diff --git a/sci-biology/foldseek/Manifest b/sci-biology/foldseek/Manifest new file mode 100644 index 00000000000..c705a097076 --- /dev/null +++ b/sci-biology/foldseek/Manifest @@ -0,0 +1 @@ +DIST foldseek-1.tar.gz 14545729 BLAKE2B 5ded5c9b35c78e8b3ec22d47c44d894f577ef1ac1ce0f3e157706d3f1951df8bdcc4036739d31211354a1128eaeb745659f5e4684c37e3767d43e1d5875a9ddd SHA512 8d2776099cd184da52ee639ea46a603fc07d4719dd4ebf57dfd01ee549b1801c48de48f36de69f1b9760ffef6c7998d3f492886a170f88bbbd14c457eeaa1cfd diff --git a/sci-biology/foldseek/foldseek-1.ebuild b/sci-biology/foldseek/foldseek-1.ebuild new file mode 100644 index 00000000000..e43fffd7399 --- /dev/null +++ b/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 +} diff --git a/sci-biology/foldseek/foldseek-9999.ebuild b/sci-biology/foldseek/foldseek-9999.ebuild new file mode 100644 index 00000000000..e8a814e80fb --- /dev/null +++ b/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 +} diff --git a/sci-biology/foldseek/metadata.xml b/sci-biology/foldseek/metadata.xml new file mode 100644 index 00000000000..b29f4ee1240 --- /dev/null +++ b/sci-biology/foldseek/metadata.xml @@ -0,0 +1,17 @@ + + + + + steineggerlab/foldseek + https://www.biorxiv.org/content/10.1101/2022.02.07.479398 + + + joel@generisbio.com + Joel Berendzen + + + 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. + + diff --git a/sci-biology/mmseqs2/Manifest b/sci-biology/mmseqs2/Manifest index dbfe859884b..4f28731619e 100644 --- a/sci-biology/mmseqs2/Manifest +++ b/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 diff --git a/sci-biology/mmseqs2/metadata.xml b/sci-biology/mmseqs2/metadata.xml index c957d777e25..49f82af2a83 100644 --- a/sci-biology/mmseqs2/metadata.xml +++ b/sci-biology/mmseqs2/metadata.xml @@ -10,7 +10,7 @@ Joel Berendzen - 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 diff --git a/sci-biology/mmseqs2/mmseqs2-13.0.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0.ebuild deleted file mode 100644 index 5b35f2e5d08..00000000000 --- a/sci-biology/mmseqs2/mmseqs2-13.0.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# 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="${RDEPEND}" - -src_configure() { - local mycmakeargs=( - # Need static libs: https://github.com/soedinglab/MMseqs2/issues/411 - -DBUILD_SHARED_LIBS=OFF - -DUSE_SYSTEM_ZSTD=ON - # Disable auto detection, build respecting cpu flags instead - -DNATIVE_ARCH=OFF - -DHAVE_AVX2="$(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 -} diff --git a/sci-biology/mmseqs2/mmseqs2-13.ebuild b/sci-biology/mmseqs2/mmseqs2-13.ebuild new file mode 100644 index 00000000000..f955fb60ef2 --- /dev/null +++ b/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 +} diff --git a/sci-biology/mmseqs2/mmseqs2-9999.ebuild b/sci-biology/mmseqs2/mmseqs2-9999.ebuild new file mode 100644 index 00000000000..a8fa1ecdd50 --- /dev/null +++ b/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 +}