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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
inherit eutils flag-o-matic multilib toolchain-funcs
EXTENSIONS="-without-extensions"
DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
SRC_URI="http://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"
}
src_compile() {
pushd core > /dev/null || die
emake \
$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
PREFIX="${EPREFIX}"/usr \
CC="$(tc-getCC)" \
CFLAGS="${CFLAGS}"
popd > /dev/null || die
}
src_test() {
export MAFFT_BINARIES="${S}"/core
cd test || die
bash ../core/mafft sample > test.fftns2 || die
bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die
bash ../core/mafft --globalpair sample > test.gins1 || die
bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die
bash ../core/mafft --localpair sample > test.lins1 || die
bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die
diff test.fftns2 sample.fftns2 || die
diff test.fftnsi sample.fftnsi || die
diff test.gins1 sample.gins1 || die
diff test.ginsi sample.ginsi || die
diff test.lins1 sample.lins1 || die
}
src_install() {
pushd core
emake PREFIX="${ED}usr" install
popd
dodoc readme
}
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