/[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 1.4 - (hide annotations) (download)
Mon Nov 19 10:27:46 2012 UTC (2 years, 1 month ago) by jlec
Branch: MAIN
Changes since 1.3: +4 -1 lines
sci-biology/allpaths: Block sci-biology/allpathslg due to file collision, #443740

(Portage version: 2.2.0_alpha142/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

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 1.4 # $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.3 2012/08/30 07:46:16 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 1.4 DEPEND="!sci-biology/allpathslg"
23     RDEPEND="${DEPEND}"
24    
25 jlec 1.2 PATCHES=( "${FILESDIR}"/${P}-gcc4.7.patch )
26 weaver 1.1
27 jlec 1.3 src_prepare() {
28     sed \
29     -e "s:-O3:${CXXFLAGS}:g" \
30     -e 's:-ggdb3::g' \
31     -i Makefile* || die
32     base_src_prepare
33     }
34    
35 weaver 1.1 src_compile() {
36     base_src_compile
37 jlec 1.2 emake install_scripts
38 weaver 1.1 }
39    
40     src_install() {
41 jlec 1.2 exeinto /usr/libexec/${P}/
42 weaver 1.1 find bin -type f -executable | xargs doexe || die
43 jlec 1.2
44     echo "PATH=\"/usr/libexec/${P}/\"" > "${S}/50${P}"
45     doenvd "${S}/50${P}" || die
46    
47     dosym /usr/libexec/${P}/RunAllPaths3G /usr/bin/RunAllPaths3G
48    
49     dodoc "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
50 weaver 1.1 }

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