VRE_RUNNER

#!/bin/bash

###
### Main Executor
###
### Script that validates software dependencies and call VRE_RUNNER.py
###


DEPENDENCIES=("python","Rscript")  # TODO add your software dependencies (e.g. DEPENDENCIES=("Rscript","docker")
PROGNAME="VRE_RUNNER.py"

# Validate dependencies

REALPATH="$(realpath "$0")"
BASEDIR="$(dirname "$REALPATH")"

case "$BASEDIR" in
/*)
  true
  ;;
*)
  BASEDIR="${PWD}/$BASEDIR"
  ;;
esac

for prog in $(echo $DEPENDENCIES | sed "s/,/ /g"); do
  type -a "$prog" >/dev/null
  if [ $? -ne 0 ]; then
    echo "UNCONFIGURED: No $prog executable found" 1>&2
    exit 1
  fi
done

# check R dependencies
Rscript -e 'if (R.Version()$major < 4) stop("Need at least R 4.0")' || exit 1
"$BASEDIR/check_r_package.R" "dataquieR" "1.0.5" || exit 1
"$BASEDIR/check_r_package.R" "openxlsx" "4.2.3" || exit 1
"$BASEDIR/check_r_package.R" "parallelly" "1.25.0" || exit 1


# Run VRE_RUNNER

source "$BASEDIR"/venv/bin/activate
exec python -u "${BASEDIR}"/"${PROGNAME}" "$@"
exit 1