diff options
-rw-r--r-- | sci-biology/abyss/Manifest | 3 | ||||
-rw-r--r-- | sci-biology/abyss/abyss-2.2.5-r1.ebuild | 58 | ||||
-rw-r--r-- | sci-biology/abyss/abyss-2.3.0-r1.ebuild | 58 | ||||
-rw-r--r-- | sci-biology/abyss/abyss-2.3.1.ebuild | 58 | ||||
-rw-r--r-- | sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch | 11 | ||||
-rw-r--r-- | sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch | 11 | ||||
-rw-r--r-- | sci-biology/abyss/metadata.xml | 18 |
7 files changed, 0 insertions, 217 deletions
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest deleted file mode 100644 index 1540aba61..000000000 --- a/sci-biology/abyss/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST abyss-2.2.5.tar.gz 1698962 BLAKE2B cb629242dd25b8ca9f9b3f9d7b7f4211a0791b02a4bbbe9c1b11bb436098d1267f37a15ec7409a62e05fd1b75c8ff2f44be20d4a9788e46dfe8b310737e2e32f SHA512 d7ac857f9a9078357c9b7e509379a8b7e0f2e75fc2495f31e30d9403d20b1129372bd51fb601ea2fa37b52cb2dfa158706c121d15ac1746cd958a09c67204ae7 -DIST abyss-2.3.0.tar.gz 1530977 BLAKE2B feda6dc6b757a9183157b01c44c6ee7ec721e95860f50a8a44d245932622c91d0f21fd347bfacc50b787f766b18e0f94b69407bbed9c771601825e63f65a8320 SHA512 efd0423dfbf4fa6c8b529a43222cdf9421369093b780b1ce9309a0b7a89ae8ccd77645a4790cbfdacb1d40814bb0aa4f5f3b225a1e0c299b9bc913cb34084a33 -DIST abyss-2.3.1.tar.gz 1531044 BLAKE2B 2365080bdcca3a1fc5af91557da0187af7f18b20d1f91111b6818a8f53991337913d8ff8cf264aaac560bfc0e860e99f6833beb0b78a56ace014c96b869bec8a SHA512 c7fb8b0a1a1346d138a0a64d2a2886b7c081ed628011b614e8ff14d1cbf4a992a8acb1cc668640c0c6a9c22802e4b0cb839f136b8e1f12fe76dae3248cec1777 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>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="project"> - <email>haskell@gentoo.org</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> |