diff options
author | clintval | 2018-06-04 17:42:43 -0700 |
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committer | clintval | 2018-06-04 17:42:43 -0700 |
commit | c8a2b211d1965dc652e62ad8486f5eb41669ce07 (patch) | |
tree | 0b934332ce7b8c7f2c00bb3244f37c6cc8db7a98 | |
parent | c1d87e6b4e5ac1a7888a18c01e8edc7252adaf13 (diff) | |
download | aur-c8a2b211d1965dc652e62ad8486f5eb41669ce07.tar.gz |
Internalized jellyfish v1 dependency
-rw-r--r-- | .SRCINFO | 6 | ||||
-rw-r--r-- | PKGBUILD | 54 |
2 files changed, 46 insertions, 14 deletions
@@ -1,15 +1,15 @@ pkgbase = kraken pkgdesc = Kraken taxonomic sequence classification system pkgver = 1.1 - pkgrel = 2 + pkgrel = 3 url = https://github.com/DerrickWood/kraken - arch = i686 arch = x86_64 license = GPL3 depends = perl - optdepends = jellyfish<=1: for building Kraken databases source = kraken-1.1.tar.gz::https://github.com/DerrickWood/kraken/archive/v1.1.tar.gz + source = jellyfish-1.1.11.tar.gz::http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz sha256sums = a4ac74c54c10920f431741c80d8a172670be12c3b352912000030fb5ea4c87a7 + sha256sums = 496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2 pkgname = kraken @@ -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 } |