annotate LICENSE @ 2:a3b158471bd3 draft

planemo upload for repository https://github.com/ncbi/egapx commit 98875ef7eda9323fc9991970103954e9097d9e73

CONTENTS

  Public Domain Notice
  Exceptions (for bundled 3rd-party code)
  Copyright F.A.Q.



================================================================================
                          PUBLIC DOMAIN NOTICE
             National Center for Biotechnology Information

This software was created as part of the author(s) official duties as a United 
States Government employee(s), is a "United States Government Work" and is not 
subject to copyright in the United States (17 USC 105). The National Library of 
Medicine (NLM) and the U.S. Government have not placed any restriction on its
use or reproduction.

The NLM disclaims all warranties, express or implied, including warranties of 
performance, merchantability, or fitness for any particular purpose.

Please cite NLM in any work or product based on this material.

EGAPx makes use of various third-party tools which carry their own licenses. 

The list of third-party tools and their licenses are provided here:
================================================================================
EXCEPTIONS (in all cases excluding NCBI-written makefiles):


Location: img/gp/third-party/STAR
Authors:  Alexander Dobin
License:  MIT License
          [https://github.com/alexdobin/STAR/blob/master/LICENSE]

Location: img/gp/third-party/samtools
Authors:  Genome Research Ltd.
License:  The MIT/Expat License
          [https://github.com/samtools/samtools/blob/develop/LICENSE]

Location: img/gp/third-party/miniprot
Authors:  Dana-Farber Cancer Institute
License:  MIT License
          [https://github.com/lh3/miniprot/blob/master/LICENSE.txt]

Location: img/gp/third-party/diamond
Authors:  Benjamin Buchfink
License:  GNU GENERAL PUBLIC LICENSE
          [https://github.com/bbuchfink/diamond/blob/master/LICENSE]

Location: img/gp/third-party/seqkit
Authors:  Wei Shen
License:  MIT License
          [https://github.com/shenwei356/seqkit/blob/master/LICENSE]

================================================================================

Copyright F.A.Q.


--------------------------------------------------------------
Q. Our product makes use of the NCBI source code, and we did changes
   and additions to that version of the NCBI code to better fit it to
   our needs. Can we copyright the code, and how?

A. You can copyright only the *changes* or the *additions* you made to the
   NCBI source code. You should identify unambiguously those sections of
   the code that were modified, e.g. by commenting any changes you made
   in the code you distribute. Therefore, your license has to make clear
   to users that your product is a combination of code that is public domain
   within the U.S. (but may be subject to copyright by the U.S. in foreign
   countries) and code that has been created or modified by you.


--------------------------------------------------------------
Q. Can we (re)license all or part of the NCBI source code?

A. No, you cannot license or relicense the source code written by NCBI
   since you cannot claim any copyright in the software that was developed
   at NCBI as a 'government work' and consequently is in the public domain
   within the U.S.


--------------------------------------------------------------
Q. What if these copyright guidelines are not clear enough or are not
   applicable to my particular case?

A. Contact us. Send your questions to '[e-mail]'.

MIT License

Copyright (c) 2024 Ross Lazarus

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:

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.