/[gentoo-x86]/sci-biology/allpaths/allpaths-3.1-r1.ebuild
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Revision 1.1 - (hide annotations) (download)
Thu Nov 8 20:54:22 2012 UTC (2 years, 1 month ago) by jlec
Branch: MAIN
sci-biology/allpaths: Fix for latest boost, #421727; fix for additional problem with gcc-4.7; enable openmp support; Respect LDFALGS and CFLAGS everywhere; make it gold resistant

(Portage version: 2.2.0_alpha142/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

1 jlec 1.1 # Copyright 1999-2012 Gentoo Foundation
2     # Distributed under the terms of the GNU General Public License v2
3     # $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.3 2012/08/30 07:46:16 jlec Exp $
4    
5     EAPI=4
6    
7     inherit base multilib
8    
9     DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
10     HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
11     SRC_URI="
12     ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
13     ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
14    
15     LICENSE="Whitehead-MIT"
16     SLOT="3"
17     KEYWORDS="~amd64 ~x86"
18     IUSE="openmp"
19    
20     S="${WORKDIR}/AllPaths"
21    
22     PATCHES=(
23     "${FILESDIR}"/${P}-gcc4.7.patch
24     "${FILESDIR}"/${P}-boost-1.50.patch
25     "${FILESDIR}"/${P}-linking.patch
26     )
27    
28     pkg_setup() {
29     if use openmp; then
30     if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
31     ewarn "OpenMP is not available in your current selected gcc"
32     die "need openmp capable gcc"
33     fi
34     fi
35     }
36    
37     src_prepare() {
38     sed \
39     -e "s:-O3:${CXXFLAGS}:g" \
40     -e 's:-ggdb3::g' \
41     -i Makefile* || die
42    
43     if use openmp; then
44     sed \
45     -e '/OPEN_MP/s:no:yes:g' \
46     -i Makefile.in || die
47     fi
48     base_src_prepare
49     export L_FLAGS="${LDFLAGS}"
50     }
51    
52     src_configure() {
53     econf \
54     --with-boost="${EPREFIX}/usr" \
55     --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)"
56     }
57    
58     src_compile() {
59     base_src_compile
60     emake install_scripts
61     }
62    
63     src_install() {
64     exeinto /usr/libexec/${P}/
65     find bin -type f -executable | xargs doexe
66    
67     echo "PATH=\"/usr/libexec/${P}/\"" > "${S}/50${P}"
68     doenvd "${S}/50${P}" || die
69    
70     dosym /usr/libexec/${P}/RunAllPaths3G /usr/bin/RunAllPaths3G
71    
72     dodoc "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
73     }

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