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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
inherit git-2
[ "$PV" == "9999" ] && inherit git-2
DESCRIPTION="Population genetics analysis package"
HOMEPAGE="http://www.popgen.dk/angsd"
if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
KEYWORDS=""
else
EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
EGIT_BRANCH="0.700"
KEYWORDS=""
fi
LICENSE="GPL-2"
SLOT="0"
IUSE=""
DEPEND="dev-lang/R
sci-libs/htslib"
RDEPEND="${DEPEND}"
# https://github.com/ANGSD/angsd/issues/9
src_prepare(){
sed -e 's@FLAGS=-O3@FLAGS=@' \
-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
-e 's@all: htshook angsd misc@all: angsd misc@' -i Makefile || die
sed -e 's@HTSLIB = .*@HTSLIB = -lhts@' \
-e 's@HTSDIR = .*@HTSDIR = /usr/include@' -i misc/Makefile || die
sed -e 's@include "../htslib/bgzf.h@include "bgzf.h@' -i misc/thetaStat.cpp || die
}
src_compile(){
emake HTS=/usr/include
}
src_install(){
dobin angsd
dodoc README.md
cd misc || die
dobin supersim thetaStat realSFS emOptim2 msToGlf smartCount printIcounts splitgl contamination NGSadmix
}
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