Mercurial > repos > siwaa > carboseq_s

comparison carboseqSimulator.xml @ 13:9ad79c2d8e0b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/75b22cbc75bbd0c301eabef3a734ca47468bb47e/toos/CarboSeqSimulator commit 75b22cbc75bbd0c301eabef3a734ca47468bb47e-dirty"
author siwaa
date Thu, 19 Sep 2024 17:57:10 +0000
parents 7e43dc776bda
children de71663fbce4
comparison
equal deleted inserted replaced
12:7e43dc776bda 13:9ad79c2d8e0b
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.16"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.16">
2 <description>To run the CarboSeq simulator</description> 2 <description>To run the CarboSeq simulator</description>
3 <environment_variables>
4 <environment_variable name="TMPDIR">\$(realpath -s tmp)</environment_variable>
5 </environment_variables>
6 <requirements> 3 <requirements>
7 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container>
8 </requirements> 5 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
10 (env | grep DOCKER_IMAGE) && 7 (env | grep DOCKER_IMAGE) &&
11 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) && 8 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
12 bash -e -c "mkdir tmp && 9 export "TMPDIR=\$(realpath -s tmp)" &&
10 bash -e -c "
11 echo \$TMPDIR &&
12 mkdir tmp &&
13 mkdir output && 13 mkdir output &&
14 unzip -d input ${input} && 14 unzip -d input ${input} &&
15 cp /usr/local/src/myscripts/semantifier.jar . && 15 cp /usr/local/src/myscripts/semantifier.jar . &&
16 cp /usr/local/src/myscripts/start_server.sh . && 16 cp /usr/local/src/myscripts/start_server.sh . &&
17 cp -r /usr/local/src/myscripts/config_mappers . && 17 cp -r /usr/local/src/myscripts/config_mappers . &&