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comparison insilicow.xml @ 2:2722892ff716 draft

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"planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit d91a7371e51377d199865ad1c6d5b70afbf2c414"
author siwaa
date Wed, 28 May 2025 08:37:22 +0000
parents f2840b46b353
children 3fe3e1e6a40b
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1:f2840b46b353 2:2722892ff716
1 <tool id="inSiliCow" name="inSiliCow" version="1.0.1"> 1 <tool id="inSiliCow" name="inSiliCow" version="1.0.2">
2 <description>to run the inSiliCow simulator</description> 2 <description>to run the inSiliCow simulator</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/insilicow/insilicow-container:6d9cbffcf24d3af29b244ea3543c53b4298077de</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/insilicow/insilicow-container:ea8a24d5d56c3d12d53303db6d47ef77382c843f</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"> 6 <command detect_errors="aggressive">
7 <![CDATA[ 7 <![CDATA[
8 echo "=================" && 8 echo "=================" &&
9 env && 9 env &&
10 echo "=================" && 10 echo "=================" &&
11 cp -r /insilicow-simulator . && 11 cp -r /insilicow-simulator . &&
12 cd insilicow-simulator/scripts && 12 cd insilicow-simulator/scripts &&
13 cp $__tool_directory__/inSiliCow-run.sh . &&
14 cp $__tool_directory__/inSiliCow-post.sh . &&
15 rm -rf examples/e* &&
16 unzip -d tmp ${in} && 13 unzip -d tmp ${in} &&
17 configDir=\$(ls -1 tmp) && 14 configDir=\$(ls -1 tmp) &&
18 mv tmp/* examples && 15 find examples/* -type d | xargs rm -R &&
16 mv -f tmp/* examples &&
19 pwd && ls && echo \$configDir && 17 pwd && ls && echo \$configDir &&
18 head -n -3 ./inSiliCow-run.sh > tmpFile &&
19 mv tmpFile ./inSiliCow-run.sh &&
20 chmod u+x ./inSiliCow-run.sh && 20 chmod u+x ./inSiliCow-run.sh &&
21 TERM="xterm-256color" ./inSiliCow-run.sh \$configDir && 21 TERM="xterm-256color" ./inSiliCow-run.sh \$configDir &&
22 cd out && 22 cd out &&
23 zip -r j* * && 23 zip -r j* * &&
24 mv *.zip ${out} 24 mv *.zip ${out}