--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/redelacSticsTool.bash	Tue Feb 06 09:21:00 2024 +0000
@@ -0,0 +1,50 @@
+cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . &&
+rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
+cp -r $4/config JavaSTICS-1.5.1-STICS-10.0.0 &&
+unzip -q $5 -d TMP &&
+export WSname=$(ls TMP) &&
+mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
+cp ${17} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
+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 &&
+/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 ${10} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
+cd JavaSTICS-1.5.1-STICS-10.0.0 &&
+(if [ "${11}" != "noAdditionalPlantOrConfig" ];
+ then
+   unzip -q -o ${11}
+fi) &&
+/usr/bin/time -p -o ./bashlog Rscript --verbose $4/redelacSticsTool.R $1 $2 $3 ${15} &&
+echo "Step 1, time to run the R script:" &&
+echo "=================================" && 
+cat ./bashlog &&
+echo "=================================" &&
+cd WS &&
+#/usr/bin/time -p -o ./bashlog zip ${13} -qq -r analyse_simulations_STICS analyse_simulations_STICS &&
+/usr/bin/time -p -o ./bashlog 7z a -tzip -mx=1 -mmt=$3 analyse_simulations_STICS analyse_simulations_STICS &&
+echo "Step 2, time to zip the results:" &&
+echo "================================" && 
+cat ./bashlog &&
+echo "================================" && 
+cp analyse_simulations_STICS.zip ${16} &&
+rm -rf analyse_simulations_STICS &&
+cd .. &&
+(if [ "${14}" != "no" ];
+  then  
+(cd WS && ls | grep -e '^[0-9]*\.[0-9]*$' | xargs -i rm {}) &&
+mv WS $WSname &&
+/usr/bin/time -p -o ./bashlog zip ${13} -y -q -r $WSname $WSname &&
+echo "Step 2, time to zip the Workspace:" &&
+echo "==================================" && 
+cat ./bashlog &&
+echo "==================================" && 
+cp $WSname.zip ${12}
+fi)