/[gentoo-x86]/sci-biology/lagan/lagan-2.0-r1.ebuild
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Revision 1.1 - (hide annotations) (download)
Tue Jul 21 08:12:46 2009 UTC (10 years, 7 months ago) by weaver
Branch: MAIN
CVS Tags: HEAD
Fix compilation with glibc-2.10, bug 273988
(Portage version: 2.2_rc30/cvs/Linux x86_64)

1 weaver 1.1 # Copyright 1999-2009 Gentoo Foundation
2     # Distributed under the terms of the GNU General Public License v2
3     # $Header: /var/cvsroot/gentoo-x86/sci-biology/lagan/lagan-2.0.ebuild,v 1.1 2009/02/27 00:23:49 weaver Exp $
4    
5     EAPI="2"
6    
7     inherit eutils
8    
9     MY_P="lagan20"
10    
11     DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA"
12     HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
13     SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
14    
15     LICENSE="GPL-2"
16     SLOT="0"
17     IUSE=""
18     KEYWORDS="~amd64 ~x86"
19    
20     DEPEND=""
21     RDEPEND=""
22    
23     S="${WORKDIR}/${MY_P}"
24    
25     src_prepare() {
26     sed -i "/use Getopt::Long;/ i use lib \"/usr/share/${PN}/lib\";" "${S}/supermap.pl" || die
27     # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline
28     sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
29     epatch "${FILESDIR}"/${P}-*.patch
30     }
31    
32     src_install() {
33     dobin lagan.pl slagan.pl mlagan
34     rm lagan.pl slagan.pl utils/Utils.pm
35     dodir /usr/share/${PN}/lib
36     insinto /usr/share/${PN}/lib
37     doins Utils.pm
38     exeinto /usr/share/${PN}/utils
39     doexe utils/*
40     exeinto /usr/share/${PN}
41     doexe *.pl anchors chaos glocal order prolagan
42     insinto /usr/share/${PN}
43     doins *.txt
44     dosym /usr/share/${PN}/supermap.pl /usr/bin/supermap
45     dosym /usr/bin/lagan.pl /usr/bin/lagan
46     dosym /usr/bin/slagan.pl /usr/bin/slagan
47     echo "LAGAN_DIR=\"/usr/share/${PN}\"" > ${S}/99${PN}
48     doenvd "${S}/99${PN}"
49     dodoc Readmes/README.*
50     }

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