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author | Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2022-01-31 14:31:37 +0100 |
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committer | Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2022-01-31 14:31:37 +0100 |
commit | 416c7d818a75d321cd8b33b1332ef0863d36f5e0 (patch) | |
tree | 15cc6e13476b5e910c84c0aeb6477edd39a0757c /sci-biology | |
parent | sci-libs/spyking-circus: bump to 1.1.0 (diff) | |
download | sci-416c7d818a75d321cd8b33b1332ef0863d36f5e0.tar.gz sci-416c7d818a75d321cd8b33b1332ef0863d36f5e0.tar.bz2 sci-416c7d818a75d321cd8b33b1332ef0863d36f5e0.zip |
sci-biology/mmseqs2: new package
Closes: https://github.com/gentoo/sci/pull/1050
Co-authored-by: Joel Berendzen <joel@generisbio.com>
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/mmseqs2/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/mmseqs2/metadata.xml | 22 | ||||
-rw-r--r-- | sci-biology/mmseqs2/mmseqs2-13.0.ebuild | 51 |
3 files changed, 74 insertions, 0 deletions
diff --git a/sci-biology/mmseqs2/Manifest b/sci-biology/mmseqs2/Manifest new file mode 100644 index 000000000..dbfe85988 --- /dev/null +++ b/sci-biology/mmseqs2/Manifest @@ -0,0 +1 @@ +DIST mmseqs2-13.0.tar.gz 10199551 BLAKE2B 282d270c2b63a186d7534add93f6c23d625c5011392dc2cdff3cf11572ff23cb527726c19f5e9b092830216fa70a788faa46b1a4a2daafee05a513bff37a8a14 SHA512 90904392edd8a619577f79d75b44461b1bb647133850cc384caddb39bcfa3de0793392521edef0e86436ea0f76c9626298bd7975aba961ac7e846786eaf2e919 diff --git a/sci-biology/mmseqs2/metadata.xml b/sci-biology/mmseqs2/metadata.xml new file mode 100644 index 000000000..c957d777e --- /dev/null +++ b/sci-biology/mmseqs2/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <upstream> + <remote-id type="github">soedinglab/mmseqs2</remote-id> + <doc>https://github.com/soedinglab/mmseqs2/wiki</doc> + </upstream> + <maintainer type="person"> + <email>joel@generisbio.com</email> + <name>Joel Berendzen</name> + </maintainer> + <longdescription> + MMseqs2 (Many-against-Many sequence searching) is a software suite toi + 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 + and exhibits very good scalability. MMseqs2 can run 10000 times + faster than BLAST. At 100 times its speed it achieves almost the + same sensitivity. It can perform profile searches with the same + sensitivity as PSI-BLAST at over 400 times its speed. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/mmseqs2/mmseqs2-13.0.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0.ebuild new file mode 100644 index 000000000..5b35f2e5d --- /dev/null +++ b/sci-biology/mmseqs2/mmseqs2-13.0.ebuild @@ -0,0 +1,51 @@ +# 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 +} |