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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
inherit eutils toolchain-funcs
DESCRIPTION="Whole genome association analysis toolset"
HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink
https://www.cog-genomics.org/plink2/"
SRC_URI="https://www.cog-genomics.org/static/bin/plink160731/plink_src.zip -> ${P}.zip"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="lapack"
DEPEND="
app-arch/unzip
virtual/pkgconfig"
RDEPEND="
sys-libs/zlib
lapack? ( virtual/lapack
virtual/cblas )"
S="${WORKDIR}/"
# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
src_prepare() {
rm -rf zlib-1.2.8 || die
sed \
-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
-i *.{c,h} || die
sed \
-e 's:g++:$(CXX):g' \
-e 's:gcc:$(CC):g' \
-e 's:gfortran:$(FC):g' \
-i Makefile || die
if ! use lapack; then
sed -e 's/^NO_LAPACK =/NO_LAPACK = 1/' -i Makefile || die
sed -e 's@^// #define NOLAPACK@#define NOLAPACK@' -i plink_common.h || die
fi
tc-export PKG_CONFIG
}
src_compile() {
local blasflags
use lapack && blasflags="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
emake \
CXX=$(tc-getCXX) \
CFLAGS="${CFLAGS}" \
ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
BLASFLAGS="$blasflags"
}
src_install() {
newbin plink p-link
}
pkg_postinst(){
einfo "plink binary is now renamed to p-link to avoid file collision"
}
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