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From: "Justin Lecher (jlec)" <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] gentoo-x86 commit in sci-chemistry/clashlist: clashlist-3.17.ebuild metadata.xml ChangeLog clashlist-3.17-r1.ebuild
Date: Thu, 07 Jun 2012 15:08:37
Message-Id: 20120607150822.DCA7B2004B@flycatcher.gentoo.org
1 jlec 12/06/07 15:08:22
2
3 Modified: clashlist-3.17.ebuild metadata.xml ChangeLog
4 Added: clashlist-3.17-r1.ebuild
5 Log:
6 sci-chemistry/clashlist: Rename cluster to molprobity-cluster, #419999
7
8 (Portage version: 2.2.0_alpha110/cvs/Linux x86_64)
9
10 Revision Changes Path
11 1.2 sci-chemistry/clashlist/clashlist-3.17.ebuild
12
13 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17.ebuild?rev=1.2&view=markup
14 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17.ebuild?rev=1.2&content-type=text/plain
15 diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17.ebuild?r1=1.1&r2=1.2
16
17 Index: clashlist-3.17.ebuild
18 ===================================================================
19 RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17.ebuild,v
20 retrieving revision 1.1
21 retrieving revision 1.2
22 diff -u -r1.1 -r1.2
23 --- clashlist-3.17.ebuild 19 Jul 2010 06:43:59 -0000 1.1
24 +++ clashlist-3.17.ebuild 7 Jun 2012 15:08:22 -0000 1.2
25 @@ -1,23 +1,25 @@
26 -# Copyright 1999-2010 Gentoo Foundation
27 +# Copyright 1999-2012 Gentoo Foundation
28 # Distributed under the terms of the GNU General Public License v2
29 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17.ebuild,v 1.1 2010/07/19 06:43:59 jlec Exp $
30 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17.ebuild,v 1.2 2012/06/07 15:08:22 jlec Exp $
31
32 -# inherit
33 +EAPI=4
34
35 DESCRIPTION="Build lists of van der Waals clashes from an input PDB file"
36 HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
37 SRC_URI="mirror://gentoo/molprobity-${PV}.tgz"
38
39 SLOT="0"
40 -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
41 LICENSE="richardson"
42 +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
43 IUSE=""
44
45 RDEPEND="
46 - sci-chemistry/cluster
47 + <=sci-chemistry/cluster-1.3.081231
48 sci-chemistry/probe"
49 DEPEND="${RDEPEND}"
50
51 +S="${WORKDIR}"
52 +
53 src_install() {
54 - dobin molprobity3/bin/clashlist || die
55 + dobin molprobity3/bin/clashlist
56 }
57
58
59
60 1.2 sci-chemistry/clashlist/metadata.xml
61
62 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/metadata.xml?rev=1.2&view=markup
63 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/metadata.xml?rev=1.2&content-type=text/plain
64 diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/metadata.xml?r1=1.1&r2=1.2
65
66 Index: metadata.xml
67 ===================================================================
68 RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/clashlist/metadata.xml,v
69 retrieving revision 1.1
70 retrieving revision 1.2
71 diff -u -r1.1 -r1.2
72 --- metadata.xml 19 Jul 2010 06:43:59 -0000 1.1
73 +++ metadata.xml 7 Jun 2012 15:08:22 -0000 1.2
74 @@ -1,16 +1,16 @@
75 <?xml version="1.0" encoding="UTF-8"?>
76 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
77 <pkgmetadata>
78 -<herd>sci-chemistry</herd>
79 -<maintainer>
80 - <email>jlec@g.o</email>
81 -</maintainer>
82 -<longdescription>
83 + <herd>sci-chemistry</herd>
84 + <maintainer>
85 + <email>jlec@g.o</email>
86 + </maintainer>
87 + <longdescription>
88 Clashlist is a simple UNIX script which uses the awk facility along with
89 the programs Probe and Cluster to build lists of van der Waals clashes
90 from an input PDB-format molecular data file (with H atoms). These lists
91 are organized such that collections of interacting residues are grouped
92 together, sorted by the worst clash. For the purposes of this analysis,
93 -a clash is defined as a van der Waals overlap >= 0.4 A.
94 +a clash is defined as a van der Waals overlap &gt;= 0.4 A.
95 </longdescription>
96 </pkgmetadata>
97
98
99
100 1.2 sci-chemistry/clashlist/ChangeLog
101
102 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/ChangeLog?rev=1.2&view=markup
103 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/ChangeLog?rev=1.2&content-type=text/plain
104 diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/ChangeLog?r1=1.1&r2=1.2
105
106 Index: ChangeLog
107 ===================================================================
108 RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/clashlist/ChangeLog,v
109 retrieving revision 1.1
110 retrieving revision 1.2
111 diff -u -r1.1 -r1.2
112 --- ChangeLog 19 Jul 2010 06:43:59 -0000 1.1
113 +++ ChangeLog 7 Jun 2012 15:08:22 -0000 1.2
114 @@ -1,6 +1,12 @@
115 # ChangeLog for sci-chemistry/clashlist
116 -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
117 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/clashlist/ChangeLog,v 1.1 2010/07/19 06:43:59 jlec Exp $
118 +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
119 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/clashlist/ChangeLog,v 1.2 2012/06/07 15:08:22 jlec Exp $
120 +
121 +*clashlist-3.17-r1 (07 Jun 2012)
122 +
123 + 07 Jun 2012; Justin Lecher <jlec@g.o> clashlist-3.17.ebuild,
124 + +clashlist-3.17-r1.ebuild, metadata.xml:
125 + Rename cluster to molprobity-cluster, #419999
126
127 *clashlist-3.17 (19 Jul 2010)
128
129
130
131
132 1.1 sci-chemistry/clashlist/clashlist-3.17-r1.ebuild
133
134 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild?rev=1.1&view=markup
135 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild?rev=1.1&content-type=text/plain
136
137 Index: clashlist-3.17-r1.ebuild
138 ===================================================================
139 # Copyright 1999-2012 Gentoo Foundation
140 # Distributed under the terms of the GNU General Public License v2
141 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild,v 1.1 2012/06/07 15:08:22 jlec Exp $
142
143 EAPI=4
144
145 DESCRIPTION="Build lists of van der Waals clashes from an input PDB file"
146 HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
147 SRC_URI="mirror://gentoo/molprobity-${PV}.tgz"
148
149 SLOT="0"
150 LICENSE="richardson"
151 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
152 IUSE=""
153
154 RDEPEND="
155 >=sci-chemistry/cluster-1.3.081231-r1
156 sci-chemistry/probe"
157 DEPEND="${RDEPEND}"
158
159 S="${WORKDIR}"
160
161 src_prepare() {
162 sed \
163 -e 's: cluster : molprobity-cluster :g' \
164 -i molprobity3/bin/clashlist || die
165 }
166
167 src_install() {
168 dobin molprobity3/bin/clashlist
169 }
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