Initial import

2 files changed, 54 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..1ed34127e17f
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,15 @@
+pkgbase = stampy
+	pkgdesc = Mapper of short reads from illumina sequencing machines onto a reference genome
+	pkgver = 1.0.23
+	pkgrel = 1
+	url = http://www.well.ox.ac.uk/project-stampy
+	arch = i686
+	arch = x86_64
+	license = custom
+	makedepends = gcc
+	depends = python2
+	source = http://www.well.ox.ac.uk/bioinformatics/Software/Stampy-latest.tgz
+	md5sums = 30bbfc2c4a2750f6cc87bbfe52394dcd
+
+pkgname = stampy
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..0e0a14bb6f67
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,39 @@
+# Maintainer: Fabio Zanini <fabio.zanini@tuebingen.mpg.de>
+pkgname=stampy
+pkgver=1.0.23
+pkgrel=1
+pkgdesc="Mapper of short reads from illumina sequencing machines onto a reference genome"
+arch=('i686' 'x86_64')
+url="http://www.well.ox.ac.uk/project-stampy"
+license=('custom')
+depends=('python2')
+makedepends=('gcc')
+source=(http://www.well.ox.ac.uk/bioinformatics/Software/Stampy-latest.tgz)
+md5sums=('30bbfc2c4a2750f6cc87bbfe52394dcd')
+
+build() {
+ 	echo $srcdir
+	cd "$srcdir/$pkgname-$pkgver"
+	# Python2 fix
+	sed -i 's/python?=python/python?=python2/' makefile
+
+	# g++ obsolete option fix
+	sed -i 's/-Wl /-Wall /' makefile
+
+	make
+
+	sed -i 's|#!/usr/bin/env python|#!/usr/bin/env python2|' stampy.py
+	# FIXME: Substitute all TABS by spaces
+	sed -i 's/	/        /g' stampy.py
+
+}
+
+package() {
+	# Install manually
+	mkdir -p "$pkgdir/opt" "$pkgdir/usr/bin" "$pkgdir/usr/share/licenses/stampy"
+	cp -r "$srcdir/$pkgname-$pkgver" "$pkgdir/opt"
+	ln -s "$pkgdir/opt/$pkgname-$pkgver/stampy.py" "$pkgdir/usr/bin/stampy"
+
+	# Install license
+	sed -n '/This is a release version/,/support./p' "$srcdir/$pkgname-$pkgver/README.txt" > "$pkgdir/usr/share/licenses/stampy/LICENSE"
+}