Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_full_clustering.xml @ 24:adf6673735f7 draft

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author petr-novak
date Wed, 05 Jun 2024 08:47:15 +0000
parents 9eee8a12fd8a
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23:5d6ff2684c5b 24:adf6673735f7
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.10.2" > 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.11.1" >
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">library://repeatexplorer/default/repex_tarean:0.3.10-a11bf65</container> 11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.11-579a65d</container>
12 </requirements> 12 </requirements>
13 <command> 13 <command>
14 export PYTHONHASHSEED=0; 14 export PYTHONHASHSEED=0;
15 export TAREAN_CPU=\$GALAXY_SLOTS; 15 export TAREAN_CPU=\$GALAXY_SLOTS;
16 export TAREAN_MAX_MEM=\$((GALAXY_MEMORY_MB*1024)); 16 export TAREAN_MAX_MEM=\$((GALAXY_MEMORY_MB*1024));