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| author |   David Seifert <soap@gentoo.org> | 2017-09-02 12:44:42 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2017-09-02 13:04:41 +0200 |
| commit | adb3bc8e64f8afe51ae31d8070b98f2a88a243ee (patch) | |
| tree | 7d03d254694354924d8bd37d8a92f55b6a055d1e /sci-biology/pysam | |
| parent | sci-visualization/visit: remove unused patches (diff) | |
| download | gentoo-adb3bc8e64f8afe51ae31d8070b98f2a88a243ee.tar.gz gentoo-adb3bc8e64f8afe51ae31d8070b98f2a88a243ee.tar.bz2 gentoo-adb3bc8e64f8afe51ae31d8070b98f2a88a243ee.zip | |
sci-biology/pysam: Bump to 0.12
Package-Manager: Portage-2.3.8, Repoman-2.3.3
Diffstat (limited to 'sci-biology/pysam')
| -rw-r--r-- | sci-biology/pysam/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/pysam/pysam-0.12.ebuild | 43 |
2 files changed, 44 insertions, 0 deletions
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 24afdea8b623..b2e7af85717f 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1,2 @@ +DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3 DIST pysam-0.9.0.tar.gz 2701721 SHA256 dd4946c8efa6786a754e2b50c6027dd03aa82c8ee6c2be3b4e51384da80b4c7c SHA512 9189ef2b56df0f5e2c84586c0c2b2cd46a77dbedd3aa6fd25ddcc4a93320038bead073206fff528ae9775f153c875838726dd0af8e4c7bf4e0c6063145e2bc06 WHIRLPOOL 6c7d459057fed3961e983b3e8563e10a47cb87f5da2fb99ca893eff9e19a8b9e4c27b5d82a978a611d615eba8052fbe3e36498ea461e03521a075d9aee8da463 diff --git a/sci-biology/pysam/pysam-0.12.ebuild b/sci-biology/pysam/pysam-0.12.ebuild new file mode 100644 index 000000000000..e181e06ac9bc --- /dev/null +++ b/sci-biology/pysam/pysam-0.12.ebuild @@ -0,0 +1,43 @@ +# 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}]" + +python_prepare_all() { + export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include + export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) + export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl" + + # 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 + : +} |