#!/bin/bash
set -e

pkg=tigr-glimmer

if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi

cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"
gunzip -r *

echo 'Begin Test'
/usr/lib/tigr-glimmer/long-orfs  -n -t 1.15 example.fa test1.longorfs
/usr/lib/tigr-glimmer/extract -t example.fa test1.longorfs > test1.train
/usr/lib/tigr-glimmer/build-icm -r test1.icm < test1.train
/usr/lib/tigr-glimmer/glimmer3 example.fa test1.icm test1
echo '---------------Passed!----------------------------'