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author | 2024-03-19 23:59:32 -0400 | |
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committer | 2024-03-20 06:17:03 +0000 | |
commit | 676077c732029914876df94a29591ae5ed6b4ba2 (patch) | |
tree | 3061e1350cfbfa0df82fa671f11e382f64217ee5 /sci-biology | |
parent | sci-biology/muscle: mark as LTO-unsafe, strict-aliasing unsafe (diff) | |
download | gentoo-676077c732029914876df94a29591ae5ed6b4ba2.tar.gz gentoo-676077c732029914876df94a29591ae5ed6b4ba2.tar.bz2 gentoo-676077c732029914876df94a29591ae5ed6b4ba2.zip |
sci-biology/muscle: add 5.1.0
Major new release, major new build system that is majorly broken. <3
scientific code.
This package has not been updated since before the import of gentoo into
git, so I shall simply assume this major version is safe. From the
homepage, it is a "major rewrite", "based on new algorithms", which is
"much more accurate, is often faster, and scales to much larger datasets".
I think that's another way of saying "same old program but with fixes".
Signed-off-by: Eli Schwartz <eschwartz93@gmail.com>
Signed-off-by: Sam James <sam@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/muscle/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch | 49 | ||||
-rw-r--r-- | sci-biology/muscle/muscle-5.1.0.ebuild | 33 |
3 files changed, 83 insertions, 0 deletions
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest index f1ec094f5a69..0741cc695e2f 100644 --- a/sci-biology/muscle/Manifest +++ b/sci-biology/muscle/Manifest @@ -1 +1,2 @@ +DIST muscle-5.1.0.tar.gz 185437 BLAKE2B b3742c37179fc8c36fb6160be4c3a8b4afa2f686bc018ec8e97a10834c1f1901b54b489faa9c365aa65c8514f378b7b5518d91a4e2fb067492e32202a06c4f64 SHA512 0cafc7ce07e5d0c261811e085e0fec8e44318a3d2604ad530ad95b370d6386143a4eeb59012e17cfc703f54bde5ee0752c3ce7fc8bb489748dbe89b2229dd6eb DIST muscle3.8.31_src.tar.gz 515267 BLAKE2B 79a8517f7a14d8ee907104e9035e1284fcabec556544508fd9b712789759448969ce39ecbefcedac62c435dc91e109b3b5b7027120691310ffebda80ca80dd9e SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce diff --git a/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch b/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch new file mode 100644 index 000000000000..a8604239105b --- /dev/null +++ b/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch @@ -0,0 +1,49 @@ +From 9ef231e4612263524a4c41ecb841cdcf0e17d011 Mon Sep 17 00:00:00 2001 +From: Eli Schwartz <eschwartz93@gmail.com> +Date: Tue, 19 Mar 2024 23:44:43 -0400 +Subject: [PATCH] Makefile: fix horribleness so that it respects build system + environment + +Do not strip, that is portage's job. Respect $CXX, don't override use +-O. +--- + Makefile | 15 ++++----------- + 1 file changed, 4 insertions(+), 11 deletions(-) + +diff --git a/Makefile b/Makefile +index df16673..086aba3 100644 +--- a/Makefile ++++ b/Makefile +@@ -19,14 +19,10 @@ OS := $(shell uname) + + CPPFLAGS := $(CPPFLAGS) -DNDEBUG -pthread + +-CXX := g++ +-ifeq ($(OS),Darwin) +- CXX := g++-11 +-endif ++CXX ?= g++ ++CXXFLAGS := $(CXXFLAGS) -fopenmp -ffast-math + +-CXXFLAGS := $(CXXFLAGS) -O3 -fopenmp -ffast-math +- +-LDFLAGS := $(LDFLAGS) -O3 -fopenmp -pthread -lpthread ${LDFLAGS2} ++LDFLAGS := $(LDFLAGS) -fopenmp -pthread -lpthread ${LDFLAGS2} + + HDRS := $(shell echo *.h) + OBJS := $(shell echo *.cpp | sed "-es/^/$(OS)\//" | sed "-es/ / $(OS)\//g" | sed "-es/\.cpp/.o/g") +@@ -35,10 +31,7 @@ SRCS := $(shell ls *.cpp *.h) + .PHONY: clean + + $(OS)/muscle : gitver.txt $(OS)/ $(OBJS) +- $(CXX) $(LDFLAGS) $(OBJS) -o $@ +- +- # Warning: do not add -d option to strip, this is not portable +- strip $(OS)/muscle ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o $@ + + gitver.txt : $(SRCS) + bash ./gitver.bash +-- +2.43.2 + diff --git a/sci-biology/muscle/muscle-5.1.0.ebuild b/sci-biology/muscle/muscle-5.1.0.ebuild new file mode 100644 index 000000000000..033c35b8ee1a --- /dev/null +++ b/sci-biology/muscle/muscle-5.1.0.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Multiple sequence comparison by log-expectation" +HOMEPAGE="https://www.drive5.com/muscle/" +SRC_URI="https://github.com/rcedgar/muscle/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" + +RDEPEND="!sci-libs/libmuscle" + +S="${WORKDIR}"/${P}/src + +PATCHES=( + "${FILESDIR}"/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch +) + +src_configure() { + tc-export CXX + printf '"%s"\n' "${PV}" > gitver.txt +} + +src_install() { + local OS=$(uname) || die + dobin ${OS}/muscle + dodoc *.txt +} |