#!/bin/bash
set -e

pkg=logol
CUR_DIR=`pwd`

export LC_ALL=C.UTF-8
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 -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"
mkdir -p ${AUTOPKGTEST_TMP}/work
cp /etc/logol/logol.properties .
cp /usr/share/logol/log4j.properties .
export LOGOL_LOG4J=${AUTOPKGTEST_TMP}/log4j.properties
sed -i 's;workingDir=/tmp/;workingDir='${AUTOPKGTEST_TMP}'/work/;' logol.properties
sed -i 's;dir.result=/var/lib/logol/results/;dir.result='${AUTOPKGTEST_TMP}'/work/;' logol.properties
sed -i 's;/var/log/logol/logol.log;'${AUTOPKGTEST_TMP}'/logol.log;g'  log4j.properties
sed -i 's;INFO;DEBUG;g'  log4j.properties
cat logol.properties > /tmp/out

LogolExec -conf logol.properties -g 1799.logol -s 1799.fasta -dna
LogolMultiExec -conf logol.properties -g 1799.logol -s 1799.fasta -dna 
