My configure.ac recipe for the proper parallel is this, setting logs_all to the GNU parallel version.

    dnl GNU parallel, skip the old non-perl version from moreutils so far
    AC_CHECK_PROGS([PARALLEL], [parallel])
    logs_all=logs-all-serial.sh.in
    if test -n "$PARALLEL"; then
      AC_MSG_CHECKING([PARALLEL version])
      parallel_version=`$PARALLEL --version 2>&1 | head -n1 | cut -c14-`
      case "$parallel_version" in
        [0-9]*) AC_MSG_RESULT([$parallel_version])
                logs_all=logs-all-parallel.sh.in
                ;;
        *invalid*)
                PARALLEL=
                parallel_version="skip old moreutils version, need GNU parallel"
      esac
      AC_MSG_RESULT([$parallel_version])
    fi
    AM_CONDITIONAL([HAVE_PARALLEL], [test -n "$PARALLEL"])