packages-metadata/t/tophat.copyright

Format: http://dep.debian.net/deps/dep5
Upstream-Name: TopHat
Upstream-Contact: Cole Trapnell <cole@cs.umd.edu>
Source: http://tophat.cbcb.umd.edu/downloads/tophat-1.4.1.tar.gz
Comment:
 Cole Trapnell wrote TopHat. TopHat is built on Bowtie, which was written by
 Ben Langmead and Cole Trapnell.  Daehwan Kim and Geo Pertea added support
 for SOLiD reads. The SeqAn-1.2 library is used in TopHat and
 Bowtie and some of its sources are included in TopHat source releases; its
 authors are Andreas Doring, David Weese, Tobias Rausch, and Knut Reinert.

Files: *
Copyright: © 2003-2010 Cole Trapnell et al
License: Artistic

Files: src/SeqAn-1.2/* 
Upstream-Name: SeqAn
Copyright: © 2007
License: LGPL-3+
 This library is free software; you can redistribute it and/or
 modify it under the terms of the GNU Lesser General Public
 License as published by the Free Software Foundation; either
 version 3 of the License, or (at your option) any later version.
 . 
 This library is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 Lesser General Public License for more details.
 .
 On Debian systems, the complete text of the GNU Lesser General Public License
 version 3 can be found in the files ‘/usr/share/common-licenses/LGPL-3’ and
 ‘/usr/share/common-licenses/GPL-3’.

Files: src/SeqAn-1.2/index_sa_lss.h
Copyright: © 1999, N. Jesper Larsson, all rights reserved.
License: qsufsort.c
 This file contains an implementation of the algorithm presented in "Faster
 Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
 Sadakane (sada@is.s.u-tokyo.ac.jp).
 .
 This software may be used freely for any purpose. However, when distributed,
 the original source must be clearly stated, and, when the source code is
 distributed, the copyright notice must be retained and any alterations in
 the code must be clearly marked. No warranty is given regarding the quality
 of this software.

Files: ax_bam.m4
Copyright: © 2010 Cole Trapnell <cole@cs.umd.edu>
License: GAP
 Copying and distribution of this file, with or without modification, are
 permitted in any medium without royalty provided the copyright notice
 and this notice are preserved.

Files: ax_check_zlib.m4
Copyright: © 2008 Loic Dachary <loic@senga.org>
License: GPL-2+ with autoconf exception
 This program is free software; you can redistribute it and/or modify it
 under the terms of the GNU General Public License as published by the
 Free Software Foundation; either version 2 of the License, or (at your
 option) any later version.
 .
 This program is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
 Public License for more details.
 .
 You should have received a copy of the GNU General Public License along
 with this program. If not, see <http://www.gnu.org/licenses/>.
 .
 As a special exception, the respective Autoconf Macro's copyright owner
 gives unlimited permission to copy, distribute and modify the configure
 scripts that are the output of Autoconf when processing the Macro. You
 need not follow the terms of the GNU General Public License when using
 or distributing such scripts, even though portions of the text of the
 Macro appear in them. The GNU General Public License (GPL) does govern
 all other use of the material that constitutes the Autoconf Macro.
 .
 This special exception to the GPL applies to versions of the Autoconf
 Macro released by the Autoconf Archive. When you make and distribute a
 modified version of the Autoconf Macro, you may extend this special
 exception to the GPL to apply to your modified version as well.

Files: debian/*
Copyright: 2011 Carlos Borroto <carlos.borroto@gmail.com>
           © 2011 Alex Mestiashvili <alex@biotec.tu-dresden.de>
License: GPL-2+

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 systems, the complete text of the Artistic License can be
 found in `/usr/share/common-licenses/Artistic'.

License: GPL-2+
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation; either version 2 of the License, or
 (at your option) any later version.
 .
 This package is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 .
 You should have received a copy of the GNU General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>
 .
 On Debian systems, the complete text of the GNU General
 Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".

1	plessy	2171	Format: http://dep.debian.net/deps/dep5
2			Upstream-Name: TopHat
3			Upstream-Contact: Cole Trapnell <cole@cs.umd.edu>
4			Source: http://tophat.cbcb.umd.edu/downloads/tophat-1.4.1.tar.gz
5			Comment:
6			Cole Trapnell wrote TopHat. TopHat is built on Bowtie, which was written by
7			Ben Langmead and Cole Trapnell. Daehwan Kim and Geo Pertea added support
8			for SOLiD reads. The SeqAn-1.2 library is used in TopHat and
9			Bowtie and some of its sources are included in TopHat source releases; its
10			authors are Andreas Doring, David Weese, Tobias Rausch, and Knut Reinert.
11
12			Files: *
13			Copyright: © 2003-2010 Cole Trapnell et al
14			License: Artistic
15
16			Files: src/SeqAn-1.2/*
17			Upstream-Name: SeqAn
18			Copyright: © 2007
19			License: LGPL-3+
20			This library is free software; you can redistribute it and/or
21			modify it under the terms of the GNU Lesser General Public
22			License as published by the Free Software Foundation; either
23			version 3 of the License, or (at your option) any later version.
24			.
25			This library is distributed in the hope that it will be useful,
26			but WITHOUT ANY WARRANTY; without even the implied warranty of
27			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
28			Lesser General Public License for more details.
29			.
30			On Debian systems, the complete text of the GNU Lesser General Public License
31			version 3 can be found in the files ‘/usr/share/common-licenses/LGPL-3’ and
32			‘/usr/share/common-licenses/GPL-3’.
33
34			Files: src/SeqAn-1.2/index_sa_lss.h
35			Copyright: © 1999, N. Jesper Larsson, all rights reserved.
36			License: qsufsort.c
37			This file contains an implementation of the algorithm presented in "Faster
38			Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
39			Sadakane (sada@is.s.u-tokyo.ac.jp).
40			.
41			This software may be used freely for any purpose. However, when distributed,
42			the original source must be clearly stated, and, when the source code is
43			distributed, the copyright notice must be retained and any alterations in
44			the code must be clearly marked. No warranty is given regarding the quality
45			of this software.
46
47			Files: ax_bam.m4
48			Copyright: © 2010 Cole Trapnell <cole@cs.umd.edu>
49			License: GAP
50			Copying and distribution of this file, with or without modification, are
51			permitted in any medium without royalty provided the copyright notice
52			and this notice are preserved.
53
54			Files: ax_check_zlib.m4
55			Copyright: © 2008 Loic Dachary <loic@senga.org>
56			License: GPL-2+ with autoconf exception
57			This program is free software; you can redistribute it and/or modify it
58			under the terms of the GNU General Public License as published by the
59			Free Software Foundation; either version 2 of the License, or (at your
60			option) any later version.
61			.
62			This program is distributed in the hope that it will be useful, but
63			WITHOUT ANY WARRANTY; without even the implied warranty of
64			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
65			Public License for more details.
66			.
67			You should have received a copy of the GNU General Public License along
68			with this program. If not, see <http://www.gnu.org/licenses/>.
69			.
70			As a special exception, the respective Autoconf Macro's copyright owner
71			gives unlimited permission to copy, distribute and modify the configure
72			scripts that are the output of Autoconf when processing the Macro. You
73			need not follow the terms of the GNU General Public License when using
74			or distributing such scripts, even though portions of the text of the
75			Macro appear in them. The GNU General Public License (GPL) does govern
76			all other use of the material that constitutes the Autoconf Macro.
77			.
78			This special exception to the GPL applies to versions of the Autoconf
79			Macro released by the Autoconf Archive. When you make and distribute a
80			modified version of the Autoconf Macro, you may extend this special
81			exception to the GPL to apply to your modified version as well.
82
83			Files: debian/*
84			Copyright: 2011 Carlos Borroto <carlos.borroto@gmail.com>
85			© 2011 Alex Mestiashvili <alex@biotec.tu-dresden.de>
86			License: GPL-2+
87
88			License: Artistic
89			This program is free software; you can redistribute it and/or modify
90			it under the terms of the Artistic License, which comes with Perl.
91			.
92			On Debian systems, the complete text of the Artistic License can be
93			found in `/usr/share/common-licenses/Artistic'.
94
95			License: GPL-2+
96			This package is free software; you can redistribute it and/or modify
97			it under the terms of the GNU General Public License as published by
98			the Free Software Foundation; either version 2 of the License, or
99			(at your option) any later version.
100			.
101			This package is distributed in the hope that it will be useful,
102			but WITHOUT ANY WARRANTY; without even the implied warranty of
103			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
104			GNU General Public License for more details.
105			.
106			You should have received a copy of the GNU General Public License
107			along with this program. If not, see <http://www.gnu.org/licenses/>
108			.
109			On Debian systems, the complete text of the GNU General
110			Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
111