commit: 5ef25a48bee2090fbcd6a9e92d4a8299c88edc67 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu May 17 19:37:29 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu May 17 19:37:29 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5ef25a48
sci-biology/SPAdes: version bump, drop old Package-Manager: Portage-2.3.36, Repoman-2.3.9 sci-biology/SPAdes/SPAdes-3.10.1.ebuild | 85 ---------------------- .../{SPAdes-3.11.1.ebuild => SPAdes-3.12.0.ebuild} | 13 ++-- .../files/SPAdes-3.10.1-fix-missing-include.patch | 10 --- 3 files changed, 8 insertions(+), 100 deletions(-) diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild deleted file mode 100644 index 3d219dbf0..000000000 --- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild +++ /dev/null @@ -1,85 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python{2_7,3_{4,5}} ) - -inherit eutils toolchain-funcs cmake-utils - -DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" -HOMEPAGE="http://cab.spbu.ru/software/spades" -SRC_URI=" - http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz - http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html - http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html -> ${P}_dipspades_manual.html - http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html - http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - dev-python/regex" -RDEPEND="${DEPEND}" -# 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 - -pkg_pretend() { - if [[ ${MERGE_TYPE} != binary ]]; then - if [[ $(tc-getCXX) == *g++ ]] ; then - if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then - eerror "You need at least sys-devel/gcc-4.7.0" - die "You need at least sys-devel/gcc-4.7.0" - fi - fi - fi -} - -src_prepare(){ - # https://github.com/Homebrew/homebrew-science/pull/5616 - epatch "${FILESDIR}"/"${P}"-fix-missing-include.patch - cp -p spades_compile.sh spades_install.sh || die - sed -e 's/make install/#make install/;s/cd $PREFIX/#cd $PREFIX/' -i spades_compile.sh || die - default -} - -src_compile(){ - mkdir build_spades || die - cd build_spades || die - cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="${ED}/usr" $* "${S}/src" || die -} - -src_install(){ - cd build_spades || die - emake install PREFIX="${ED}"/usr - # cmake-utils_src_install # dies with "${S}" does not appear to contain CMakeLists.txt - # BUG: move *.py files to standard site-packages/ subdirectories - insinto /usr/share/"${PN}" - dodoc "${DISTDIR}"/${P}_*manual.html -} diff --git a/sci-biology/SPAdes/SPAdes-3.11.1.ebuild b/sci-biology/SPAdes/SPAdes-3.12.0.ebuild similarity index 70% rename from sci-biology/SPAdes/SPAdes-3.11.1.ebuild rename to sci-biology/SPAdes/SPAdes-3.12.0.ebuild index 1842fca37..b56180a1a 100644 --- a/sci-biology/SPAdes/SPAdes-3.11.1.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.12.0.ebuild @@ -10,11 +10,14 @@ inherit eutils toolchain-funcs DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" HOMEPAGE="http://cab.spbu.ru/software/spades" SRC_URI=" - http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz - http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html - http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html -> ${P}_dipspades_manual.html - http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html - http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html" + https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz + http://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html + http://cab.spbu.ru/files/release${PV}/manual.md -> ${P}_manual.md + http://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html + http://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html + http://spades.bioinf.spbau.ru/release3.11.1/dipspades_manual.html -> ${P}_dipspades_manual.html" +# DEPRECATED in 3.12.0: dipSPAdes pipeline for highly polymorphic diploid genomes +# (still present in the release but no longer supported) LICENSE="GPL-2" SLOT="0" diff --git a/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch b/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch deleted file mode 100644 index bb6d75797..000000000 --- a/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- SPAdes-3.10.1/src/common/utils/segfault_handler.hpp.ori 2017-05-13 22:43:01.296207276 +0200 -+++ SPAdes-3.10.1/src/common/utils/segfault_handler.hpp 2017-05-13 22:43:41.437310225 +0200 -@@ -12,6 +12,7 @@ - #include "boost/noncopyable.hpp" - - #include <signal.h> -+#include <functional> - - struct segfault_handler : boost::noncopyable { - typedef std::function<void()> callback_t;