add script to convert from DL2 to DL3

bash_scripts/run_dl2_to_dl3.sh

+#!/bin/bash
+#Script to Run the dl3_tool over a set of DL2 REAL data.
+#Change paths according to your system
+
+#Some variables for retrieving the input files
+DATES=( 20201120 ) #Dates to analyze
+SOURCE="Crab" #name of source
+SRCRA="83.63308333deg" #source ra
+SRCDEC="22.0145deg" #source dec
+VERSION="v0.9.2" #lstchain version
+CLEANING="tailcut84" #tailcut
+INPUT_DIR="/fefs/aswg/workspace/alice.donini/Analysis/data/" #Base directory where to find the dl2 data
+
+#Variables for the output directory
+#SUFFIX="tuned_dynamic_cleaning_source_independent" #Optional suffix to add to a folder
+CUT="standard" #Name of the cut applied to data ( nocuts, softcut, hardcut, hardestcut )
+
+#Configuration file to be used if not standard cut
+#CONFIG="/fefs/aswg/workspace/alice.donini/Analysis/config/config_dl3_tool${CUT}.json"
+
+#IRF file
+IRF="/fefs/aswg/workspace/alice.donini/Analysis/data/IRF/irf_40deg.fits.gz"
+
+#Script (in ./cta-lstchain/tools/)
+SCRIPT="/fefs/aswg/workspace/alice.donini/Software/cta-lstchain/lstchain/tools/lstchain_create_dl3_file.py"
+
+for date in "${DATES[@]}" #Run over dates
+do
+    #Define and create an output path for each date
+    OUTPUT_PATH="/fefs/aswg/workspace/alice.donini/Analysis/data/DL3/$SOURCE/$date/$VERSION/$CLEANING"
+    `mkdir -p $OUTPUT_PATH`
+
+    FILES=`ls ${INPUT_DIR}/DL2/$SOURCE/${date}/${VERSION}/${CLEANING}/*.h5`
+    # Run over the merged run files
+    mkdir -p jobs/dl3/${date}
+    for f in $FILES
+    do
+        b=$(basename $f)
+        run=${b:13:-3}
+        if [[ $run != *"."* ]]; then
+            FILE=${INPUT_DIR}/DL2/${SOURCE}/${date}/${VERSION}/${CLEANING}/dl2_LST-1.Run$run.h5
+            #Execute the script. You can remove the "srun --mem=20g -o out.txt" part if you don't want to use the IT cluster
+            #srun --mem=20g -o out.txt python $SCRIPT -d $FILE -o $OUTPUT_PATH --input-irf $IRF --source-name $SRCNAME --source-ra $SRCRA --source-dec $SRCDEC --config $CONFIG --overwrite &
+            echo "File $b"
+            rm -rf jobs/dl3/${date}/run_dl3_${run}${CUT}.sh
+
+            echo "#!/bin/bash
+#SBATCH -N 3
+#SBATCH --mem 100000
+ulimit -l unlimited
+ulimit -s unlimited
+ulimit -a
+
+            python $SCRIPT -d $FILE -o $OUTPUT_PATH --input-irf $IRF --source-name $SOURCE --source-ra $SRCRA --source-dec $SRCDEC --overwrite " >> jobs/dl3/${date}/run_dl3_${run}${CUT}.sh
+            # python $SCRIPT -d $FILE -o $OUTPUT_PATH --input-irf $IRF --source-name $SOURCE --source-ra $SRCRA --source-dec $SRCDEC --config $CONFIG --overwrite " >> jobs/dl3/${date}/run_dl3_${run}${CUT}.sh
+            chmod gu+x jobs/dl3/${date}/run_dl3_${run}${CUT}.sh
+            sbatch jobs/dl3/${date}/run_dl3_${run}${CUT}.sh
+        fi
+    done
+done