Mercurial > repos > siwaa > redelac_stics_s

comparison redelacSticsSimulator.bash @ 7:2586f7dbcde1 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e/tools/REDELACSticsSimulator commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e-dirty"
author siwaa
date Mon, 02 Oct 2023 13:51:01 +0000
parents 41f652e6616f
children 65c00476f417
comparison
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6:41f652e6616f 7:2586f7dbcde1
1 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . && 1 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . &&
2 unzip -qq $4 -d TMP && 2 /usr/bin/time -p -o ./bashlog unzip -qq $5 -d TMP &&
3 echo "Step 0, time to unzip the Workspace:" &&
4 echo "====================================" &&
5 cat ./bashlog &&
6 echo "====================================" &&
3 export WSname=$(ls TMP) && 7 export WSname=$(ls TMP) &&
4 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS && 8 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
5 cp $5 JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv && 9 cp $6 JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
6 cd JavaSTICS-1.5.1-STICS-10.0.0 && 10 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
7 Rscript --verbose $3/redelacSticsSimulator.R $1 $2 && 11 /usr/bin/time -p -o ./bashlog Rscript --verbose $4/redelacSticsSimulator.R $1 $2 $3 &&
12 echo "Step 1, time to run the R script:" &&
13 echo "=================================" &&
14 cat ./bashlog &&
15 echo "=================================" &&
16 cd WS &&
17 /usr/bin/time -p -o ./bashlog zip -qq -r analyse_simulations_STICS analyse_simulations_STICS &&
18 echo "Step 2, time to zip the results:" &&
19 echo "================================" &&
20 cat ./bashlog &&
21 echo "================================" &&
22 cp analyse_simulations_STICS.zip $8 &&
23 rm -rf analyse_simulations_STICS &&
24 cd .. &&
8 mv WS $WSname && 25 mv WS $WSname &&
9 zip -qq -r $WSname $WSname && 26 /usr/bin/time -p -o ./bashlog zip -qq -r $WSname $WSname &&
10 cp $WSname.zip $6 && 27 echo "Step 3, time to zip the Workspace:" &&
11 cp results.RData $7 28 echo "==================================" &&
12 29 cat ./bashlog &&
30 echo "==================================" &&
31 cp $WSname.zip $7