Gentoo Archives: gentoo-commits

From: Andrew Ammerlaan <andrewammerlaan@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mmseqs2/
Date: Mon, 31 Jan 2022 13:32:12
Message-Id: 1643635897.416c7d818a75d321cd8b33b1332ef0863d36f5e0.andrewammerlaan@gentoo
1 commit: 416c7d818a75d321cd8b33b1332ef0863d36f5e0
2 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
3 AuthorDate: Mon Jan 31 13:31:37 2022 +0000
4 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
5 CommitDate: Mon Jan 31 13:31:37 2022 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=416c7d81
7
8 sci-biology/mmseqs2: new package
9
10 Closes: https://github.com/gentoo/sci/pull/1050
11 Co-authored-by: Joel Berendzen <joel <AT> generisbio.com>
12 Package-Manager: Portage-3.0.30, Repoman-3.0.3
13 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
14
15 sci-biology/mmseqs2/metadata.xml | 22 ++++++++++++++
16 sci-biology/mmseqs2/mmseqs2-13.0.ebuild | 51 +++++++++++++++++++++++++++++++++
17 2 files changed, 73 insertions(+)
18
19 diff --git a/sci-biology/mmseqs2/metadata.xml b/sci-biology/mmseqs2/metadata.xml
20 new file mode 100644
21 index 000000000..c957d777e
22 --- /dev/null
23 +++ b/sci-biology/mmseqs2/metadata.xml
24 @@ -0,0 +1,22 @@
25 +<?xml version="1.0" encoding="UTF-8"?>
26 +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
27 +<pkgmetadata>
28 + <upstream>
29 + <remote-id type="github">soedinglab/mmseqs2</remote-id>
30 + <doc>https://github.com/soedinglab/mmseqs2/wiki</doc>
31 + </upstream>
32 + <maintainer type="person">
33 + <email>joel@××××××××××.com</email>
34 + <name>Joel Berendzen</name>
35 + </maintainer>
36 + <longdescription>
37 + MMseqs2 (Many-against-Many sequence searching) is a software suite toi
38 + search and cluster huge protein and nucleotide sequence sets.
39 + MMseqs2 is open source GPL-licensed software implemented in C++.
40 + The software is designed to run on multiple cores and servers
41 + and exhibits very good scalability. MMseqs2 can run 10000 times
42 + faster than BLAST. At 100 times its speed it achieves almost the
43 + same sensitivity. It can perform profile searches with the same
44 + sensitivity as PSI-BLAST at over 400 times its speed.
45 + </longdescription>
46 +</pkgmetadata>
47
48 diff --git a/sci-biology/mmseqs2/mmseqs2-13.0.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0.ebuild
49 new file mode 100644
50 index 000000000..5b35f2e5d
51 --- /dev/null
52 +++ b/sci-biology/mmseqs2/mmseqs2-13.0.ebuild
53 @@ -0,0 +1,51 @@
54 +# Copyright 2021-2022 Gentoo Authors
55 +# Distributed under the terms of the GNU General Public License v2
56 +
57 +EAPI=8
58 +
59 +inherit bash-completion-r1 cmake
60 +
61 +MY_PN="MMseqs2"
62 +
63 +# Must be manually updated with each release
64 +COMMIT="45111b641859ed0ddd875b94d6fd1aef1a675b7e"
65 +
66 +DESCRIPTION="Fast and sensitive sequence search and clustering"
67 +HOMEPAGE="https://github.com/soedinglab/MMseqs2"
68 +SRC_URI="https://github.com/soedinglab/${MY_PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
69 +S="${WORKDIR}/${MY_PN}-${COMMIT}"
70 +
71 +LICENSE="GPL-3"
72 +SLOT="0"
73 +KEYWORDS="~amd64"
74 +IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2"
75 +
76 +RDEPEND="
77 + app-arch/zstd[static-libs]
78 + sys-libs/zlib
79 + app-arch/bzip2
80 +"
81 +DEPEND="${RDEPEND}"
82 +
83 +src_configure() {
84 + local mycmakeargs=(
85 + # Need static libs: https://github.com/soedinglab/MMseqs2/issues/411
86 + -DBUILD_SHARED_LIBS=OFF
87 + -DUSE_SYSTEM_ZSTD=ON
88 + # Disable auto detection, build respecting cpu flags instead
89 + -DNATIVE_ARCH=OFF
90 + -DHAVE_AVX2="$(usex cpu_flags_x86_avx2)"
91 + -DHAVE_SSE4_1="$(usex cpu_flags_x86_sse4_1)"
92 + -DHAVE_SSE2="$(usex cpu_flags_x86_sse2)"
93 + # We also have cpu flags for ppc/arm/s390x
94 + -DVERSION_OVERRIDE=${PV}
95 + )
96 + cmake_src_configure
97 +}
98 +
99 +src_install(){
100 + cmake_src_install
101 + # move the bashcomp to correct dir
102 + newbashcomp "${ED}/usr/util/bash-completion.sh" "${PN}"
103 + rm -r "${ED}/usr/util/" || die
104 +}