1 files changed, 55 insertions, 0 deletions
diff --git a/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild
new file mode 100644
index 000000000..6cbd139d8
--- /dev/null
+++ b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit bash-completion-r1 cmake
+
+MY_PN="MMseqs2"
+
+# Must be manually updated with each release
+COMMIT="45111b641859ed0ddd875b94d6fd1aef1a675b7e"
+
+DESCRIPTION="Fast and sensitive sequence search and clustering"
+HOMEPAGE="https://github.com/soedinglab/MMseqs2"
+SRC_URI="https://github.com/soedinglab/${MY_PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_PN}-${COMMIT}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2"
+
+RDEPEND="
+	app-arch/zstd[static-libs]
+	sys-libs/zlib
+	app-arch/bzip2
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-properly-handle-cpuflags.patch"
+)
+
+src_configure() {
+	local mycmakeargs=(
+		# Need static libs: https://github.com/soedinglab/MMseqs2/issues/411
+		-DBUILD_SHARED_LIBS=OFF
+		-DUSE_SYSTEM_ZSTD=ON
+		# Disable auto detection, build respecting cpu flags instead
+		-DNATIVE_ARCH=OFF
+		-DHAVE_AVX2="$(usex cpu_flags_x86_avx2)"
+		-DHAVE_SSE4_1="$(usex cpu_flags_x86_sse4_1)"
+		-DHAVE_SSE2="$(usex cpu_flags_x86_sse2)"
+		# We also have cpu flags for ppc/arm/s390x
+		-DVERSION_OVERRIDE=${PV}
+	)
+	cmake_src_configure
+}
+
+src_install(){
+	cmake_src_install
+	# move the bashcomp to correct dir
+	newbashcomp "${ED}/usr/util/bash-completion.sh" "${PN}"
+	rm -r "${ED}/usr/util/" || die
+}