[med-svn] r6165 - trunk/packages/gbrowse/trunk/debian

Sun Mar 6 10:24:23 UTC 2011

Author: plessy
Date: 2011-03-06 10:24:19 +0000 (Sun, 06 Mar 2011)
New Revision: 6165

Modified:
   trunk/packages/gbrowse/trunk/debian/copyright
Log:
First copyright review for Gbrowse. Please proofread me !

The following two files have unknown licenses:

Files: contrib/GeneFinder/genefinder/readseq.c
Copyright: ?\194?\169 R Durbin, 1994
License: unknown

Files: htdocs/css/dropdown/default_theme.css htdocs/css/dropdown/dropdown.css
Copyright: ?\194?\169 2008 Live Web Institute. All Rights Reserved.
License: unknown

readseq.c is most probably free, but for the CSS files, I have no idea.


Modified: trunk/packages/gbrowse/trunk/debian/copyright
===================================================================

--- trunk/packages/gbrowse/trunk/debian/copyright	2011-03-05 15:39:14 UTC (rev 6164)
+++ trunk/packages/gbrowse/trunk/debian/copyright	2011-03-06 10:24:19 UTC (rev 6165)
@@ -4,19 +4,157 @@
 Name: GBrowse
 
 Files: *
-Copyright: Lincoln Stein <lincoln.stein at gmail.com>
-License: Artistic or GPL-1+
+Copyright: © 2002 Cold Spring Harbor Laboratory and University of California, Berkeley
+ © 2008 H. Mark Okada <hmokada at hotmail.com>.
+ © 2001,2003,2005,2008 Cold Spring Harbor Laboratory
+ © 2010 Ontario Institute for Cancer Research
+License: GPL-1+ or Artistic-2.0
+ The Generic Genome Browser package versions between 1.0 and 1.8 and
+ all associated files are Copyright (c) 2002 Cold Spring Harbor
+ Laboratory and University of California, Berkeley. Versions 1.9 and
+ higher are copyright (c) 2010 Ontario Institute for Cancer Research.
+ .
+ This package and its accompanying libraries is free software; you can
+ redistribute it and/or modify it under the terms of the GPL (either
+ version 1, or at your option, any later version) or the Artistic
+ License 2.0.  Refer to LICENSE for the full license text.
+ .
+ CSHL makes no representations whatsoever as to the SOFTWARE contained
+ herein.  It is experimental in nature and is provided WITHOUT WARRANTY
+ OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER
+ WARRANTY, EXPRESS OR IMPLIED.  CSHL MAKES NO REPRESENTATION OR
+ WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR
+ OTHER PROPRIETARY RIGHT.
+ .
+ By downloading this SOFTWARE, your Institution hereby indemnifies CSHL
+ against any loss, claim, damage or liability, of whatsoever kind or
+ nature, which may arise from your Institution's respective use,
+ handling or storage of the SOFTWARE.
+ .
+ If publications result from research using this SOFTWARE, we ask that
+ CSHL, University of California, Berkeley and the Ontario Institute for
+ Cancer Research be acknowledged and/or credit be given to
+ CSHL/Berkeley/OICR scientists, as scientifically appropriate.
 
+Files: bin/auto_install_databases.pl
+ bin/bed2gff3.pl
+ bin/bp_load_gff.pl
+ bin/gtf2gff3.pl
+ bin/load_genbank.pl
+ bin/make_das_conf.pl
+ bin/process_gadfly.pl
+ bin/process_ncbi_human.pl
+ bin/process_ncbi_human.pl
+ bin/process_sgd.pl
+ bin/ucsc_genes2gff.pl
+ cgi-bin/gbrowse_img
+ conf/plugins/Aligner.pm
+ conf/plugins/AttributeHiliter.pm
+ conf/plugins/RestrictionAnnotator.pm
+ conf/plugins/SequenceDumper.pm
+ conf/plugins/SimpleTrackFinder.pm
+ conf/plugins/Spectrogram.pm
+ conf/plugins/TrackFinder.pm
+ contrib/Coverage/plugin/Coverage.pm
+ docs/pod/GBROWSE_IMG.pod
+ docs/pod/MAKE_IMAGES_HOWTO.pod
+ docs/pod/PLUGINS_HOWTO.pod
+ htdocs/gbrowse_karyotype_help.html
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
+ lib/Bio/Graphics/Browser2/CAlign.pm
+ lib/Bio/Graphics/Browser2/Markup.pm
+ lib/Bio/Graphics/Browser2/OptionPick.pm
+ lib/Bio/Graphics/Browser2/PadAlignment.pm
+ lib/Bio/Graphics/Browser2/Realign.pm
+ lib/CGI/Toggle.pm
+ libalign/CAlign.pm
+Copyright: © 2001–4 Cold Spring Harbor Laboratory
+ © Jason Stajich and Cold Spring Harbor Laboratories 2002
+ © 2009 Ontario Institute for Cancer Research
+ © 2007, University of Utah
+ © 2002 Regional Blood Center of Ribeirao Preto
+ © 2002 Advanced Biomedical Computing Center, SAIC/NCI-Frederick.
+License: GPL-1+ or Artistic
+ This library is free software; you can redistribute it and/or modify
+ it under the same terms as Perl itself.  See DISCLAIMER.txt for
+ disclaimers of warranty.
+
+Files: t/Test.pm
+Copyright: © 1998-1999 Joshua Nathaniel Pritikin.  All rights reserved.
+License: Artistic
+ This package is free software and is provided "as is" without express
+ or implied warranty.  It may be used, redistributed and/or modified
+ under the terms of the Perl Artistic License (see
+ http://www.perl.com/perl/misc/Artistic.html)
+
+Files: contrib/GeneFinder/genefinder/readseq.c
+Copyright: © R Durbin, 1994
+License: unknown
+
+Files: htdocs/css/dropdown/default_theme.css htdocs/css/dropdown/dropdown.css
+Copyright: © 2008 Live Web Institute. All Rights Reserved.
+License: unknown
+
+Files: docs/pod/INSTALL.MacOSX.pod
+Copyright @ 2003 Cold Spring Harbor Laboratory
+License: missing, most probably same as Perl
+ Material in this document is copyright 2001-2003 by the Cold Spring
+ Harbor Laboratory. This information is provided "AS-IS" without any
+ warranty, expressed or implied.
+
+Files: htdocs/js/*.js
+Copyright: © 2005-2010 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
+ © 2005-2010 Ivan Krstic (http://blogs.law.harvard.edu/ivan)
+ © 2005-2010 Jon Tirsen (http://www.tirsen.com)
+ © 2007,2008 Sheldon McKay, Cold Spring Harbor Laboratory
+License: MIT (doublecheck it is “the” MIT license)
+
+Files: htdocs/js/prototype.js
+Copyright: © 2005-2010 Sam Stephenson
+ © 2009, The Dojo Foundation
+License: Dojo
+ Released under the MIT, BSD, and GPL Licenses.
+ More information: http://sizzlejs.com/
+
+Files: htdocs/js/x_cook.js
+Copyright: © 2004 Michael Foster
+License: LGPL
+
+Files: htdocs/subtracktable.js
+Copyright: © 2005-2009 Matt Kruse (javascripttoolbox.com)
+License: MIT or GPL 
+ Dual licensed under the MIT and GPL licenses. 
+ This basically means you can use this code however you want for
+ free, but don't claim to have written it yourself!
+ Donations always accepted: http://www.JavascriptToolbox.com/donate/
+ . 
+ Please do not link to the .js files on javascripttoolbox.com from
+ your site. Copy the files locally to your server instead.
+
 Files: debian/*
 Copyright: 2011, Olivier Sallou <olivier.sallou at irisa.fr>
-License: Artistic or GPL-1+
+License: Artistic-2.0 or GPL-1+
 
-License: Artistic
- This program is free software; you can redistribute it and/or modify
- it under the terms of the Artistic License, which comes with Perl.
+License: MIT (doublecheck it is “the” MIT license)
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
  .
- On Debian GNU/Linux systems, the complete text of the Artistic License
- can be found in `/usr/share/common-licenses/Artistic'.
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
 
 License: GPL-1+
  This program is free software; you can redistribute it and/or modify
@@ -26,3 +164,184 @@
  .
  On Debian GNU/Linux systems, the complete text of version 1 of the
  General Public License can be found in `/usr/share/common-licenses/GPL-1'.
+
+License: Artistic
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the Artistic License, which comes with Perl.
+ .
+ On Debian GNU/Linux systems, the complete text of the Artistic License
+ can be found in `/usr/share/common-licenses/Artistic'.
+
+License: Artistic-2.0
+ Copyright (c) 2000-2006, The Perl Foundation.
+ .
+ Everyone is permitted to copy and distribute verbatim copies of this license 
+ document, but changing it is not allowed.
+ .
+ .
+  Preamble
+ This license establishes the terms under which a given free software Package may 
+ be copied, modified, distributed, and/or redistributed. The intent is that the 
+ Copyright Holder maintains some artistic control over the development of that 
+ Package while still keeping the Package available as open source and free 
+ software.
+ .
+ You are always permitted to make arrangements wholly outside of this license 
+ directly with the Copyright Holder of a given Package. If the terms of this 
+ license do not permit the full use that you propose to make of the Package, you 
+ should contact the Copyright Holder and seek a different licensing arrangement.
+ .
+ .
+  Definitions
+ "Copyright Holder" means the individual(s) or organization(s) named in the 
+ copyright notice for the entire Package.
+ .
+ "Contributor" means any party that has contributed code or other material to the 
+ Package, in accordance with the Copyright Holder's procedures.
+ .
+ "You" and "your" means any person who would like to copy, distribute, or modify 
+ the Package.
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+ .
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+ (9) Works (including, but not limited to, modules and scripts) that merely 
+ extend or make use of the Package, do not, by themselves, cause the Package to 
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