4 files changed, 95 insertions, 3 deletions
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
index 27cd7bd28fd3..17669dfb8b6c 100644
--- a/sci-biology/muscle/Manifest
+++ b/sci-biology/muscle/Manifest
@@ -1,4 +1,7 @@
+AUX 0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch 1344 BLAKE2B 2e9d4fb92df8f5726dd731b103cc4b4fe8fc18a22f171b13f00ce7dd4df7aa3806f1c0e59e6f54eb75b8d866ebcc8fae940d961fa083d6bca0c745ba163d28e7 SHA512 d0d5e12d61c159b62e1dcdf229eaaca16b453ed95adfb06402073706bd91cd748c0a4db169fc1ac9f07a955acf3fcf2017f6c45dcb8da8e34b3ad6ba0cc5c5ad
 AUX 3.8.31-make.patch 922 BLAKE2B 57f112a4538b1b0a791f9e151e0e27ba8c6af2beefb6ce95f064edd183315e17a09d92a9cd0a368907e2b4a1571463669e5ef83e96758603fa4807780ea98bc0 SHA512 c948991ab4f7b7d6e05ab63df00ea6ac576587e63f808c377cc86f4e3863c7cee207569d7f0a8572a8fcf81f2e23d9dd6b1270447a0028910301d74554ab1fac
+DIST muscle-5.1.0.tar.gz 185437 BLAKE2B b3742c37179fc8c36fb6160be4c3a8b4afa2f686bc018ec8e97a10834c1f1901b54b489faa9c365aa65c8514f378b7b5518d91a4e2fb067492e32202a06c4f64 SHA512 0cafc7ce07e5d0c261811e085e0fec8e44318a3d2604ad530ad95b370d6386143a4eeb59012e17cfc703f54bde5ee0752c3ce7fc8bb489748dbe89b2229dd6eb
 DIST muscle3.8.31_src.tar.gz 515267 BLAKE2B 79a8517f7a14d8ee907104e9035e1284fcabec556544508fd9b712789759448969ce39ecbefcedac62c435dc91e109b3b5b7027120691310ffebda80ca80dd9e SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce
-EBUILD muscle-3.8.31.ebuild 584 BLAKE2B ab2cbaa5046807ae92065e39b81179768f3b94eac6a28ffff1b9f670b8b74a9bff5ef6a4169c76189360bb7f7fe43a4804c95a837f739f66939e9a538cd4f9c0 SHA512 0f7f1a9f877cef9b54b19e884c315aaf03566011bfdbb3a0b061324382a581059bf756d1125db78dcbf8a83f92b57b425a555d2de6101cd8e2fe42cdfe8243fe
+EBUILD muscle-3.8.31.ebuild 778 BLAKE2B f6a676dd5f3e1ef4c9c1dd9192e836029a49cec4a4fb7d5a8cbee158493bb03e07bb3a70f7d6a28ede11b9ba2de8c712eba128369a5eb33811dfb6ce8efd4f93 SHA512 7ffb3867c528823db408a76c94f84c31f93114216202b4819b718e88dac4687c6b48decff026e96a74d8ff3639364dbcdec3b4f2b39fb778eb50a894520df866
+EBUILD muscle-5.1.0.ebuild 693 BLAKE2B 00abefc4b1a777639ea2cc84653bcc3db1a06c09730b39302ccb1b7468918e4ee7fd194da2c1ea251ac4ea4f75428f48d002cfb8974b9cf6563608e1f5ccddf2 SHA512 057e7db90995b4ce98d26c7afbb6d4225357da531f32efb9379040442511c054ea8be6ab3af8e534472afa22950f3d29a39426c41af4a289413ee938b8d954ba
 MISC metadata.xml 341 BLAKE2B 6b03204418f247ef22fd3237509b77f74c4e3a8f2df5874c387fb0c63a8e36fc3fff55ee252409cf541fbedc1cef37a4ba58dd73b647cc3ae2e6ce5d653b5e34 SHA512 e921eda7a3135f20b64253b388af339085f7f5c020f72a082dab4a6600fbe8841f236348974886f177a3196c83ed0fb25954128b272c3e92544f1880f49fa809
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-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild
index e47f5f66cf46..faefc5b1a280 100644
--- a/sci-biology/muscle/muscle-3.8.31.ebuild
+++ b/sci-biology/muscle/muscle-3.8.31.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-inherit toolchain-funcs
+inherit flag-o-matic toolchain-funcs
 
 MY_P="${PN}${PV}_src"
 
@@ -22,6 +22,14 @@ S="${WORKDIR}"/${PN}${PV}/src
 PATCHES=( "${FILESDIR}"/${PV}-make.patch )
 
 src_configure() {
+	# -Werror=strict-aliasing
+	# https://bugs.gentoo.org/862276
+	# Fixed upstream in later releases
+	#
+	# Do not trust with LTO either.
+	append-flags -fno-strict-aliasing
+	filter-lto
+
 	tc-export CXX
 }
 
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..84c0c2266804
--- /dev/null
+++ b/sci-biology/muscle/muscle-5.1.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit 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 -> ${P}.tar.gz"
+S="${WORKDIR}"/${P}/src
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+
+RDEPEND="!sci-libs/libmuscle"
+
+PATCHES=(
+	"${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
+}