sci-biology/abyss: move the new versions to ::gentoo

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

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>