Gentoo Archives: gentoo-commits

From: Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/kraken/
Date: Thu, 30 Jun 2016 21:20:12
Message-Id: 1467321592.94465f706e18530fe400311e03ae114e59a679af.mmokrejs@gentoo
1 commit: 94465f706e18530fe400311e03ae114e59a679af
2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Thu Jun 30 21:19:52 2016 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Thu Jun 30 21:19:52 2016 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=94465f70
7
8 sci-biology/kraken: new package with huge requirements
9
10 Package-Manager: portage-2.2.28
11
12 sci-biology/kraken/kraken-0.10.5.ebuild | 55 +++++++++++++++++++++++++++++++++
13 sci-biology/kraken/metadata.xml | 12 +++++++
14 2 files changed, 67 insertions(+)
15
16 diff --git a/sci-biology/kraken/kraken-0.10.5.ebuild b/sci-biology/kraken/kraken-0.10.5.ebuild
17 new file mode 100644
18 index 0000000..540c73d
19 --- /dev/null
20 +++ b/sci-biology/kraken/kraken-0.10.5.ebuild
21 @@ -0,0 +1,55 @@
22 +# Copyright 1999-2016 Gentoo Foundation
23 +# Distributed under the terms of the GNU General Public License v2
24 +# $Id$
25 +
26 +EAPI=5
27 +
28 +PERL_EXPORT_PHASE_FUNCTIONS=no
29 +inherit perl-module
30 +
31 +DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups"
32 +HOMEPAGE="http://ccb.jhu.edu/software/kraken
33 + http://genomebiology.com/2014/15/3/R46"
34 +SRC_URI="http://ccb.jhu.edu/software/kraken/dl/kraken-0.10.5-beta.tgz
35 + http://ccb.jhu.edu/software/kraken/MANUAL.html"
36 +
37 +LICENSE="GPL-3"
38 +SLOT="0"
39 +KEYWORDS="~amd64"
40 +IUSE=""
41 +
42 +DEPEND=""
43 +RDEPEND="${DEPEND}
44 + dev-lang/perl
45 + net-misc/wget"
46 +
47 +S="${WORKDIR}"/kraken-0.10.5-beta
48 +
49 +src_prepare(){
50 + sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die
51 + echo "exit 0" >> install_kraken.sh || die
52 +}
53 +
54 +src_compile(){
55 + ./install_kraken.sh destdir || die
56 +}
57 +
58 +src_install(){
59 + dohtml "${DISTDIR}"/MANUAL.html
60 + perl_set_version
61 + insinto ${VENDOR_LIB}/${PN}
62 + doins destdir/*.pm
63 + insinto /usr/share/${PN}/util
64 + doins destdir/*.pl
65 + chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util
66 + rm -f destdir/krakenlib.pm
67 + dobin destdir/*
68 +}
69 +
70 +pkg_postinst(){
71 + ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs"
72 + ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read"
73 + ewarn "http://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space"
74 + ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM"
75 + ewarn "Results can be visualized with http://sourceforge.net/p/krona/home/krona"
76 +}
77
78 diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml
79 new file mode 100644
80 index 0000000..f68a1b6
81 --- /dev/null
82 +++ b/sci-biology/kraken/metadata.xml
83 @@ -0,0 +1,12 @@
84 +<?xml version="1.0" encoding="UTF-8"?>
85 +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
86 +<pkgmetadata>
87 + <maintainer type="person">
88 + <email>mmokrejs@×××××××××××××××.cz</email>
89 + <name>Martin Mokrejs</name>
90 + </maintainer>
91 + <maintainer type="project">
92 + <email>sci-biology@g.o</email>
93 + <name>Gentoo Biology Project</name>
94 + </maintainer>
95 +</pkgmetadata>