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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit toolchain-funcs
MY_P="lagan20"
DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA"
HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
RDEPEND="dev-lang/perl"
S="${WORKDIR}/${MY_P}"
PATCHES=(
"${FILESDIR}/${PN}-2.0-flags.patch"
"${FILESDIR}/${PN}-2.0-gcc4.3.patch"
"${FILESDIR}/${PN}-2.0-fix-c++14.patch"
"${FILESDIR}/${PN}-2.0-qa-implicit-declarations.patch"
)
src_prepare() {
sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die
# NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h
# where libc getline is erroneously used instead of own getline
sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
default
}
src_compile() {
emake \
CC=$(tc-getCC) \
CXX=$(tc-getCXX) \
CXXFLAGS="${CXXFLAGS}" \
CFLAGS="${CFLAGS}"
}
src_install() {
newbin lagan.pl lagan
newbin slagan.pl slagan
dobin mlagan
rm -f lagan.pl slagan.pl utils/Utils.pm || die
insinto /usr/$(get_libdir)/${PN}/lib
doins Utils.pm
exeinto /usr/$(get_libdir)/${PN}/utils
doexe utils/*
exeinto /usr/$(get_libdir)/${PN}
doexe *.pl anchors chaos glocal order prolagan
insinto /usr/$(get_libdir)/${PN}
doins *.txt
dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap
echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > 99${PN} || die
doenvd 99${PN}
dodoc Readmes/README.*
}
|
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