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# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit eutils flag-o-matic multilib 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"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
IUSE="threads"
S="${WORKDIR}"/${P}${EXTENSIONS}
src_prepare() {
# epatch "${FILESDIR}"/${PN}-7.037-respect.patch
use threads && append-cppflags -Denablemultithread
# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
sed \
-e 's:$(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_compile() {
cd core || die
emake \
$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
PREFIX="${EPREFIX}"/usr \
CC="$(tc-getCC)" \
CFLAGS="${CFLAGS} -Wno-unused-result"
}
src_test() {
export MAFFT_BINARIES="${S}"/core
cd test || die
bash ../core/mafft sample > test.fftns2 || die
bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die
bash ../core/mafft --globalpair sample > test.gins1 || die
bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die
bash ../core/mafft --localpair sample > test.lins1 || die
bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die
diff test.fftns2 sample.fftns2 || die
diff test.fftnsi sample.fftnsi || die
diff test.gins1 sample.gins1 || die
diff test.ginsi sample.ginsi || die
diff test.lins1 sample.lins1 || die
}
src_install() {
dodoc readme
cd core || die
emake PREFIX="${ED}usr" install
}
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