/[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 1.5 - (show annotations) (download)
Wed Nov 20 07:29:19 2013 UTC (9 months, 1 week ago) by jlec
Branch: MAIN
CVS Tags: HEAD
Changes since 1.4: +1 -1 lines
FILE REMOVED
superseeded by sci-biology/allpathslg
Upstream wants anybody to move over

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 1.4 2012/11/19 10:27:46 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 DEPEND="!sci-biology/allpathslg"
23 RDEPEND="${DEPEND}"
24
25 PATCHES=( "${FILESDIR}"/${P}-gcc4.7.patch )
26
27 src_prepare() {
28 sed \
29 -e "s:-O3:${CXXFLAGS}:g" \
30 -e 's:-ggdb3::g' \
31 -i Makefile* || die
32 base_src_prepare
33 }
34
35 src_compile() {
36 base_src_compile
37 emake install_scripts
38 }
39
40 src_install() {
41 exeinto /usr/libexec/${P}/
42 find bin -type f -executable | xargs doexe || die
43
44 echo "PATH=\"/usr/libexec/${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 }

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