 +0000 |
parents | 397394c00bf7 |
children | ffe53359f758 |
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5:397394c00bf7 | 6:4b3af335dca8 |
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1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8" > | 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="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" /> |
7 <exit_code range="1:" level="fatal" description="Error" /> | 7 <exit_code range="1:" level="fatal" description="Error" /> |
8 </stdio> | 8 </stdio> |
9 <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description> | 9 <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description> |
10 <requirements> | 10 <requirements> |
11 <container type="singularity">shub://repeatexplorer/repex_tarean:0.3.8.dbaa07f</container> | 11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container> |
12 </requirements> | 12 </requirements> |
13 <command> | 13 <command> |
14 export PYTHONHASHSEED=0; | 14 export PYTHONHASHSEED=0; |
15 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon | 15 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon |
16 | 16 |