diff options
Diffstat (limited to 'PKGBUILD')
-rw-r--r-- | PKGBUILD | 54 |
1 files changed, 43 insertions, 11 deletions
@@ -1,27 +1,55 @@ # Maintainer: Clint Valentine <valentine.clint@gmail.com> +_jellyfishver=1.1.11 pkgname=kraken pkgver=1.1 -pkgrel=2 +pkgrel=3 pkgdesc="Kraken taxonomic sequence classification system" -arch=('i686' 'x86_64') +arch=('x86_64') url=https://github.com/DerrickWood/"${pkgname}" license=('GPL3') depends=('perl') -optdepends=('jellyfish<=1: for building Kraken databases') -source=("${pkgname}"-"${pkgver}".tar.gz::https://github.com/DerrickWood/"${pkgname}"/archive/v"${pkgver}".tar.gz) -sha256sums=('a4ac74c54c10920f431741c80d8a172670be12c3b352912000030fb5ea4c87a7') +source=( + "${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}"-"${pkgver}" prepare() { - cd "${srcdir}"/"${pkgname}"-"${pkgver}" + 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" "${script}" + done + + sed -i "s# check_for_jellyfish.sh##g" scripts/build_kraken_db.sh + sed -i "s#jellyfish#${_installation_dir}/jellyfish#g" scripts/build_kraken_db.sh + popd + + pushd "${srcdir}"/jellyfish-"${_jellyfishver}" + ./configure --prefix="${_installation_dir}" + make clean + popd } build() { cd "${srcdir}"/"${pkgname}"-"${pkgver}" make -C src + + cd "${srcdir}"/jellyfish-"${_jellyfishver}" + make +} + +check() { + cd "${srcdir}"/jellyfish-"${_jellyfishver}" + # make check } package() { @@ -31,11 +59,8 @@ package() { make -C src install - for scripts in scripts/*; do - sed -i "s|#####=KRAKEN_DIR=#####|${_installation_dir}|g" "${scripts}" - sed -i "s|#####=VERSION=#####|${pkgver}|g" "${scripts}" - - install -Dm775 "${scripts}" "${pkgdir}""${_installation_dir}"/ + for script in scripts/*; do + install -Dm775 "${script}" "${pkgdir}""${_installation_dir}"/ done install -D -m644 LICENSE "${pkgdir}"/usr/share/licenses/"${pkgname}"_v"${pkgver}"/LICENSE @@ -49,4 +74,11 @@ package() { for file in "${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_"${_jellyfishver}"/LICENSE + install -D -m644 HalfLICENSE "${pkgdir}"/usr/share/licenses/jellyfish_"${_jellyfishver}"/HalfLICENSE + install -D -m644 README "${pkgdir}"/usr/share/doc/jellyfish-"${_jellyfishver}"/README + + install -Dm775 bin/jellyfish "${pkgdir}${_installation_dir}"/jellyfish } |