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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
DESCRIPTION="Population genetics analysis package"
HOMEPAGE="http://www.popgen.dk/angsd"
SRC_URI="https://github.com/ANGSD/angsd/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
DEPEND="
dev-lang/R
sci-libs/htslib:0="
RDEPEND="${DEPEND}"
# https://github.com/ANGSD/angsd/issues/9
src_prepare(){
default
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(){
einstalldocs
dobin angsd
cd misc || die
dobin \
supersim haploToPlink ibs thetaStat realSFS msToGlf msHOT2glf smartCount \
printIcounts splitgl contamination contamination2 NGSadmix ngsPSMC scounts
}
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