#!/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!----------------------------'