cronjob_Galaxy_Array.sh

#!/bin/bash -l
                                
conda activate root_env
                              
echo "Running environment at ${CONDA_PREFIX}"

#if [-z "$(ls -A /data/cmsdaq/DimensionBench/Arrays/ArrayData)" ] && echo "Not Empty" || echo "Empty"
#if [ -z "$(ls -A /data/cmsdaq/DimensionBench/Arrays/ArrayData)" ]

#begin=$(date +%s) 
begin=$SECONDS

if [ -z "$(ls -A /data/cmsdaq/DimensionBench/Arrays/ArrayData_tmp)" ]


then
   echo "++++++++++++++++++++++++++++++"
   echo "No raw data in this directory"
   echo "++++++++++++++++++++++++++++++"

else
   echo "+++++++++++++++++++++++++++++++"
   echo "New raw data in this directory"
   echo "+++++++++++++++++++++++++++++++"


# Added this part to move files from ArrayData_tmp to ArrayData and run cronjob smoothly 


for file in /data/cmsdaq/DimensionBench/Arrays/ArrayData_tmp/*-*.TXT; do

    mv "$file" "/data/cmsdaq/DimensionBench/Arrays/ArrayData/$(basename "$file")"
    echo "+++++++++++++++++++++++++++++++++++++++++++++++"
    echo "$file moved to ArrayData directory!"
    echo "Executing Galaxy analysis code ..." 
    echo "+++++++++++++++++++++++++++++++++++++++++++++++"


cd /home/cmsdaq/GalaxyAnalysis/



echo "++++++++++++++++++++++++++++++++++++"
echo " Adding Run Number to raw data file"
echo "++++++++++++++++++++++++++++++++++++"


python3 AddRunNumb-Galaxy-Array.py

echo "++++++++++++++++++++++++++++++"
echo " Starting LYSO Array Analysis"
echo "++++++++++++++++++++++++++++++"


python3 runAll_Galaxy_Array.py --inputdir /data/cmsdaq/DimensionBench/Arrays/ArrayData/

#end=$(date +%s)

#tottime=$(expr $end - $begin)

tottime=$(($SECONDS - $begin))

echo "+++++++++++++++++++++++++++++++++++++++++++"
echo "Execution time for 1 LYSO Array is: $(($tottime/60)) min $(($tottime%60)) sec"
echo "+++++++++++++++++++++++++++++++++++++++++++"

done

conda deactivate
cd ~/


fi