Mercurial > repos > patrick_chabrier > carboseq_s

comparison carboseqSimulator.xml @ 3:40f76111ab6c draft

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author siwaa
date Tue, 25 Jun 2024 14:58:11 +0000
parents bf6c51b72a10
children b5a6c2d3e5e7
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2:bf6c51b72a10 3:40f76111ab6c
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.2"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.3">
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 ${input} &&
10 set -a ;source /usr/local/src/myscripts/.env && 10 set -a ;source /usr/local/src/myscripts/.env &&
11 mkdir tmp && 11 mkdir tmp &&
12 export TMP=$(pwd)/tmp && 12 export TMP=\$(realpath -s 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}&& 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}&&
14 mv output/* ${output}" 14 mv output/* ${output}"
15 ]]> 15 ]]>
16 </command> 16 </command>
17 <inputs> 17 <inputs>