commit: eeef69fea4f72eb2bd4400a11d80f3a5db0a3d92 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sat Jan 2 13:09:32 2021 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Sun Jan 3 06:25:30 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=eeef69fe
sci-biology/pysam: remove, package is in ::gentoo Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> Signed-off-by: Horea Christian <chr <AT> chymera.eu> sci-biology/pysam/metadata.xml | 12 --------- sci-biology/pysam/pysam-0.15.3.ebuild | 46 ----------------------------------- 2 files changed, 58 deletions(-) diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml deleted file mode 100644 index 6182254bd..000000000 --- a/sci-biology/pysam/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">pysam</remote-id> - <remote-id type="github">pysam-developers/pysam</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pysam/pysam-0.15.3.ebuild b/sci-biology/pysam/pysam-0.15.3.ebuild deleted file mode 100644 index 4224df0be..000000000 --- a/sci-biology/pysam/pysam-0.15.3.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 python3_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.org/project/pysam/"; -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" - -# current code wraps 3rd-party code from htslib-1.9, samtools-1.9 and bcftools-1.9 -RDEPEND="=sci-libs/htslib-1.9*:=" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}]" - -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 - : -}
