/[gentoo-x86]/sci-biology/allpaths/allpaths-3.1.ebuild
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Contents of /sci-biology/allpaths/allpaths-3.1.ebuild

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Revision 1.3 - (show annotations) (download)
Thu Aug 30 07:46:16 2012 UTC (2 years, 3 months ago) by jlec
Branch: MAIN
Changes since 1.2: +9 -1 lines
sci-biology/allpaths: Respect CXXFLAGS

(Portage version: 2.2.0_alpha123/cvs/Linux x86_64)

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 1.2 2012/08/30 07:32:21 jlec Exp $
4
5 EAPI=4
6
7 inherit base
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-${PV}.tgz
13 ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
14
15 LICENSE="Whitehead-MIT"
16 SLOT="3"
17 IUSE=""
18 KEYWORDS="~amd64 ~x86"
19
20 S="${WORKDIR}/AllPaths"
21
22 PATCHES=( "${FILESDIR}"/${P}-gcc4.7.patch )
23
24 src_prepare() {
25 sed \
26 -e "s:-O3:${CXXFLAGS}:g" \
27 -e 's:-ggdb3::g' \
28 -i Makefile* || die
29 base_src_prepare
30 }
31
32 src_compile() {
33 base_src_compile
34 emake install_scripts
35 }
36
37 src_install() {
38 exeinto /usr/libexec/${P}/
39 find bin -type f -executable | xargs doexe || die
40
41 echo "PATH=\"/usr/libexec/${P}/\"" > "${S}/50${P}"
42 doenvd "${S}/50${P}" || die
43
44 dosym /usr/libexec/${P}/RunAllPaths3G /usr/bin/RunAllPaths3G
45
46 dodoc "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
47 }

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