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authorChristian Krause2016-01-10 11:44:28 +0100
committerChristian Krause2016-01-10 11:44:28 +0100
commitce0e65b4a554c65329bc40d6de30120fda1aa0ea (patch)
tree35760f062f5f98cd24d74bcce1f4430b3eb4be41 /PKGBUILD
parent1c012681f904e3b3f380cb3eaefe5730f2357d8c (diff)
downloadaur-ce0e65b4a554c65329bc40d6de30120fda1aa0ea.tar.gz
bcftools-1.3-1
Diffstat (limited to 'PKGBUILD')
-rw-r--r--PKGBUILD29
1 files changed, 12 insertions, 17 deletions
diff --git a/PKGBUILD b/PKGBUILD
index 3327eeea3a3..9f21ce0cc10 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,47 +1,42 @@
# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
pkgname=bcftools
-pkgver=1.2
-pkgrel=3
+pkgver=1.3
+pkgrel=1
pkgdesc="Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"
arch=('i686' 'x86_64')
url="http://samtools.github.io/bcftools/"
license=('GPL')
depends=('gsl' 'htslib' 'perl')
-source=($pkgname-$pkgver.tar.gz::https://github.com/samtools/bcftools/archive/$pkgver.tar.gz
- bcftools-profile.sh
+source=(https://github.com/samtools/$pkgname/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2
makefile-system-htslib.patch)
-md5sums=('87efbd0092b6e4828c17842c9ae57ec9'
- '50efd8fdb3f4c11a5dff7748c666d90e'
- '5ae8f6433b42acf1f4bc7b7658a10805')
+md5sums=('17f1f7d9e4a03d64a114b43ca896899f'
+ '697d169f4a729c0fc61720490b60ea5e')
prepare() {
cd $srcdir/$pkgname-$pkgver
+ # prevent shipped htslib to be used
+ rm -rf htslib-1.3
+
# patch Makefile to make it work with a system-provided htslib
- patch -Np1 -i $srcdir/makefile-system-htslib.patch
+ patch -i $srcdir/makefile-system-htslib.patch
}
build() {
cd $srcdir/$pkgname-$pkgver
- make USE_GPL=1
+ make -e prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1
}
check() {
cd $srcdir/$pkgname-$pkgver
- make USE_GPL=1 test
+ make -e prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 test
}
package() {
cd $srcdir/$pkgname-$pkgver
- make USE_GPL=1 DESTDIR=$pkgdir prefix=/usr install
-
- for plugin in plugins/*.so ; do
- install -Dm755 $plugin $pkgdir/usr/lib/bcftools/$(basename $plugin)
- done
-
- install -Dm644 $srcdir/bcftools-profile.sh $pkgdir/etc/profile.d/bcftools.sh
+ make -e prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 DESTDIR=$pkgdir install
}