commit: 34773140d758b76b35f70f857f7b27ee06503921 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Tue Jan 25 14:24:18 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue Jan 25 14:24:18 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34773140
sci-biology/SPAdes: bump to 3.15.3 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> sci-biology/SPAdes/SPAdes-3.15.1.ebuild | 55 --------------------------------- sci-biology/SPAdes/SPAdes-3.15.3.ebuild | 36 +++++++++++++++++++++ 2 files changed, 36 insertions(+), 55 deletions(-) diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild deleted file mode 100644 index 853524984..000000000 --- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" -HOMEPAGE="https://cab.spbu.ru/software/spades"; -SRC_URI=" - https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz - https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html - https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html - https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html" -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" - -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - dev-python/regex" -RDEPEND="${DEPEND}" -BDEPEND="dev-util/cmake" -# BUG: -# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used, -# not *.so or *.a are even used) -# -# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their -# existing packages -# nlopt -# llvm -# python_libs -# bamtools -# ConsensusCore -# ssw -# jemalloc -# htrie -# getopt_pp -# cppformat -# cityhash -# samtools -# bwa - -# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary? -# bwa-0.7.12 -# bwa-0.6.2 - -src_compile(){ - PREFIX="${ED}"/usr ./spades_compile.sh || die -} - -src_install(){ - # BUG: move *.py files to standard site-packages/ subdirectories - insinto /usr/share/"${PN}" - dodoc "${DISTDIR}"/${P}_*manual.html -} diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild new file mode 100644 index 000000000..553c21e21 --- /dev/null +++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) +inherit python-single-r1 + +DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" +HOMEPAGE="https://cab.spbu.ru/software/spades"; +SRC_URI=" + https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz + https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html + https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html + https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + sys-libs/zlib + app-arch/bzip2 + dev-python/regex + ${PYTHON_DEPS} +" +RDEPEND="${DEPEND}" +BDEPEND="dev-util/cmake" + +src_install(){ + einstalldocs + # WORKAROUND: This script does both compile and install in one go + PREFIX="${ED}"/usr ./spades_compile.sh || die +}
