/[gentoo-x86]/sci-biology/allpaths/allpaths-3.1-r1.ebuild
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Revision 1.1 - (show annotations) (download)
Thu Nov 8 20:54:22 2012 UTC (22 months, 1 week 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 # 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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