Mercurial > repos > siwaa > redelac_stics_t

comparison redelacSticsTool.bash @ 0:7f8f474a7bd7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
author siwaa
date Tue, 06 Feb 2024 09:21:00 +0000
parents
children aa575691d6f0
comparison
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-1:000000000000 0:7f8f474a7bd7
1 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . &&
2 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
3 cp -r $4/config JavaSTICS-1.5.1-STICS-10.0.0 &&
4 unzip -q $5 -d TMP &&
5 export WSname=$(ls TMP) &&
6 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
7 cp ${17} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
8 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
9 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
10 /usr/bin/time -p -o ./bashlog unzip -q $6 -d TMPbis &&
11 echo "Step 0, time to unzip the Workspace:" &&
12 echo "====================================" &&
13 cat ./bashlog &&
14 echo "====================================" &&
15 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
16 cp $7 JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
17 cp $8 JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
18 cp $9 JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
19 cp ${10} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
20 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
21 (if [ "${11}" != "noAdditionalPlantOrConfig" ];
22 then
23 unzip -q -o ${11}
24 fi) &&
25 /usr/bin/time -p -o ./bashlog Rscript --verbose $4/redelacSticsTool.R $1 $2 $3 ${15} &&
26 echo "Step 1, time to run the R script:" &&
27 echo "=================================" &&
28 cat ./bashlog &&
29 echo "=================================" &&
30 cd WS &&
31 #/usr/bin/time -p -o ./bashlog zip ${13} -qq -r analyse_simulations_STICS analyse_simulations_STICS &&
32 /usr/bin/time -p -o ./bashlog 7z a -tzip -mx=1 -mmt=$3 analyse_simulations_STICS analyse_simulations_STICS &&
33 echo "Step 2, time to zip the results:" &&
34 echo "================================" &&
35 cat ./bashlog &&
36 echo "================================" &&
37 cp analyse_simulations_STICS.zip ${16} &&
38 rm -rf analyse_simulations_STICS &&
39 cd .. &&
40 (if [ "${14}" != "no" ];
41 then
42 (cd WS && ls | grep -e '^[0-9]*\.[0-9]*$' | xargs -i rm {}) &&
43 mv WS $WSname &&
44 /usr/bin/time -p -o ./bashlog zip ${13} -y -q -r $WSname $WSname &&
45 echo "Step 2, time to zip the Workspace:" &&
46 echo "==================================" &&
47 cat ./bashlog &&
48 echo "==================================" &&
49 cp $WSname.zip ${12}
50 fi)