commit: 481e43cca963debc0db30e5c751dda55dc4ea5d7 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Jun 19 18:04:28 2022 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Jun 19 18:04:28 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=481e43cc
sci-biology/mafft: add 7.490 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/mafft/Manifest | 1 + sci-biology/mafft/mafft-7.490.ebuild | 62 ++++++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest index cc67db0ab402..bb9ba76f1c82 100644 --- a/sci-biology/mafft/Manifest +++ b/sci-biology/mafft/Manifest @@ -1 +1,2 @@ DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9 +DIST mafft-7.490-without-extensions-src.tgz 605510 BLAKE2B f432ea3001f1d9c18cecea50d19f48570ffe7edf56e64088f8854acc1ee17fd7c1696244133f90ae0bf916f4499becfbfa8a770ca51a370219191f2a29f73db4 SHA512 dd87b731fdee48828da93c715ef480de474870de2fa42727e8d34b62bc136fb486dd9079ca2acdf1745f0a621fe4f413e25c05f7534f1673b6f9c1199ce70b8e diff --git a/sci-biology/mafft/mafft-7.490.ebuild b/sci-biology/mafft/mafft-7.490.ebuild new file mode 100644 index 000000000000..a5ff0a5764d6 --- /dev/null +++ b/sci-biology/mafft/mafft-7.490.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"; +SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"; +S="${WORKDIR}/${P}${EXTENSIONS}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" + +src_prepare() { + default + + sed \ + -e 's/(PREFIX)\/man/(PREFIX)\/share\/man/' \ + -e 's:$(LDFLAGS)::g' \ + -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ + -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ + -e '/INSTALL/s: -s : :g' \ + -i core/Makefile || die +} + +src_configure() { + append-cflags -Wno-unused-result +} + +src_compile() { + emake -C core \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die "Tests failed" + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die "Tests failed" + bash ../core/mafft --globalpair sample > test.gins1 || die "Tests failed" + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die "Tests failed" + bash ../core/mafft --localpair sample > test.lins1 || die "Tests failed" + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die "Tests failed" + + diff test.fftns2 sample.fftns2 || die "Tests failed" + diff test.fftnsi sample.fftnsi || die "Tests failed" + diff test.gins1 sample.gins1 || die "Tests failed" + diff test.ginsi sample.ginsi || die "Tests failed" + diff test.lins1 sample.lins1 || die "Tests failed" +} + +src_install() { + emake -C core DESTDIR="${D}" STRIP=":" PREFIX="${EPREFIX}"/usr install + dodoc readme +}
