run hermsk

hermsk.sh

#!/bin/bash

function die() {
  echo "Error: ${@}!" >&2
  exit 1
}

: "${INPUT_DATA_PATH:=~/develop/hermsk/mpauli/}"

input=
if [[ -f "$1" ]]; then
  if [[ "$1" =~ ^/ ]]; then # absolute
    input="$1"
  else
    input="$(pwd)/$1"
  fi
else
  input="${INPUT_DATA_PATH}$1.dat"
fi

[[ -f "$input" ]] || die "No input '$input' ('$1') found"

echo "Input: $input"

outpath=$(pwd)
echo "Out: $outpath"

resprefix=$(basename "$input")
resprefix=${resprefix%.dat}
echo "Result prefix: $resprefix"

: "${hermsk:=$(pwd)/hermsk}"

[[ -x "$hermsk" ]] || die "No executable '$hermsk' found"

echo "Executable: $hermsk"

tmp=$(mktemp -d) || die "tmpdir"
trap "rm -rf -- '$tmp'" EXIT

if cd "$tmp" && ln -s "$input" 'input.dat' && "$hermsk"; then
  for i in *.out; do
    mv -- "$i" "$outpath/$resprefix-$i"
  done
else
  trap - EXIT
  echo "Error while executing hermsk!  Tmp dir: $tmp"
  exit 1
fi