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