LICENSE

The default license of this repository is the MIT License (copied below), but
LICENSE files in subdirectories override this default. As a result, the
majority of the source code falls under the MIT license, however, some parts
are under two different non-commercial licenses: These parts are 
a) the Genome Browser Web CGI programs, are under a non-commercial license by UC
b) the BLAT program suite, licensed by Kent Informatics and under a different 
non-commercial license. Their directories are listed below.

As a result, if you are a non-commercial entity, you can use all the source
code for free. However, if you are commercial, you may need to buy a license if
you want to install a web-based Genome Browser locally or use BLAT locally,
either as the blat/gfServer/gfClient command line programs or the webBlat GUI
running locally on your servers.
 
All other UCSC Genome Browser command-line tools and their required
libraries are released under the MIT License. This includes our various file
format converters, such as bedToBigBed and wigToBigWig, and any tools to create
files needed for track hubs. They can be redistributed in any way necessary.

The following sections list all licenses and which directories are covered by 
which one.

FREE Licenses:

1. As described above, the default is the MIT license (attached below) 
  - this includes, for example, all code to read and write the Genome Browser
    file formats, such as bigBed and bigWig, and the command line tools for
    these, bedToBigBed, wigToBigWig and the tagStorm tools and the parasol job
    scheduler.
  - also, third-party code for reading BAM files bundled for convenience,
    in src/htslib (MIT)
2. A modified BSD license for src/htslib/cram/, see src/htslib/LICENSE. 
   Copyright (C) 2012-2014 Genome Research Ltd.
3. A public domain "with attribution" license for sorting bigWig files, 
   see src/optimalLeaf/LICENSE

NON-COMMERCIAL licenses:

4. A non-commercial license from UC for the genome browser interactive web code in 
   the following subdirectories of src/hg/ (see the LICENSE files in these directories):
     cgilib hgApi hgCollection hgFileSearch hgFileUi hgGateway
     hgGene hgGenome hgIntegrator hgPal hgPcr hgPhyloPlace hgPublicSessions
     hgSession hgSuggest hgTables hgTrackUi hgTracks hgVai hgc hubApi near
     visiGene liftOver
5. A non-commercial license from Kent Informatics for the BLAT and isPCR code
   in src/blat/, src/isPcr and src/jkOwnLib/, for more information see
   https://genome.ucsc.edu/license/ and http://www.kentinformatics.com/

See https://genome.ucsc.edu/license/ for more details and on how to obtain a license
for commercial use for the case (4) and (5): Commercial users interested in the 
interactive Genome Browser web software listed under (4) should contact
genomebrowser@ucsc.edu. Those interested in BLAT, so any code listed under (5),
should contact kent@soe.ucsc.edu.

The code in src/htslib is distributed under a dual license as noted in the LICENSE
file in that directory.

Mandatory acknowledgements for third party open source libraries that are used but not
distributed as part of this source tree are provided at https://genome.ucsc.edu/license/
---- 

MIT License

Copyright (C) 2001 UC Regents

Permission is hereby granted, free of charge, to any person or non-commercial
entity 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.