/[gentoo-x86]/sci-biology/allpaths/allpaths-3.1-r1.ebuild
Gentoo

Contents of /sci-biology/allpaths/allpaths-3.1-r1.ebuild

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.4 - (show annotations) (download)
Wed Nov 20 07:29:19 2013 UTC (9 months, 3 weeks ago) by jlec
Branch: MAIN
CVS Tags: HEAD
Changes since 1.3: +1 -1 lines
FILE REMOVED
superseeded by sci-biology/allpathslg
Upstream wants anybody to move over

1 # Copyright 1999-2013 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-r1.ebuild,v 1.3 2013/07/17 06:17:01 jlec Exp $
4
5 EAPI=5
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-${PV}.tgz
13 ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
14
15 LICENSE="Whitehead-MIT"
16 SLOT="3"
17 KEYWORDS="~amd64 ~x86"
18 IUSE="openmp"
19
20 DEPEND="!sci-biology/allpathslg"
21 RDEPEND="${DEPEND}"
22
23 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 }

  ViewVC Help
Powered by ViewVC 1.1.20