Mercurial > repos > siwaa > redelac_stics_g

diff redelacSticsInputGenerator.bash @ 10:f707c2fb725b draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e"
author siwaa
date Mon, 02 Oct 2023 13:49:57 +0000
parents 2a6d7d053ba7
children 3db1f57029a7
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line diff
--- a/redelacSticsInputGenerator.bash	Mon Sep 25 16:25:51 2023 +0000
+++ b/redelacSticsInputGenerator.bash	Mon Oct 02 13:49:57 2023 +0000
@@ -6,15 +6,31 @@
 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
-unzip -q $6 -d TMPbis &&
+/usr/bin/time -p -o ./bashlog unzip -q $6 -d TMPbis &&
+echo "Step 0, time to unzip the Workspace:" &&
+echo "====================================" && 
+cat ./bashlog &&
+echo "====================================" && 
 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
 cp $7 JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
 cp $8 JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
 cp $9 JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
 cp ${10} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
-Rscript --verbose $4/redelacSticsInputGenerator.R $1 $2 $3 &&
+if [[ "$11" != "noAdditionalPlantOrConfig" ]]
+then
+   unzip -o ${10}
+fi
+/usr/bin/time -p -o ./bashlog Rscript --verbose $4/redelacSticsInputGenerator.R $1 $2 $3 &&
+echo "Step 1, time to run the R script:" &&
+echo "=================================" && 
+cat ./bashlog &&
+echo "=================================" && 
 rm WS/1* &&
 mv WS $WSname &&
-zip -q -r $WSname $WSname &&
-cp $WSname.zip ${11}
+/usr/bin/time -p -o ./bashlog zip -q -r $WSname $WSname &&
+echo "Step 2, time to zip the Workspace:" &&
+echo "==================================" && 
+cat ./bashlog &&
+echo "==================================" && 
+cp $WSname.zip ${12}