Mercurial > repos > patrick_chabrier > carboseq_s

comparison carboseqSimulator.xml @ 8:74a8deeedd19 draft

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author patrick_chabrier
date Thu, 04 Jul 2024 14:15:56 +0000
parents fe6b69ede424
children 32bda6e69c5a
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7:fe6b69ede424 8:74a8deeedd19
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.6"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.7">
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</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 (java -Dquarkus.http.port=8282 -jar $__tool_directory__/semantifier.jar &) &&
8 env &&
7 (env | grep DOCKER_IMAGE) && 9 (env | grep DOCKER_IMAGE) &&
8 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) && 10 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
9 bash -e -c "mkdir output && 11 bash -e -c "mkdir output &&
10 unzip -d input ${input} && 12 unzip -d input ${input} &&
11 mkdir tmp && 13 mkdir tmp &&
12 export TMPDIR="\${PWD}/tmp" && 14 export TMPDIR="\${PWD}/tmp" &&
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}&& 15 Rscript $__tool_directory__/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&&
14 mv output/* ${output}" 16 mv output/* ${output}"
15 ]]> 17 ]]>
16 </command> 18 </command>
17 <inputs> 19 <inputs>
18 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/> 20 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>