blob: e4c2be65afeade495ada72d6674bcf8449a4ad34 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
|
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
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
}
|