commit: b1ad15e7a10105fb9f0905ea5aac0835a62b46f3 Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com> AuthorDate: Fri Jan 10 16:32:20 2020 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Jan 10 16:52:47 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b1ad15e7
sci-biology/pysamstats: version bump sci-biology/pysam: version bump I am not sure if the path pysam-0.12-fix-buildsystem.patch is still needed or not. Nevertheless, the modules do not import properly into python so the ebuild needs more work. Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com> sci-biology/pysam/metadata.xml | 12 ++++++ sci-biology/pysam/pysam-0.15.3.ebuild | 46 ++++++++++++++++++++++ ...stats-0.24.2.ebuild => pysamstats-1.1.2.ebuild} | 9 +++-- 3 files changed, 64 insertions(+), 3 deletions(-) diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml new file mode 100644 index 000000000..6182254bd --- /dev/null +++ b/sci-biology/pysam/metadata.xml @@ -0,0 +1,12 @@ +<?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 new file mode 100644 index 000000000..4224df0be --- /dev/null +++ b/sci-biology/pysam/pysam-0.15.3.ebuild @@ -0,0 +1,46 @@ +# 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 + : +} diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild similarity index 77% rename from sci-biology/pysamstats/pysamstats-0.24.2.ebuild rename to sci-biology/pysamstats/pysamstats-1.1.2.ebuild index d6e1350a4..06bb7c69b 100644 --- a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild +++ b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -17,6 +17,9 @@ SLOT="0" KEYWORDS="" # needs working pysam, see bug #645060 IUSE="" -DEPEND="dev-python/cython - >=sci-biology/pysam-0.8.4" +DEPEND=" + dev-python/cython + dev-python/numpy + dev-python/pytables + >=sci-biology/pysam-0.15.1" RDEPEND="${DEPEND}"
