Recursively add multiple root data files into one.

combineData.sh

#!/bin/bash

prefix="cascade"

dataDir="data/prometheus/"
subDir=""

postfixes="pid_complete
reco_complete
cascade_ana-0"

tempFile="temp.root"

printHelp() {
    echo "./combineData.sh <subDir> <prefix> [filesAtOnce]"
    echo
    echo "Merging files in directory ${dataDir}<subDir>. Files should start"
    echo "with <prefix>_[0..9]. Optionally, you can choose how many files"
    echo "should be merged at once (default: 1)."
    exit
}

if test "$1" != ""; then
    subDir=$1
else
    printHelp
fi

if test "$2" != ""; then
    prefix=$2
else
    printHelp
fi

filesAtOnce="1"
if test "$3" != ""; then
    if [[ $3 =~ ^[0-9]+$ ]]; then
        filesAtOnce=$3
    fi
fi

cd $dataDir/$subDir
for postfix in $postfixes; do
    files=`ls ${prefix}_*_${postfix}.root`
    filesArray=( $files )
    arraylength=${#filesArray[@]}

    echo
    echo "Merging ${arraylength} files for ${postfix}."

    master="${prefix}__master__${postfix}.root"

    currentEntryList=()
    for (( i = 0; i < ${arraylength}; i+=1));
    do
        currentEntry=${filesArray[0]}
        currentEntryList+=($currentEntry)

        if [[ ${#currentEntryList[@]} -ge $filesAtOnce || $((i+1)) -eq $arraylength ]]; then
            if [[ "$i" -lt $filesAtOnce ]]; then
                echo "hadd -f $master ${currentEntryList[@]}"
                hadd -f $master ${currentEntryList[@]}
            else
                # echo "mv $master 'temp.root'"
                mv $master "temp.root"
                echo "hadd -f $master ${currentEntryList[@]} $tempFile"
                hadd -f $master ${currentEntryList[@]} "temp.root"
            fi

            currentEntryList=()
        fi

        filesArray=( ${filesArray[@]/$currentEntry} )
    done

    if [[ -e $tempFile ]]; then
        rm $tempFile
    fi

    echo
    echo "Merging done. Final file written: ${master}"
    echo
    echo "------------------------------------------"
done

An input-file based version is over here: https://gist.github.com/AndiH/121e3d89fc647fb65338