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# Maintainer: Maël Kerbiriou <m431.kerbiriou@gmail.com>
pkgname=bwa-mem2-git
_pkgname=bwa-mem2
pkgver=r183.d43752d
pkgrel=1
pkgdesc="The next version of Burrows-Wheeler Aligner MEM algorithm"
arch=('i686' 'x86_64')
url="https://github.com/bwa-mem2/bwa-mem2"
license=('custom')
depends=('gcc-libs' 'zlib')
source=("git+https://github.com/bwa-mem2/bwa-mem2"
"git+https://github.com/intel/safestringlib.git")
md5sums=('SKIP' 'SKIP')
# For compiling for native instruction set only, set this to false:
MULTI=${MULTI:-true}
pkgver() {
cd "$_pkgname"
printf "r%s.%s" "$(git rev-list --count HEAD)" "$(git rev-parse --short HEAD)"
}
prepare() {
cd "$srcdir/$_pkgname"
git submodule init
git config submodule.ext/safestringlib.url ${srcdir}/safestringlib
git submodule update
}
build() {
cd "$srcdir/$_pkgname"
if [ "$MULTI" = true ] ; then
make multi
else
make arch=native
fi
}
package() {
cd "$srcdir/$_pkgname"
install -Dm755 bwa-mem2 "$pkgdir/usr/bin/bwa-mem2"
install -Dm644 LICENSE "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
if [ "$MULTI" = true ] ; then
install -Dm755 bwa-mem2.avx2 "$pkgdir/usr/bin/bwa-mem2.avx2"
install -Dm755 bwa-mem2.avx512bw "$pkgdir/usr/bin/bwa-mem2.avx512bw"
install -Dm755 bwa-mem2.sse41 "$pkgdir/usr/bin/bwa-mem2.sse41"
fi
}
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