1 files changed, 57 insertions, 0 deletions
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..ed6d64fab56b
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,57 @@
+# 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'
+         '05b136769fff4ab6c0962877390e96d8')
+
+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
+}
+
+check() {
+  cd $srcdir/$pkgname-$pkgver
+
+  make check
+}
+
+package() {
+  cd $srcdir/$pkgname-$pkgver
+
+  make DESTDIR=$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 $srcdir/$pkgname-$pkgver/*.h $pkgdir/usr/include/bam
+
+  install -Dm644 libbam.a $pkgdir/usr/lib/libbam.a
+
+  install -Dm644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE
+}