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# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
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/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="dev-lang/perl"
S="${WORKDIR}/${MY_P}"
PATCHES=(
"${FILESDIR}"/${P}-makefile.patch
"${FILESDIR}"/${P}-conflicting-getline.patch
"${FILESDIR}"/${P}-gcc-4.8.patch
"${FILESDIR}"/${P}-ambiguous-end.patch
"${FILESDIR}"/${P}-gcc-9.patch
"${FILESDIR}"/${P}-gcc-10.patch
"${FILESDIR}"/${P}-C99-static-inline.patch
"${FILESDIR}"/${P}-qa-implicit-declarations.patch
)
src_prepare() {
default
sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/lagan/lib\";" \
supermap.pl || die
}
src_configure() {
tc-export CC CXX
}
src_install() {
newbin lagan.pl lagan
newbin slagan.pl slagan
dobin mlagan
rm lagan.pl slagan.pl utils/Utils.pm || die
insinto /usr/$(get_libdir)/lagan/lib
doins Utils.pm
exeinto /usr/$(get_libdir)/lagan/utils
doexe utils/*
exeinto /usr/$(get_libdir)/lagan
doexe *.pl anchors chaos glocal order prolagan
insinto /usr/$(get_libdir)/lagan
doins *.txt
dosym ../$(get_libdir)/lagan/supermap.pl /usr/bin/supermap
newenvd - 99lagan <<- _EOF_
LAGAN_DIR="${EPREFIX}/usr/$(get_libdir)/lagan"
_EOF_
dodoc Readmes/README.*
}
|
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