/[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 - (hide annotations) (download)
Thu Aug 30 07:46:16 2012 UTC (23 months, 3 weeks 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 jlec 1.2 # Copyright 1999-2012 Gentoo Foundation
2 weaver 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.ebuild,v 1.2 2012/08/30 07:32:21 jlec Exp $
4 weaver 1.1
5 jlec 1.2 EAPI=4
6 weaver 1.1
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 jlec 1.2 SRC_URI="
12     ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
13 weaver 1.1 ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
14    
15     LICENSE="Whitehead-MIT"
16     SLOT="3"
17     IUSE=""
18 jlec 1.2 KEYWORDS="~amd64 ~x86"
19 weaver 1.1
20 jlec 1.2 S="${WORKDIR}/AllPaths"
21 weaver 1.1
22 jlec 1.2 PATCHES=( "${FILESDIR}"/${P}-gcc4.7.patch )
23 weaver 1.1
24 jlec 1.3 src_prepare() {
25     sed \
26     -e "s:-O3:${CXXFLAGS}:g" \
27     -e 's:-ggdb3::g' \
28     -i Makefile* || die
29     base_src_prepare
30     }
31    
32 weaver 1.1 src_compile() {
33     base_src_compile
34 jlec 1.2 emake install_scripts
35 weaver 1.1 }
36    
37     src_install() {
38 jlec 1.2 exeinto /usr/libexec/${P}/
39 weaver 1.1 find bin -type f -executable | xargs doexe || die
40 jlec 1.2
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 weaver 1.1 }

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