1 files changed, 46 insertions, 0 deletions
diff --git a/sci-biology/pysam/pysam-0.9.0.ebuild b/sci-biology/pysam/pysam-0.9.0.ebuild
new file mode 100644
index 000000000000..5fcecfb99db9
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.9.0.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5} )
+
+inherit distutils-r1 python-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="https://github.com/pysam-developers/pysam http://pypi.python.org/pypi/pysam"
+SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="=sci-libs/htslib-1.3*"
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+
+PATCHES=(
+	"${FILESDIR}/${P}-missing-config.h.patch"
+)
+
+src_prepare() {
+	default
+
+	export HTSLIB_INCLUDE_DIR=${EPREFIX}/usr/include
+	export HTSLIB_LIBRARY_DIR=${EPREFIX}/usr/$(get_libdir)
+	export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+
+	sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
+		-i cy_build.py || die
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+}
+
+src_compile() {
+	# TODO
+	# empty compile, as the build system runs the whole build again in install
+	:
+}