b2r.sh

#!/bin/bash
# https://stackoverflow.com/a/23930212/1801749
read -r -d '' HELP << END
Submit b2r jobs to Slurm
 
Usage:
/path/to/b2r.sh /path/to/input/files/folder
END

echo "parse arguments..."
if [ $# -lt 1 ]; then echo "$HELP"; exit; fi # missing arguments
test -d "$1" || { echo "$1 doesn't exist. Quit."; exit; }
if [ ${1:0:1} != '/' ]; then # relative path
  fullpath=$PWD/$1
else # absolute path
  fullpath=$1
fi

echo "check CSV files in $1..."
njobs=`ls -1 $1/SIS*Raw_*_*.csv 2>/dev/null | wc -l`
if [ $njobs -le 0 ]; then echo "no CSV file in $1. Quit."; exit; fi

echo "process $njobs CSV files..."
for file in `ls -1 $fullpath/SIS*Raw_*_*.csv`; do
  name=$(basename -- $file) # remove path from file name
  # skip processed CSV files
  out=${name%csv}root; if [ -f $fullpath/$out ]; then continue; fi

  log=${name%csv}log; err=${name%csv}err; script=${name%csv}sh
  number=${name##*_}; number=${number%.csv} # get number from file name
  echo "#!/bin/bash" > $script
  echo "root -b -q $PWD/b2r.C'(\"$file\")'" >> $script
  sbatch -J b2r$number -o $log -e $err $script
done

echo "check progress..."
while true; do
  njobs=`squeue | egrep " b2r[0-9]+" | wc -l`
  if [ $njobs -eq 0 ]; then break; fi
  squeue | head -n 1; squeue | egrep " b2r[0-9]+"; sleep 3
done
chmod 664 *.err *.log &>/dev/null
chmod 775 *_*.sh &>/dev/null
chmod 664 *.root &>/dev/null