diff options
| -rw-r--r-- | .SRCINFO | 14 | ||||
| -rw-r--r-- | PKGBUILD | 26 | ||||
| -rw-r--r-- | makefile-system-htslib.patch | 13 |
3 files changed, 21 insertions, 32 deletions
@@ -1,20 +1,20 @@ +# Generated by mksrcinfo v8 +# Sun Jan 10 10:05:21 UTC 2016 pkgbase = samtools pkgdesc = tools for manipulating next-generation sequencing data - pkgver = 1.2 - pkgrel = 2 + pkgver = 1.3 + pkgrel = 1 url = http://www.htslib.org/ arch = i686 arch = x86_64 license = custom - depends = perl depends = htslib + depends = perl optdepends = luajit: needed for r2plot.lua vcfutils.lua optdepends = python2: needed for varfilter.py options = staticlibs - source = samtools-1.2.tar.gz::https://github.com/samtools/samtools/archive/1.2.tar.gz - source = makefile-system-htslib.patch - md5sums = 2748356ef392c0694ca1142de37cf2aa - md5sums = 00f3b0b730f37cd7c8ff12376a9a0c6a + source = https://github.com/samtools/samtools/releases/download/1.3/samtools-1.3.tar.bz2 + md5sums = 7ab98b5c988e254d9bb5d796bf9337c9 pkgname = samtools @@ -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) diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch deleted file mode 100644 index bd46ac328d44..000000000000 --- a/makefile-system-htslib.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff -aur samtools-1.2/Makefile samtools-1.2-patched/Makefile ---- samtools-1.2/Makefile 2015-02-02 16:18:41.000000000 +0100 -+++ samtools-1.2-patched/Makefile 2015-06-30 15:48:41.006563956 +0200 -@@ -83,7 +83,9 @@ - - # Adjust $(HTSDIR) to point to your top-level htslib directory - HTSDIR = ../htslib -+ifneq ("$(wildcard $(HTSDIR)/htslib.mk)","") - include $(HTSDIR)/htslib.mk -+endif - HTSLIB = $(HTSDIR)/libhts.a - BGZIP = $(HTSDIR)/bgzip - |