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Revision 1.3 - (hide annotations) (download)
Wed Jul 17 06:17:01 2013 UTC (15 months ago) by jlec
Branch: MAIN
Changes since 1.2: +3 -3 lines
sci-biology/allpaths: Bump to EAPI=5

(Portage version: 2.2.0_alpha188/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

1 jlec 1.3 # Copyright 1999-2013 Gentoo Foundation
2 jlec 1.1 # Distributed under the terms of the GNU General Public License v2
3 jlec 1.3 # $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1-r1.ebuild,v 1.2 2012/11/19 10:27:46 jlec Exp $
4 jlec 1.1
5 jlec 1.3 EAPI=5
6 jlec 1.1
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-${PV}.tgz
13     ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
14    
15     LICENSE="Whitehead-MIT"
16     SLOT="3"
17     KEYWORDS="~amd64 ~x86"
18     IUSE="openmp"
19    
20 jlec 1.2 DEPEND="!sci-biology/allpathslg"
21     RDEPEND="${DEPEND}"
22    
23 jlec 1.1 S="${WORKDIR}/AllPaths"
24    
25     PATCHES=(
26     "${FILESDIR}"/${P}-gcc4.7.patch
27     "${FILESDIR}"/${P}-boost-1.50.patch
28     "${FILESDIR}"/${P}-linking.patch
29     )
30    
31     pkg_setup() {
32     if use openmp; then
33     if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
34     ewarn "OpenMP is not available in your current selected gcc"
35     die "need openmp capable gcc"
36     fi
37     fi
38     }
39    
40     src_prepare() {
41     sed \
42     -e "s:-O3:${CXXFLAGS}:g" \
43     -e 's:-ggdb3::g' \
44     -i Makefile* || die
45    
46     if use openmp; then
47     sed \
48     -e '/OPEN_MP/s:no:yes:g' \
49     -i Makefile.in || die
50     fi
51     base_src_prepare
52     export L_FLAGS="${LDFLAGS}"
53     }
54    
55     src_configure() {
56     econf \
57     --with-boost="${EPREFIX}/usr" \
58     --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)"
59     }
60    
61     src_compile() {
62     base_src_compile
63     emake install_scripts
64     }
65    
66     src_install() {
67     exeinto /usr/libexec/${P}/
68     find bin -type f -executable | xargs doexe
69    
70     echo "PATH=\"/usr/libexec/${P}/\"" > "${S}/50${P}"
71     doenvd "${S}/50${P}" || die
72    
73     dosym /usr/libexec/${P}/RunAllPaths3G /usr/bin/RunAllPaths3G
74    
75     dodoc "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
76     }

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