Mercurial > repos > patrick_chabrier > carboseq_s

comparison carboseqSimulator.xml @ 2:bf6c51b72a10 draft

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author siwaa
date Tue, 25 Jun 2024 14:02:45 +0000
parents 8e2dd4aec727
children 40f76111ab6c
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1:8e2dd4aec727 2:bf6c51b72a10
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.1"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.2">
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-695457e0</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop-695457e0</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 bash -e -c "mkdir inputs && 7 bash -e -c "mkdir inputs &&
8 mkdir output && 8 mkdir output &&
9 unzip -d input ${input} && 9 unzip -d input ${input} &&
10 set -a ;source /usr/local/src/myscripts/.env && 10 set -a ;source /usr/local/src/myscripts/.env &&
11 mkdir tmp &&
12 export TMP=$(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}&&
12 mv output/* ${output}" 14 mv output/* ${output}"
13 ]]> 15 ]]>
14 </command> 16 </command>
15 <inputs> 17 <inputs>