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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
inherit toolchain-funcs
DESCRIPTION="Multiple alignment of large DNA sequences"
HOMEPAGE="http://baboon.math.berkeley.edu/mavid/"
SRC_URI="http://bio.math.berkeley.edu/mavid/download/mavid-package-${PV}.tar.gz"
LICENSE="mavid"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
DEPEND=""
RDEPEND="
sci-biology/clustalw
sci-biology/fastdnaml"
S="${WORKDIR}"/${PN}-package-${PV}
src_prepare() {
sed \
-e 's:OPT_CPP_OPTIONS =:OPT_CPP_OPTIONS ?=:g' \
-e 's:DEBUG_CPP_OPTIONS =:DEBUG_CPP_OPTIONS ?=:g' \
-i $(find -type f -name Makefile) || die
}
src_compile() {
emake \
CPP=$(tc-getCXX) \
BASE_CPP_OPTIONS="${CXXFLAGS}" \
DEBUG_CPP_OPTIONS="${CXXFLAGS}" \
OPT_CPP_OPTIONS="${CXXFLAGS}"
}
src_install() {
local i
dobin mavid/{mavid,mavid.pl}
for i in checkfasta cut_alignment extract_seq extract_tree fasta2phylip phylip2fasta project_alignment randtree root_tree tree_dists; do
dobin utils/$i/$i
done
dodoc examples/*
newdoc mavid/README README.mavid
}
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