[med-svn] [spades] 01/01: add more licenses
Sascha Steinbiss
sascha at steinbiss.name
Mon Feb 8 11:16:21 UTC 2016
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sascha-guest pushed a commit to branch master
in repository spades.
commit 07bff24dd122672caf7c8da4ed7d82e8a601435b
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Mon Feb 8 11:16:11 2016 +0000
add more licenses
---
debian/copyright | 138 +++++++++++++++++++++++++++++++++++++++++++++++++++----
1 file changed, 129 insertions(+), 9 deletions(-)
diff --git a/debian/copyright b/debian/copyright
index 069b81a..11fbde4 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -28,6 +28,20 @@ Copyright: 2014-2016 Andreas Tille <tille at debian.org>
2016 Sascha Steinbiss <sascha at steinbiss.name>
License: GPL-2+
+Files: src/ionhammer/seqeval/*
+Copyright: (C) 2012-2013 Ion Torrent Systems, Inc. All Rights Reserved
+License: GPL-2+
+Comment:
+ Assumed to be under GPL-2+ as well, cf. https://github.com/iontorrent/TS
+
+Files: src/spades_pipeline/lucigen_nxmate.py
+Copyright: 2011-2014 Saint-Petersburg Academic University
+ 2015 Saint Petersburg State University
+ 2014 Lucigen Corp
+License: GPL-2+
+Comment:
+ Assumed to be under GPL-2+ due to upstream's source header.
+
License: GPL-2+
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
@@ -78,14 +92,9 @@ License: BSD-3-clause-Akiba
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Files: src/include/xmath.h
+ src/include/sparsehash/*
Copyright: (c) 2005 Google Inc.
License: BSD-3-clause-Google
-
-Files: src/include/sparsehash/*
-Copyright: (c) 2005 Google Inc.
-License: BSD-3-clause-Google
-
-License: BSD-3-clause-Google
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
@@ -160,7 +169,8 @@ Copyright: (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stro
License: MIT
Files: ext/include/kseq/*
-Copyright: (c) 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
+ ext/src/samtools/bcftools/kmin.*
+Copyright: (c) 2008-2011 Attractive Chaos <attractor at live.co.uk>
License: MIT
Files: ext/include/libcxx/sort.hpp
@@ -169,6 +179,17 @@ License: MIT
Comment: This file is taken from LLVM's libc++.
See http://llvm.org/docs/DeveloperPolicy.html#license.
+Files: ext/include/nlopt/bobyqa/*
+Copyright: (c) 2009 M. J. D. Powell (mjdp at cam.ac.uk)
+ (c) 2010 Massachusetts Institute of Technology
+License: MIT
+
+Files: ext/include/nlopt/cobyla/*
+Copyright: (c) 1992, Michael J. D. Powell (M.J.D.Powell at damtp.cam.ac.uk)
+ (c) 2004, Jean-Sebastien Roy (js at jeannot.org)
+ (c) 2008, Steven G. Johnson (stevenj at alum.mit.edu)
+License: MIT
+
Files: ext/include/nlopt/*
ext/src/nlopt/*
Copyright: (c) 2007-2012 Massachusetts Institute of Technology
@@ -176,11 +197,17 @@ License: MIT
Files: ext/src/samtools/*
Copyright: (c) 2008-2009 Genome Research Ltd.
+ (c) 2003-2006, 2008-2010 Heng Li
+ (c) 2008 Broad Institute / Massachusetts Institute of Technology
License: MIT
Files: ext/src/ssw/*
-Copyright: (c) 2012-1015 Boston College <zhangmp at bc.edu>
+ src/include/ssw/ssw.h
+Copyright: (c) 2012-1015 Boston College
License: MIT
+Comment:
+ Please find original license attribution for this code at:
+ https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
Files: ext/include/yaml-cpp/*
ext/src/yaml-cpp/*
@@ -234,6 +261,14 @@ Files: ext/include/cppformat/*
ext/src/cppformat/*
Copyright: (c) 2012-2014 Victor Zverovich
License: BSD-2-clause
+
+Files: src/include/io/mpmc_bounded.hpp
+Copyright: (c) 2015 Saint Petersburg State University
+ (c) 2011-2014 Saint Petersburg Academic University
+ (c) 2011 Dmitry Vyukov. All rights reserved.
+License: BSD-2-clause
+
+License: BSD-2-clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
.
@@ -297,4 +332,89 @@ License: GPL-3+
this program. If not, see <http://www.gnu.org/licenses/>.
.
On Debian systems, the complete text of the GNU General
- Public License can be found in `/usr/share/common-licenses/GPL-3'.
\ No newline at end of file
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.
+
+Files: src/cmake/Modules/GetGitRevisionDescription.*
+Copyright: 2009-2010 Iowa State University
+License: Boost-1
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
+ .
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
+ must be included in all copies of the Software, in whole or in part, and
+ all derivative works of the Software, unless such copies or derivative
+ works are solely in the form of machine-executable object code generated by
+ a source language processor.
+ .
+ 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, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+
+Files: src/hammer/quake_correct/gzstream.*
+Copyright: (C) 2001 Deepak Bandyopadhyay
+ (C) 2001 Lutz Kettner
+License: LGPL-2.1
+ 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 2.1 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.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+Files: src/include/mph_index/MurmurHash3.h
+ src/mph_index/MurmurHash3.cpp
+License: public-domain
+Comment:
+ MurmurHash3 was written by Austin Appleby, and is placed in the public
+ domain. The author hereby disclaims copyright to this source code.
+
+Files: ext/src/bamtools/api/internal/io/pbgzf/util.c
+Copyright: (C) 1996-2008 Julian R Seward. All rights reserved.
+License: BSDlike-libbzip2
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ 2. The origin of this software must not be misrepresented; you must
+ not claim that you wrote the original software. If you use this
+ software in a product, an acknowledgment in the product
+ documentation would be appreciated but is not required.
+ .
+ 3. Altered source versions must be plainly marked as such, and must
+ not be misrepresented as being the original software.
+ .
+ 4. The name of the author may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+ OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+ DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+ GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
--
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