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#!/bin/bash
set -e
pkg=resfinder
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 db_resfinder
cp -a /usr/share/resfinder/db/* db_resfinder
find -name '*.gz' -exec gunzip '{}' ';'
# Move data to deprecated dir as functional tests seek relative path
mv data deprecated/
echo "Indexing files as needed"
cd db_resfinder
python3 INSTALL.py 2> /dev/null
cd ..
cd db_pointfinder
python3 INSTALL.py 2> /dev/null
cd ..
echo "Running tests"
python3 deprecated/functional_tests.py \
-db_res db_resfinder \
-db_point db_pointfinder \
-b /usr/bin/blastn \
-k /usr/bin/kma
echo "Cleanup"
rm -rf db_*
echo "PASS"
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