fix mmseqs, add foldseek

sci-biology/foldseek/Manifest

@@ -0,0 +1 @@
+DIST foldseek-1.tar.gz 14545729 BLAKE2B 5ded5c9b35c78e8b3ec22d47c44d894f577ef1ac1ce0f3e157706d3f1951df8bdcc4036739d31211354a1128eaeb745659f5e4684c37e3767d43e1d5875a9ddd SHA512 8d2776099cd184da52ee639ea46a603fc07d4719dd4ebf57dfd01ee549b1801c48de48f36de69f1b9760ffef6c7998d3f492886a170f88bbbd14c457eeaa1cfd

sci-biology/foldseek/foldseek-1.ebuild

@@ -0,0 +1,43 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Fast and sensitive comparison of large structure sets"
+HOMEPAGE="https://github.com/steineggerlab/foldseek"
+# To be consistent with upstream, this must be updated with each release
+SUB_PV="3c64211"
+MY_PV="${PV}-${SUB_PV}"
+
+SRC_URI="https://github.com/steineggerlab/${PN}/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# Need static libs per https://github.com/soedinglab/MMseqs2/issues/411
+DEPEND="
+	sys-libs/zlib[static-libs]
+	app-arch/bzip2[static-libs]
+	app-arch/zstd[static-libs]
+"
+DEPEND="${RDEPEND}
+	app-shells/bash-completion
+"
+
+S="${WORKDIR}/${PN}-${MY_PV}"
+
+src_configure() {
+        local mycmakeargs=(
+                -DBUILD_SHARED_LIBS=OFF
+                -DUSE_SYSTEM_ZSTD=ON
+                # In principle, we should be using system cpu flags
+                # but cmake flags for SSE, SSE3, and SSE4_2 aren't
+                # defined, resulting in no CPU flags getting recognized.
+                # Ditto for static bundled mmseqs and gemmi libs.
+                -DVERSION_OVERRIDE=${MY_PV}
+        )
+        cmake_src_configure
+}

sci-biology/foldseek/foldseek-9999.ebuild

@@ -0,0 +1,32 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake git-r3
+
+DESCRIPTION="Fast and sensitive comparison of large structure sets"
+HOMEPAGE="https://github.com/steineggerlab/foldseek"
+EGIT_REPO_URI="https://github.com/steineggerlab/foldseek"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+
+# Need static libs per https://github.com/soedinglab/MMseqs2/issues/411
+DEPEND="
+	sys-libs/zlib[static-libs]
+	app-arch/bzip2[static-libs]
+	app-arch/zstd[static-libs]
+"
+DEPEND="${RDEPEND}
+	app-shells/bash-completion
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=OFF
+		-DUSE_SYSTEM_ZSTD=ON
+	)
+	cmake_src_configure
+}

sci-biology/foldseek/metadata.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+    <upstream>
+        <remote-id type="github">steineggerlab/foldseek</remote-id>
+        <doc>https://www.biorxiv.org/content/10.1101/2022.02.07.479398</doc>
+    </upstream>
+    <maintainer type="person">
+        <email>joel@generisbio.com</email>
+        <name>Joel Berendzen</name>
+    </maintainer>
+    <longdescription>
+		Foldseek enables fast and sensitive comparisons of large structure sets.
+		It reaches sensitivities similar to state-of-the-art aligners while
+		being at least 20,000 times faster.
+    </longdescription>
+</pkgmetadata>

sci-biology/mmseqs2/Manifest

@@ -1 +1 @@
-DIST mmseqs2-13.0.tar.gz 10199551 BLAKE2B 282d270c2b63a186d7534add93f6c23d625c5011392dc2cdff3cf11572ff23cb527726c19f5e9b092830216fa70a788faa46b1a4a2daafee05a513bff37a8a14 SHA512 90904392edd8a619577f79d75b44461b1bb647133850cc384caddb39bcfa3de0793392521edef0e86436ea0f76c9626298bd7975aba961ac7e846786eaf2e919
+DIST mmseqs2-13.tar.gz 10196433 BLAKE2B d7c388a0bd0daebf8e3389d0de3f2ec3a9a42a76c2c2e9266326f47888ce3b7ecb201373e06b7e7b1ff6878e8e7e4d00dedde0d3e937384e9cecfdf2e33840b5 SHA512 2dc34d28ca29ca8b1fff31f5d92e10f3e9fe2cd5da3ce96073245b87e80e2dc43bbdb232ca21fd93880575edc87038463497c3ae1633004703985f8db301ffb4

sci-biology/mmseqs2/metadata.xml

@@ -10,7 +10,7 @@
         <name>Joel Berendzen</name>
     </maintainer>
     <longdescription>
-        MMseqs2 (Many-against-Many sequence searching) is a software suite toi
+        MMseqs2 (Many-against-Many sequence searching) is a software suite to
         search and cluster huge protein and nucleotide sequence sets.
         MMseqs2 is open source GPL-licensed software implemented in C++.
         The software is designed to run on multiple cores and servers

sci-biology/mmseqs2/mmseqs2-13.ebuild

@@ -0,0 +1,48 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit bash-completion-r1 cmake
+
+DESCRIPTION="Fast and sensitive sequence search and clustering"
+HOMEPAGE="https://github.com/soedinglab/MMseqs2"
+MY_PN="MMseqs2"
+SUB_PV="45111" # this is a hex value and must be updated with each release
+MY_PV="${PV}-${SUB_PV}"
+
+SRC_URI="https://github.com/soedinglab/${MY_PN}/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# This package only builds correctly native and does not respect
+# CPU flags, despite a subset of them being defined as cmake flags.
+
+# Need static libs per https://github.com/soedinglab/MMseqs2/issues/411
+DEPEND="
+	sys-libs/zlib[static-libs]
+	app-arch/bzip2[static-libs]
+	app-arch/zstd[static-libs]
+"
+DEPEND="${RDEPEND}
+	app-shells/bash-completion
+"
+
+S="${WORKDIR}/${MY_PN}-${MY_PV}"
+
+src_configure() {
+        local mycmakeargs=(
+                -DBUILD_SHARED_LIBS=OFF
+                -DUSE_SYSTEM_ZSTD=ON
+                -DVERSION_OVERRIDE=${MY_PV}
+        )
+        cmake_src_configure
+}
+
+src_install(){
+	cmake_src_install
+	newbashcomp "${ED}/usr/util/bash-completion.sh" mmseqs
+	rm -r "${ED}/usr/util/" || die
+}

sci-biology/mmseqs2/mmseqs2-9999.ebuild

@@ -0,0 +1,41 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit bash-completion-r1 cmake git-r3
+
+DESCRIPTION="Fast and sensitive sequence search and clustering"
+HOMEPAGE="https://github.com/soedinglab/MMseqs2"
+MY_PN="MMseqs2"
+EGIT_REPO_URI="https://github.com/soedinglab/MMseqs2"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2"
+
+# Need static libs per https://github.com/soedinglab/MMseqs2/issues/411
+DEPEND="
+	sys-libs/zlib[static-libs]
+	app-arch/bzip2[static-libs]
+	app-arch/zstd[static-libs]
+"
+DEPEND="${RDEPEND}
+	app-shells/bash-completion
+"
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=OFF
+		-DUSE_SYSTEM_ZSTD=ON
+		# Live version will be built native
+	)
+	cmake_src_configure
+}
+
+src_install(){
+	cmake_src_install
+	newbashcomp "${ED}/usr/util/bash-completion.sh" mmseqs
+	rm -r "${ED}/usr/util/" || die
+}