[gentoo-commits] repo/gentoo:master commit in: sci-biology/mafft/

["David Seifert" <soap@gentoo.org>]

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
+}