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#!/bin/bash
set -e
pkg=hilive
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/tutorial/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip *.fa.gz
mkdir -p index
hilive-build -i hiv1.fa -o index/hiv1
tar xaf BaseCalls.tar.gz
hilive -b BaseCalls -i index/hiv1 -r 100R --lanes 1 --tiles 1101
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