diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/pysam/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/pysam/pysam-0.12.0.1.ebuild | 47 |
2 files changed, 48 insertions, 0 deletions
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index c95db9a1dcd7..b01df416d508 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1,2 @@ +DIST pysam-0.12.0.1.tar.gz 2672020 SHA256 04837bf0b1313e57d50076f228463262b9982c410b973eb184c033528f83d523 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d WHIRLPOOL 5bd9f29e7458cac3839aaa9703d4c5740b1268644947f31ce7d3ddd12e0ec1948611ca5228323ce9b3b8fa5a5e0623c6fa0a0e2ce7f197fdb81aa5465915af36 DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3 diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild new file mode 100644 index 000000000000..1f4f58fdfe29 --- /dev/null +++ b/sci-biology/pysam/pysam-0.12.0.1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE=" + https://github.com/pysam-developers/pysam + https://pypi.python.org/pypi/pysam" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.5*:=" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" + +PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch ) + +python_prepare_all() { + # unbundle htslib + export HTSLIB_MODE="external" + export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include + export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) + rm -r htslib || die + + # prevent setup.py from adding RPATHs + 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 + + distutils-r1_python_prepare_all +} + +src_compile() { + # TODO + # empty compile, as the build system runs the whole build again in install + : +} |