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commit: 416c7d818a75d321cd8b33b1332ef0863d36f5e0 |
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Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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AuthorDate: Mon Jan 31 13:31:37 2022 +0000 |
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Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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CommitDate: Mon Jan 31 13:31:37 2022 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=416c7d81 |
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|
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sci-biology/mmseqs2: new package |
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|
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Closes: https://github.com/gentoo/sci/pull/1050 |
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Co-authored-by: Joel Berendzen <joel <AT> generisbio.com> |
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Package-Manager: Portage-3.0.30, Repoman-3.0.3 |
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Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> |
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|
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sci-biology/mmseqs2/metadata.xml | 22 ++++++++++++++ |
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sci-biology/mmseqs2/mmseqs2-13.0.ebuild | 51 +++++++++++++++++++++++++++++++++ |
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2 files changed, 73 insertions(+) |
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|
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diff --git a/sci-biology/mmseqs2/metadata.xml b/sci-biology/mmseqs2/metadata.xml |
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new file mode 100644 |
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index 000000000..c957d777e |
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--- /dev/null |
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+++ b/sci-biology/mmseqs2/metadata.xml |
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@@ -0,0 +1,22 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <upstream> |
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+ <remote-id type="github">soedinglab/mmseqs2</remote-id> |
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+ <doc>https://github.com/soedinglab/mmseqs2/wiki</doc> |
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+ </upstream> |
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+ <maintainer type="person"> |
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+ <email>joel@××××××××××.com</email> |
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+ <name>Joel Berendzen</name> |
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+ </maintainer> |
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+ <longdescription> |
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+ MMseqs2 (Many-against-Many sequence searching) is a software suite toi |
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+ search and cluster huge protein and nucleotide sequence sets. |
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+ MMseqs2 is open source GPL-licensed software implemented in C++. |
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+ The software is designed to run on multiple cores and servers |
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+ and exhibits very good scalability. MMseqs2 can run 10000 times |
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+ faster than BLAST. At 100 times its speed it achieves almost the |
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+ same sensitivity. It can perform profile searches with the same |
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+ sensitivity as PSI-BLAST at over 400 times its speed. |
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+ </longdescription> |
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+</pkgmetadata> |
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|
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diff --git a/sci-biology/mmseqs2/mmseqs2-13.0.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0.ebuild |
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new file mode 100644 |
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index 000000000..5b35f2e5d |
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--- /dev/null |
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+++ b/sci-biology/mmseqs2/mmseqs2-13.0.ebuild |
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@@ -0,0 +1,51 @@ |
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+# Copyright 2021-2022 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=8 |
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+ |
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+inherit bash-completion-r1 cmake |
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+ |
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+MY_PN="MMseqs2" |
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+ |
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+# Must be manually updated with each release |
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+COMMIT="45111b641859ed0ddd875b94d6fd1aef1a675b7e" |
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+ |
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+DESCRIPTION="Fast and sensitive sequence search and clustering" |
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+HOMEPAGE="https://github.com/soedinglab/MMseqs2" |
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+SRC_URI="https://github.com/soedinglab/${MY_PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" |
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+S="${WORKDIR}/${MY_PN}-${COMMIT}" |
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+ |
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+LICENSE="GPL-3" |
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+SLOT="0" |
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+KEYWORDS="~amd64" |
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+IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2" |
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+ |
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+RDEPEND=" |
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+ app-arch/zstd[static-libs] |
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+ sys-libs/zlib |
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+ app-arch/bzip2 |
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+" |
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+DEPEND="${RDEPEND}" |
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+ |
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+src_configure() { |
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+ local mycmakeargs=( |
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+ # Need static libs: https://github.com/soedinglab/MMseqs2/issues/411 |
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+ -DBUILD_SHARED_LIBS=OFF |
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+ -DUSE_SYSTEM_ZSTD=ON |
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+ # Disable auto detection, build respecting cpu flags instead |
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+ -DNATIVE_ARCH=OFF |
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+ -DHAVE_AVX2="$(usex cpu_flags_x86_avx2)" |
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+ -DHAVE_SSE4_1="$(usex cpu_flags_x86_sse4_1)" |
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+ -DHAVE_SSE2="$(usex cpu_flags_x86_sse2)" |
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+ # We also have cpu flags for ppc/arm/s390x |
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+ -DVERSION_OVERRIDE=${PV} |
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+ ) |
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+ cmake_src_configure |
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+} |
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+ |
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+src_install(){ |
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+ cmake_src_install |
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+ # move the bashcomp to correct dir |
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+ newbashcomp "${ED}/usr/util/bash-completion.sh" "${PN}" |
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+ rm -r "${ED}/usr/util/" || die |
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+} |