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# Maintainer: Clint Valentine <valentine.clint@gmail.com>
_jellyfishver=1.1.11
pkgname=kraken
pkgver=1.1
pkgrel=4
pkgdesc="Kraken taxonomic sequence classification system"
arch=('x86_64')
url=https://github.com/DerrickWood/"${pkgname}"
license=('GPL3')
depends=('perl')
source=(
"${pkgname}"-"${pkgver}".tar.gz::https://github.com/DerrickWood/"${pkgname}"/archive/v"${pkgver}".tar.gz
jellyfish-"${_jellyfishver}".tar.gz::http://www.cbcb.umd.edu/software/jellyfish/jellyfish-"${_jellyfishver}".tar.gz
)
sha256sums=(
'a4ac74c54c10920f431741c80d8a172670be12c3b352912000030fb5ea4c87a7'
'496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2'
)
_installation_dir=/usr/share/"${pkgname}"-"${pkgver}"
prepare() {
pushd "${srcdir}"/"${pkgname}"-"${pkgver}"
sed -i "s#\$(KRAKEN_DIR)#${pkgdir}${_installation_dir}#g" src/Makefile
make -C src clean
for script in scripts/*; do
sed -i "s|#####=KRAKEN_DIR=#####|${_installation_dir}|g" "${script}"
sed -i "s|#####=VERSION=#####|${pkgver}|g" "${script}"
done
sed -i "s# check_for_jellyfish.sh##g" scripts/build_kraken_db.sh
sed -i "s# jellyfish # jellyfish-v1 #g" scripts/build_kraken_db.sh
popd
pushd "${srcdir}"/jellyfish-"${_jellyfishver}"
./configure --prefix=/usr
make clean
popd
}
build() {
cd "${srcdir}"/"${pkgname}"-"${pkgver}"
make -C src
cd "${srcdir}"/jellyfish-"${_jellyfishver}"
make
}
check() {
cd "${srcdir}"/jellyfish-"${_jellyfishver}"
# make check
}
package() {
cd "${srcdir}"/"${pkgname}"-"${pkgver}"
mkdir -p "${pkgdir}""${_installation_dir}"
make -C src install
for script in scripts/*; do
install -Dm775 "${script}" "${pkgdir}""${_installation_dir}"/
done
install -D -m644 LICENSE "${pkgdir}"/usr/share/licenses/"${pkgname}"/LICENSE
install -D -m644 README.md "${pkgdir}"/usr/share/doc/"${pkgname}"/README.md
install -D -m644 CHANGELOG "${pkgdir}"/usr/share/doc/"${pkgname}"/CHANGELOG
for doc in docs/*; do
install -D -m644 "${doc}" "${pkgdir}"/usr/share/doc/"${pkgname}"/"${doc}"
done
for file in "${pkgdir}${_installation_dir}"/kraken*; do
install -Dm775 "${file}" "${pkgdir}"/usr/bin/$( basename "${file}" )
done
cd "${srcdir}"/jellyfish-"${_jellyfishver}"
install -D -m644 LICENSE "${pkgdir}"/usr/share/licenses/jellyfish_v"${_jellyfishver}"/LICENSE
install -D -m644 HalfLICENSE "${pkgdir}"/usr/share/licenses/jellyfish_v"${_jellyfishver}"/HalfLICENSE
install -D -m644 README "${pkgdir}"/usr/share/doc/jellyfish-v"${_jellyfishver}"/README
make DESTDIR="${pkgdir}" install
rm -r "${pkgdir}"/usr/share/man
mv "${pkgdir}"/usr/bin/jellyfish "${pkgdir}"/usr/bin/jellyfish-v1
}
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