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# Maintainer: Alex Peltzer ("alexpe87") <alexpe.aur@mailbox.org>
# Former Maintainer (thanks dude!) : Christian Krause ("wookietreiber") <christian.krause@mailbox.org>
# Contributor: Markus Heuser <markus.heuser@web.de>
pkgname=samtools
pkgver=1.10
pkgrel=2
pkgdesc="tools for manipulating next-generation sequencing data"
arch=('i686' 'x86_64')
url="http://www.htslib.org/"
license=('custom')
depends=('htslib=1.10')
optdepends=('luajit: needed for r2plot.lua vcfutils.lua')
source=(https://github.com/samtools/samtools/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2)
sha256sums=('7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585')
prepare() {
cd $srcdir/$pkgname-$pkgver
# prevent shipped htslib to be used
rm -rf htslib-$pkgver || exit 1
}
build() {
cd $srcdir/$pkgname-$pkgver
./configure \
--prefix=/usr \
--with-htslib=system
make
}
check() {
cd $srcdir/$pkgname-$pkgver
make check
}
package() {
cd $srcdir/$pkgname-$pkgver
make DESTDIR=$pkgdir install
for file in misc/*.lua ; do
install -Dm755 $file $pkgdir/usr/bin/$(basename $file)
done
install -d $pkgdir/usr/include/bam
install -Dm644 *.h $pkgdir/usr/include/bam
install -Dm644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE
}
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