Mercurial > repos > petr-novak > repeatexplorer2_testing

changeset 18:4308d3e572ee draft

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Uploaded
author petr-novak
date Thu, 01 Feb 2024 09:43:43 +0000
parents 5cca2c9aa4ad
children 3d0ba5734776
files repex_full_clustering.xml
diffstat 1 files changed, 2 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/repex_full_clustering.xml	Mon Jan 29 15:58:25 2024 +0000
+++ b/repex_full_clustering.xml	Thu Feb 01 09:43:43 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.4" >
+<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.9.1" >
     <stdio>
       <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" />
       <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
@@ -8,14 +8,12 @@
     </stdio>
     <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description>
    <requirements>
-     <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container>
+     <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.9-579a65d</container>
    </requirements>
 <command>
       export PYTHONHASHSEED=0;
       export TAREAN_CPU=\$GALAXY_SLOTS;
       export TAREAN_MAX_MEM=\$((GALAXY_MEMORY_MB*1024));
-      echo \$GALAXY_MEMORY_MB;
-      echo "TAREAN_MAX_MEM=\$TAREAN_MAX_MEM" ;
       seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
 
       #if $advanced_options.advanced: