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-rw-r--r--PKGBUILD47
1 files changed, 47 insertions, 0 deletions
diff --git a/PKGBUILD b/PKGBUILD
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+# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
+
+pkgname=bcftools
+pkgver=1.2
+pkgrel=3
+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
+ makefile-system-htslib.patch)
+md5sums=('87efbd0092b6e4828c17842c9ae57ec9'
+ '50efd8fdb3f4c11a5dff7748c666d90e'
+ '5ae8f6433b42acf1f4bc7b7658a10805')
+
+prepare() {
+ cd $srcdir/$pkgname-$pkgver
+
+ # patch Makefile to make it work with a system-provided htslib
+ patch -Np1 -i $srcdir/makefile-system-htslib.patch
+}
+
+build() {
+ cd $srcdir/$pkgname-$pkgver
+
+ make USE_GPL=1
+}
+
+check() {
+ cd $srcdir/$pkgname-$pkgver
+
+ make 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
+}