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# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
# Contributor: Markus Heuser <markus.heuser@web.de>
pkgname=samtools
pkgver=1.2
pkgrel=1
pkgdesc="tools for manipulating next-generation sequencing data"
arch=('i686' 'x86_64')
url="http://www.htslib.org/"
license=('custom')
depends=('perl' 'htslib')
optdepends=('luajit: needed for r2plot.lua vcfutils.lua'
'python2: needed for varfilter.py')
options=('staticlibs')
source=($pkgname-$pkgver.tar.gz::https://github.com/samtools/samtools/archive/$pkgver.tar.gz
makefile-system-htslib.patch)
md5sums=('2748356ef392c0694ca1142de37cf2aa'
'00f3b0b730f37cd7c8ff12376a9a0c6a')
prepare() {
cd $srcdir/$pkgname-$pkgver
# patch Makefile to make it work with a system-provided htslib
patch -Np1 -i $srcdir/makefile-system-htslib.patch
sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \
-i misc/varfilter.py
}
build() {
cd $srcdir/$pkgname-$pkgver
make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts
}
check() {
cd $srcdir/$pkgname-$pkgver
make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts check
}
package() {
cd $srcdir/$pkgname-$pkgver
make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts DESTDIR=$pkgdir prefix=/usr 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 libbam.a $pkgdir/usr/lib/libbam.a
install -Dm644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE
}
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