commit: 55988add1d9840ba07f1eea2067a77b6eba3a9e5 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Thu Jan 13 11:17:24 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Thu Jan 13 11:18:40 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=55988add
sci-biology/abyss: move the new versions to ::gentoo Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> sci-biology/abyss/abyss-2.2.5-r1.ebuild | 58 ---------------------- sci-biology/abyss/abyss-2.3.0-r1.ebuild | 58 ---------------------- sci-biology/abyss/abyss-2.3.1.ebuild | 58 ---------------------- .../files/abyss-2.2.5-ContigProperties.h.patch | 11 ---- .../files/abyss-2.2.5-PathConsensus-assert.patch | 11 ---- sci-biology/abyss/metadata.xml | 18 ------- 6 files changed, 214 deletions(-) diff --git a/sci-biology/abyss/abyss-2.2.5-r1.ebuild b/sci-biology/abyss/abyss-2.2.5-r1.ebuild deleted file mode 100644 index d9134813b..000000000 --- a/sci-biology/abyss/abyss-2.2.5-r1.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"; -SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost:= - misc-haskell? ( - dev-libs/gmp:0= - dev-libs/libffi:0= - ) - mpi? ( sys-cluster/openmpi )" -DEPEND="${RDEPEND} - misc-haskell? ( - dev-lang/ghc - )" - -PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch - "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch - ) - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -src_prepare() { - default - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - econf $(use_enable openmp) --enable-maxk=256 -} diff --git a/sci-biology/abyss/abyss-2.3.0-r1.ebuild b/sci-biology/abyss/abyss-2.3.0-r1.ebuild deleted file mode 100644 index d9134813b..000000000 --- a/sci-biology/abyss/abyss-2.3.0-r1.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"; -SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost:= - misc-haskell? ( - dev-libs/gmp:0= - dev-libs/libffi:0= - ) - mpi? ( sys-cluster/openmpi )" -DEPEND="${RDEPEND} - misc-haskell? ( - dev-lang/ghc - )" - -PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch - "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch - ) - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -src_prepare() { - default - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - econf $(use_enable openmp) --enable-maxk=256 -} diff --git a/sci-biology/abyss/abyss-2.3.1.ebuild b/sci-biology/abyss/abyss-2.3.1.ebuild deleted file mode 100644 index d9134813b..000000000 --- a/sci-biology/abyss/abyss-2.3.1.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"; -SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost:= - misc-haskell? ( - dev-libs/gmp:0= - dev-libs/libffi:0= - ) - mpi? ( sys-cluster/openmpi )" -DEPEND="${RDEPEND} - misc-haskell? ( - dev-lang/ghc - )" - -PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch - "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch - ) - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -src_prepare() { - default - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - econf $(use_enable openmp) --enable-maxk=256 -} diff --git a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch deleted file mode 100644 index 95181f082..000000000 --- a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- abyss-2.2.5/Common/ContigProperties.h.ori 2020-09-18 20:42:12.000000000 +0200 -+++ abyss-2.2.5/Common/ContigProperties.h 2021-04-14 12:31:23.682158000 +0200 -@@ -171,7 +171,7 @@ - template <typename T> - ContigProperties& operator+=(ContigProperties& a, const T& b) - { -- assert((int)a.length + (int)b.distance > 0); -+ assert((int)a.length + (int)b.distance >= 0); - a.length += b.distance; - return a; - } diff --git a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch deleted file mode 100644 index 754e25acc..000000000 --- a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- abyss-2.2.5/MergePaths/PathConsensus.cpp 2020-09-18 20:42:12.000000000 +0200 -+++ abyss-2.2.5/MergePaths/PathConsensus.cpp 2021-04-12 22:26:28.780547000 +0200 -@@ -379,7 +379,7 @@ - unsigned overlap, Sequence& seq, - const Sequence& s, const ContigNode& node, const Path& path) - { -- assert(s.length() > overlap); -+ assert(s.length() >= overlap); - Sequence ao; - Sequence bo(s, 0, overlap); - Sequence o; diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml deleted file mode 100644 index 47116e507..000000000 --- a/sci-biology/abyss/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Haskell</name> - </maintainer> - <use> - <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag> - </use> - <upstream> - <remote-id type="github">bcgsc/abyss</remote-id> - </upstream> -</pkgmetadata>
