Mercurial > repos > patrick_chabrier > carboseq_s

comparison carboseqSimulator.xml @ 7:fe6b69ede424 draft

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author patrick_chabrier
date Mon, 01 Jul 2024 11:06:13 +0000
parents 29b8cd5389bf
children 74a8deeedd19
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6:29b8cd5389bf 7:fe6b69ede424
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.5"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.6">
2 <description>To run the CarboSeq simulator</description> 2 <description>To run the CarboSeq simulator</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop-98fae214</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 (env | grep DOCKER_IMAGE) &&
8 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
7 bash -e -c "mkdir output && 9 bash -e -c "mkdir output &&
8 unzip -d input ${input} && 10 unzip -d input ${input} &&
9 mkdir tmp && 11 mkdir tmp &&
10 export TMPDIR="\${PWD}/tmp" && 12 export TMPDIR="\${PWD}/tmp" &&
11 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&& 13 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&&