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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/beast-mcmc: metadata.xml ChangeLog beast-mcmc-1.5.1.ebuild beast-mcmc-9999.ebuild
Date: Fri, 02 Oct 2009 21:47:25
Message-Id: E1Mtpy4-0006fB-52@stork.gentoo.org
1 weaver 09/10/02 21:47:12
2
3 Added: metadata.xml ChangeLog beast-mcmc-1.5.1.ebuild
4 beast-mcmc-9999.ebuild
5 Log:
6 Import from Science overlay and rewrite
7 (Portage version: 2.2_rc30/cvs/Linux x86_64)
8
9 Revision Changes Path
10 1.1 sci-biology/beast-mcmc/metadata.xml
11
12 file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/beast-mcmc/metadata.xml?rev=1.1&view=markup
13 plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/beast-mcmc/metadata.xml?rev=1.1&content-type=text/plain
14
15 Index: metadata.xml
16 ===================================================================
17 <?xml version="1.0" encoding="UTF-8"?>
18 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
19 <pkgmetadata>
20 <maintainer>
21 <email>weaver@g.o</email>
22 <name>Andrey Kislyuk</name>
23 </maintainer>
24 <herd>sci-biology</herd>
25 </pkgmetadata>
26
27
28
29 1.1 sci-biology/beast-mcmc/ChangeLog
30
31 file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/beast-mcmc/ChangeLog?rev=1.1&view=markup
32 plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/beast-mcmc/ChangeLog?rev=1.1&content-type=text/plain
33
34 Index: ChangeLog
35 ===================================================================
36 # ChangeLog for sci-biology/beast-mcmc
37 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
38 # $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/ChangeLog,v 1.1 2009/10/02 21:47:11 weaver Exp $
39
40 *beast-mcmc-9999 (02 Oct 2009)
41 *beast-mcmc-1.5.1 (02 Oct 2009)
42
43 02 Oct 2009; Andrey Kislyuk <weaver@g.o> +metadata.xml,
44 +beast-mcmc-1.5.1.ebuild, +beast-mcmc-9999.ebuild:
45 Import from Science overlay and rewrite
46
47
48
49
50 1.1 sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild
51
52 file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild?rev=1.1&view=markup
53 plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild?rev=1.1&content-type=text/plain
54
55 Index: beast-mcmc-1.5.1.ebuild
56 ===================================================================
57 # Copyright 1999-2009 Gentoo Foundation
58 # Distributed under the terms of the GNU General Public License v2
59 # $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild,v 1.1 2009/10/02 21:47:11 weaver Exp $
60
61 EAPI="2"
62
63 ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/"
64
65 WANT_ANT_TASKS="ant-junit4"
66 EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-1,jdom-jaxen-1.0"
67 JAVA_ANT_REWRITE_CLASSPATH="true"
68 JAVA_ANT_ENCODING="latin1"
69 JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
70
71 #inherit java-pkg-2 java-ant-2 eutils subversion
72 inherit java-pkg-2 java-ant-2 eutils
73
74 DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
75 HOMEPAGE="http://code.google.com/p/beast-mcmc/"
76 #SRC_URI=""
77 SRC_URI="mirror://gentoo/${P}.tar.bz2"
78
79 LICENSE="LGPL-3"
80 SLOT="0"
81 KEYWORDS="~amd64 ~x86"
82 IUSE=""
83
84 # TODO: sys-cluster/mpijava
85 COMMON_DEPS="dev-java/colt:0
86 dev-java/jdom:1.0
87 dev-java/itext:0
88 dev-java/junit:4
89 dev-java/jebl:0
90 dev-java/matrix-toolkits-java
91 dev-java/commons-math:1
92 dev-java/jdom-jaxen:1.0"
93 DEPEND=">=virtual/jdk-1.5
94 ${COMMON_DEPS}"
95 RDEPEND=">=virtual/jre-1.5
96 ${COMMON_DEPS}"
97
98 S="${WORKDIR}/beast_release_${PV//./_}"
99
100 src_prepare() {
101 sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die
102 cd lib
103 rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
104 java-pkg_jar-from jdom-1.0
105 java-pkg_jar-from colt
106 java-pkg_jar-from itext
107 java-pkg_jar-from jebl
108 java-pkg_jar-from matrix-toolkits-java
109 java-pkg_jar-from commons-math-1
110 java-pkg-2_src_prepare
111 }
112
113 src_compile() {
114 eant dist_all_BEAST -f build_BEAST_MCMC.xml \
115 -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
116 eant dist -f build_pathogen.xml \
117 -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
118 }
119
120 src_install() {
121 java-pkg_dojar bin/dist/*.jar dist/*.jar
122
123 java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
124 # java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
125 java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
126 java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
127 java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
128 java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
129
130 insinto /usr/share/${PN}
131 doins -r examples || die
132 dodoc NOTIFY doc/*.pdf
133 }
134
135 src_test() {
136 eant junit -f build_BEAST_MCMC.xml \
137 -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
138 }
139
140
141
142 1.1 sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
143
144 file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild?rev=1.1&view=markup
145 plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild?rev=1.1&content-type=text/plain
146
147 Index: beast-mcmc-9999.ebuild
148 ===================================================================
149 # Copyright 1999-2009 Gentoo Foundation
150 # Distributed under the terms of the GNU General Public License v2
151 # $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild,v 1.1 2009/10/02 21:47:11 weaver Exp $
152
153 EAPI="2"
154
155 ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/"
156
157 WANT_ANT_TASKS="ant-junit4"
158 EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-1,jdom-jaxen-1.0"
159 JAVA_ANT_REWRITE_CLASSPATH="true"
160 JAVA_ANT_ENCODING="latin1"
161 JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
162
163 inherit java-pkg-2 java-ant-2 eutils subversion
164
165 DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
166 HOMEPAGE="http://code.google.com/p/beast-mcmc/"
167 SRC_URI=""
168 #SRC_URI="mirror://gentoo/${P}.tar.bz2"
169
170 LICENSE="LGPL-3"
171 SLOT="0"
172 KEYWORDS=""
173 IUSE=""
174
175 # TODO: sys-cluster/mpijava
176 COMMON_DEPS="dev-java/colt:0
177 dev-java/jdom:1.0
178 dev-java/itext:0
179 dev-java/junit:4
180 dev-java/jebl:0
181 dev-java/matrix-toolkits-java
182 dev-java/commons-math:1
183 dev-java/jdom-jaxen:1.0"
184 DEPEND=">=virtual/jdk-1.5
185 ${COMMON_DEPS}"
186 RDEPEND=">=virtual/jre-1.5
187 ${COMMON_DEPS}"
188
189 S="${WORKDIR}/beast_release_${PV//./_}"
190
191 src_prepare() {
192 sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die
193 cd lib
194 rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
195 java-pkg_jar-from jdom-1.0
196 java-pkg_jar-from colt
197 java-pkg_jar-from itext
198 java-pkg_jar-from jebl
199 java-pkg_jar-from matrix-toolkits-java
200 java-pkg_jar-from commons-math-1
201 java-pkg-2_src_prepare
202 }
203
204 src_compile() {
205 eant dist_all_BEAST -f build_BEAST_MCMC.xml \
206 -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
207 eant dist -f build_pathogen.xml \
208 -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
209 }
210
211 src_install() {
212 java-pkg_dojar bin/dist/*.jar dist/*.jar
213
214 java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
215 # java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
216 java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
217 java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
218 java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
219 java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
220
221 insinto /usr/share/${PN}
222 doins -r examples || die
223 dodoc NOTIFY doc/*.pdf
224 }
225
226 src_test() {
227 eant junit -f build_BEAST_MCMC.xml \
228 -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
229 }
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