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 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/redelacSticsInputGenerator.R $1 $2 $3 &&
echo "Step 1, time to run the R script:" &&
echo "=================================" && 
cat ./bashlog &&
echo "=================================" && 
rm WS/1* &&
mv WS $WSname &&
/usr/bin/time -p -o ./bashlog zip ${13} -q -r $WSname $WSname &&
echo "Step 2, time to zip the Workspace:" &&
echo "==================================" && 
cat ./bashlog &&
echo "==================================" && 
cp $WSname.zip ${12}