diff options
Diffstat (limited to 'PKGBUILD')
| -rw-r--r-- | PKGBUILD | 26 |
1 files changed, 14 insertions, 12 deletions
@@ -2,26 +2,24 @@ # Contributor: Markus Heuser <markus.heuser@web.de> pkgname=samtools -pkgver=1.2 -pkgrel=2 +pkgver=1.3 +pkgrel=1 pkgdesc="tools for manipulating next-generation sequencing data" arch=('i686' 'x86_64') url="http://www.htslib.org/" license=('custom') -depends=('perl' 'htslib') +depends=('htslib' 'perl') 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/$pkgver.tar.gz - makefile-system-htslib.patch) -md5sums=('2748356ef392c0694ca1142de37cf2aa' - '00f3b0b730f37cd7c8ff12376a9a0c6a') +source=(https://github.com/samtools/$pkgname/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2) +md5sums=('7ab98b5c988e254d9bb5d796bf9337c9') prepare() { cd $srcdir/$pkgname-$pkgver - # patch Makefile to make it work with a system-provided htslib - patch -Np1 -i $srcdir/makefile-system-htslib.patch + # prevent shipped htslib to be used + rm -rf htslib-1.3 sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \ -i misc/varfilter.py @@ -30,19 +28,23 @@ prepare() { build() { cd $srcdir/$pkgname-$pkgver - make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts + ./configure \ + --prefix=/usr \ + --with-htslib=system + + make } check() { cd $srcdir/$pkgname-$pkgver - make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts check + make check } package() { cd $srcdir/$pkgname-$pkgver - make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts DESTDIR=$pkgdir prefix=/usr install + make DESTDIR=$pkgdir install for file in misc/*.lua ; do install -Dm755 $file $pkgdir/usr/bin/$(basename $file) |