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# maintainer: bipin <kbipinkumar@pm.me>
pkgbase=mmseqs2
pkgname=('mmseqs2-sse4' 'mmseqs2-avx2')
_pkgbase=${pkgbase//mm/MM}
pkgver=16.747c6
_pkgver=16-747c6
pkgrel=5
pkgdesc="ultra fast and sensitive search and clustering suite. https://doi.org/10.1038/nbt.3988"
arch=('x86_64')
url="https://github.com/soedinglab/mmseqs2"
license=('MIT')
makedepends=('cmake' 'zlib' 'openmp' 'vim' 'perl')
source=("$_pkgbase-$_pkgver.tar.gz::https://github.com/soedinglab/MMseqs2/archive/refs/tags/${_pkgver}.tar.gz"
"bash-completion.patch"
"fix_util_installation.patch"
)
install=bash-completion.install
sha256sums=('faeb6841feb8e028651c2391de1346c55c2091a96520b625525d27b99d07ef1d'
'39432896625dca6240e7f4f6dffebd05f40a1d0de2c724d7123cb63e2464e791'
'ca25afde5447ec6b72e0a6ca9874eb6b5b93c2ec52ff3f10e4b3929d1aea1e71')
prepare() {
cd $_pkgbase-$_pkgver
# add package specific information needed to enable bash autocompletion
patch -p1 < ${srcdir}/bash-completion.patch
# Prevent CMake from installing util/ contents to nonstandard /usr/util location.
patch -p1 < ${srcdir}/fix_util_installation.patch
}
build() {
cd $_pkgbase-$_pkgver
# 'mmseqs2-sse4'
cmake -B build1 \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_BUILD_TYPE=None \
-DHAVE_SSE4_1=1 \
-DNATIVE_ARCH=0 \
-DCMAKE_C_FLAGS="${CFLAGS} ${CPPFLAGS}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS} ${CPPFLAGS}" \
-DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \
-DCMAKE_SHARED_LINKER_FLAGS="${LDFLAGS}" \
-Wno-dev \
-DVERSION_OVERRIDE="${_pkgver}"-BioArchLinux_sse4
# 'mmseqs2-AVX2'
cmake -B build2 \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_BUILD_TYPE=None \
-DNATIVE_ARCH=0 \
-DHAVE_AVX2=1 \
-DCMAKE_C_FLAGS="${CFLAGS} ${CPPFLAGS}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS} ${CPPFLAGS}" \
-DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \
-DCMAKE_SHARED_LINKER_FLAGS="${LDFLAGS}" \
-Wno-dev \
-DVERSION_OVERRIDE="${_pkgver}"-BioArchLinux_avx2
# Build 'mmseqs2-sse4'
MAKEFLAGS=-j1 cmake --build build1
# Build 'mmseqs2-AVX2'
MAKEFLAGS=-j1 cmake --build build2
}
package_mmseqs2-sse4() {
depends=('gcc-libs' 'glibc' 'zlib' 'zstd' 'openmp' 'bzip2' 'bash')
optdepends=('r: For running bundled rscript file')
provides=('mmseqs2')
conflicts=('mmseqs2-avx2')
pkgdesc="ultra fast and sensitive search and clustering suite optimised for SSE4 instructions. https://doi.org/10.1038/nbt.3988"
cd $_pkgbase-$_pkgver
DESTDIR="$pkgdir" cmake --install build1
install -Dm644 LICENSE.md -t "$pkgdir/usr/share/licenses/${pkgname}"
cd util
install -Dm755 bash-completion.sh "${pkgdir}"/usr/share/${pkgbase}/bash-completion.sh
install -Dm644 format_substitution_matrix.R "${pkgdir}"/usr/share/${pkgbase}/format_substitution_matrix.R
}
package_mmseqs2-avx2() {
depends=('gcc-libs' 'glibc' 'zlib' 'zstd' 'openmp' 'bzip2' 'bash')
optdepends=('r: For running bundled rscript file')
provides=('mmseqs2')
conflicts=('mmseqs2-sse4')
pkgdesc="ultra fast and sensitive search and clustering suite optimised for AVX2 instructions. https://doi.org/10.1038/nbt.3988"
cd $_pkgbase-$_pkgver
DESTDIR="$pkgdir" cmake --install build2
install -Dm644 LICENSE.md -t "$pkgdir/usr/share/licenses/${pkgname}"
cd util
install -Dm755 bash-completion.sh "${pkgdir}"/usr/share/${pkgbase}/bash-completion.sh
install -Dm644 format_substitution_matrix.R "${pkgdir}"/usr/share/${pkgbase}/format_substitution_matrix.R
}
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