run_jobs.sh

#!/bin/bash
#mkdir -p /output/$jName/$fileName/$jNumber
if [ -z "$AZURE_INPUT_DATA_URI" ]
then
    echo "AZURE_DATA_URI is given. Starting downloading data from $AZURE_INPUT_DATA_URI..."
    azcopy cp "$AZURE_INPUT_DATA_URI" "/sample" --recursive
fi

CN=$((fileName*1000))
FN="pythia8_Geant4_10.0_withCharmandBeauty${CN}_mu.root"
#source $(alienv printenv FairShip/latest)
alienv -w /sw setenv  FairShip/latest  -c /bin/bash  -c "python \$FAIRSHIP/macro/run_simScript.py   $opts --MuonBack --sameSeed 1 --seed 1 -f /sample/$FN  --nEvents $nEvents  --firstEvent $mfirstEvent --output /tmp/$jName/$fileName/$jNumber  --muShieldDesign $muShieldDesign"
alienv -w /sw setenv  FairShip/latest  -c /bin/bash -c "python \$FAIRSHIP/macro/ShipReco.py -g /tmp/$jName/$fileName/$jNumber/geofile_full.conical.MuonBack-TGeant4.root -f /tmp/$jName/$fileName/$jNumber/ship.conical.MuonBack-TGeant4.root"
mv ship.conical.MuonBack-TGeant4_rec.root /tmp/$jName/$fileName/$jNumber/
#cp /tmp/$jName/$fileName/$jNumber/*  /output #/$jName/$fileName/$jNumber/

if [ ! -z "$AZURE_OUTPUT_DATA_URI" ]
then
    echo "Starting uploading results to $AZURE_OUTPUT_DATA_URI..."
    azcopy cp "/tmp/$jName/$fileName/$jNumber/*" "$AZURE_OUTPUT_DATA_URI" --recursive
else
    echo "AZURE_OUTPUT_DATA_URI wasn't given given"
fi