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From: "Andrey Kislyuk (weaver)" <weaver@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] gentoo-x86 commit in sci-biology/gatk: metadata.xml gatk-9999.ebuild gatk-1.2.ebuild ChangeLog
Date: Mon, 31 Oct 2011 21:18:27
Message-Id: 20111031211817.CA6A92004B@flycatcher.gentoo.org
1 weaver 11/10/31 21:18:17
2
3 Added: metadata.xml gatk-9999.ebuild gatk-1.2.ebuild
4 ChangeLog
5 Log:
6 New package, ebuild written by me
7
8 (Portage version: 2.2.0_alpha45/cvs/Linux x86_64)
9
10 Revision Changes Path
11 1.1 sci-biology/gatk/metadata.xml
12
13 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/gatk/metadata.xml?rev=1.1&view=markup
14 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/gatk/metadata.xml?rev=1.1&content-type=text/plain
15
16 Index: metadata.xml
17 ===================================================================
18 <?xml version="1.0" encoding="UTF-8"?>
19 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
20 <pkgmetadata>
21 <maintainer>
22 <email>weaver@g.o</email>
23 <name>Andrey Kislyuk</name>
24 </maintainer>
25 <herd>sci-biology</herd>
26 </pkgmetadata>
27
28
29
30 1.1 sci-biology/gatk/gatk-9999.ebuild
31
32 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild?rev=1.1&view=markup
33 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild?rev=1.1&content-type=text/plain
34
35 Index: gatk-9999.ebuild
36 ===================================================================
37 # Copyright 1999-2011 Gentoo Foundation
38 # Distributed under the terms of the GNU General Public License v2
39 # $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild,v 1.1 2011/10/31 21:18:17 weaver Exp $
40
41 EAPI=4
42
43 MY_HASH=885c33a
44
45 EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
46
47 EANT_BUILD_TARGET="dist"
48 EANT_NEEDS_TOOLS="true"
49 JAVA_ANT_REWRITE_CLASSPATH="true"
50
51 #inherit java-pkg-2 java-ant-2 git
52 inherit java-pkg-2 java-ant-2
53
54 DESCRIPTION="The Genome Analysis Toolkit"
55 HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
56 #SRC_URI="https://github.com/broadgsa/gatk/tarball/${PV} -> ${P}.tar.gz"
57 SRC_URI=""
58
59 LICENSE="as-is"
60 SLOT="0"
61 IUSE=""
62 KEYWORDS=""
63
64 COMMON_DEPS=""
65 DEPEND=">=virtual/jdk-1.6
66 ${COMMON_DEPS}"
67 RDEPEND=">=virtual/jre-1.6
68 ${COMMON_DEPS}"
69
70 S="${WORKDIR}/broadgsa-gatk-${MY_HASH}"
71
72 src_prepare() {
73 sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die
74 java-pkg-2_src_prepare
75 }
76
77 src_install() {
78 java-pkg_dojar dist/*.jar
79 java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar
80 java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar
81 }
82
83
84
85 1.1 sci-biology/gatk/gatk-1.2.ebuild
86
87 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/gatk/gatk-1.2.ebuild?rev=1.1&view=markup
88 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/gatk/gatk-1.2.ebuild?rev=1.1&content-type=text/plain
89
90 Index: gatk-1.2.ebuild
91 ===================================================================
92 # Copyright 1999-2011 Gentoo Foundation
93 # Distributed under the terms of the GNU General Public License v2
94 # $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-1.2.ebuild,v 1.1 2011/10/31 21:18:17 weaver Exp $
95
96 EAPI=4
97
98 MY_HASH=885c33a
99
100 EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
101
102 EANT_BUILD_TARGET="dist"
103 EANT_NEEDS_TOOLS="true"
104 JAVA_ANT_REWRITE_CLASSPATH="true"
105
106 #inherit java-pkg-2 java-ant-2 git
107 inherit java-pkg-2 java-ant-2
108
109 DESCRIPTION="The Genome Analysis Toolkit"
110 HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
111 SRC_URI="https://github.com/broadgsa/gatk/tarball/${PV} -> ${P}.tar.gz"
112
113 LICENSE="as-is"
114 SLOT="0"
115 IUSE=""
116 KEYWORDS="~amd64"
117
118 COMMON_DEPS=""
119 DEPEND=">=virtual/jdk-1.6
120 ${COMMON_DEPS}"
121 RDEPEND=">=virtual/jre-1.6
122 ${COMMON_DEPS}"
123
124 S="${WORKDIR}/broadgsa-gatk-${MY_HASH}"
125
126 src_prepare() {
127 sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die
128 java-pkg-2_src_prepare
129 }
130
131 src_install() {
132 java-pkg_dojar dist/*.jar
133 java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar
134 java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar
135 }
136
137
138
139 1.1 sci-biology/gatk/ChangeLog
140
141 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/gatk/ChangeLog?rev=1.1&view=markup
142 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/gatk/ChangeLog?rev=1.1&content-type=text/plain
143
144 Index: ChangeLog
145 ===================================================================
146 # ChangeLog for sci-biology/gatk
147 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
148 # $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.1 2011/10/31 21:18:17 weaver Exp $
149
150 *gatk-9999 (31 Oct 2011)
151 *gatk-1.2 (31 Oct 2011)
152
153 31 Oct 2011; Andrey Kislyuk <weaver@g.o> +gatk-1.2.ebuild,
154 +gatk-9999.ebuild, +metadata.xml:
155 New package, ebuild written by me
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