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author | David Seifert <soap@gentoo.org> | 2017-09-17 12:53:46 +0200 |
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committer | David Seifert <soap@gentoo.org> | 2017-09-17 12:53:46 +0200 |
commit | 25236fc56b39f744e9c57b3b6fc6255a50c6207f (patch) | |
tree | 8aaffcdcaee0468d4b855082ce7533bfee159bc8 /sci-biology/pysam/pysam-0.12.0.1.ebuild | |
parent | net-ftp/filezilla: restore ~ppc keywords (diff) | |
download | gentoo-25236fc56b39f744e9c57b3b6fc6255a50c6207f.tar.gz gentoo-25236fc56b39f744e9c57b3b6fc6255a50c6207f.tar.bz2 gentoo-25236fc56b39f744e9c57b3b6fc6255a50c6207f.zip |
sci-biology/pysam: Version bump to 0.12.0.1
Package-Manager: Portage-2.3.8, Repoman-2.3.3
Diffstat (limited to 'sci-biology/pysam/pysam-0.12.0.1.ebuild')
-rw-r--r-- | sci-biology/pysam/pysam-0.12.0.1.ebuild | 47 |
1 files changed, 47 insertions, 0 deletions
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 + : +} |