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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=6
inherit git-r3
DESCRIPTION="Population genetics analysis package"
HOMEPAGE="http://www.popgen.dk/angsd"
EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
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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