Mercurial > repos > patrick_chabrier > carboseq_s

comparison carboseqSimulator.xml @ 5:4c1a7c22e770 draft

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author siwaa
date Wed, 26 Jun 2024 06:43:43 +0000
parents b5a6c2d3e5e7
children 29b8cd5389bf
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4:b5a6c2d3e5e7 5:4c1a7c22e770
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.3"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.4">
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 output &&
8 mkdir output &&
9 unzip -d input ${input} && 8 unzip -d input ${input} &&
10 set -a ;source /usr/local/src/myscripts/.env &&
11 mkdir tmp && 9 mkdir tmp &&
12 export TMP=\$(realpath -s tmp) && 10 export TMPDIR="\${PWD}/tmp" &&
13 pwd &&
14 ls &&
15 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}&& 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}&&
16 mv output/* ${output}" 12 mv output/* ${output}"
17 ]]> 13 ]]>
18 </command> 14 </command>
19 <inputs> 15 <inputs>