94c1a35520847138f6b7ceb9a702022a561e95e4 max Thu Nov 18 06:05:43 2021 -0800 More fixes to the license files, refs #27614 diff --git src/hg/htdocs/license/index.html src/hg/htdocs/license/index.html index 7ffa5f0f..f44852f 100755 --- src/hg/htdocs/license/index.html +++ src/hg/htdocs/license/index.html @@ -1,144 +1,152 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Licensing" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Graphics: No permission is needed to reproduce a graphic produced by the Genome Browser</h1> <p>Permission is granted for reuse of all graphics produced by the UCSC Genome Browser website. There is no need to contact us to get permission. If your publisher, notably Elsevier, insists on getting approval, please direct them to this webpage. However, when you use the UCSC Genome Browser in your work, please cite one of our <a href="../goldenPath/pubs.html">publications</a>.</p> <br> <h1>Data: No license is needed for the data files and database tables used by the Genome Browser</h1> <p> As far as the UCSC Genome Browser group is concerned, the raw table data and binary files used to create the graphics by the browser is freely available for both public and commercial use. This applies to data that is downloaded as files via http, https, ftp or rsync, and equally when data is accessed through the public MySQL server or via the web API. </p> <p>Sometimes, the source databases or authors place restrictions on the data. In very rare cases, the genomes come with citation requirements. The README.txt file in the download directory of each assembly shows the original restrictions pertaining to the genome sequence itself by the original authors; most assemblies do not have any restrictions. </p> <p> Certain genome annotation data, mostly on the human genome and in the domain of clinical genetics, have specific restrictions. Usually the data must be obtained from the source database directly in the original format or licensed, rather from UCSC. Examples are HGMD, LOVD, OMIM, Decipher, Genomenom, Genehancer and COSMIC, as well as any GISAID-derived data on viral genomes. Please see the respective track documentation pages on these assemblies for more details, by selecting the assembly and clicking the track title in the genome browser.</p> <br> <h1 id="free">Software: Most command-line tools and directories are freely available for all uses</h1> <p> The majority of the Genome Browser source code is available under the MIT license, see <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE" target=_blank>the file LICENSE in our source code repository</a>. As such, the Unix command line utilities needed to build tracks and track hub files, or that can be part of computational pipelines except BLAT/liftOver, and our hundreds of tools to filter , sort, rearrange, join and process genome annotation files, can be used by anyone freely and they can be redistributed via package managers and installation tools, even for commercial use. Notable examples are bedToBigBed, wigToBigWig, overlapSelect, featureBits, pslMap, pslFilter and pslCDnaFilter. </p> <p> -The exception are kent/src/blat, kent/src/jkOwnLib and the -the programs that produce the graphical images and the graphical user interface -for the UCSC Genome Browser, the following subdirectories under kent/src/hg: +The exception are source code directories with special LICENSE files in them. +These are kent/src/blat, kent/src/jkOwnLib and the programs that produce +the graphical images and the graphical user interface +for the UCSC Genome Browser, so the following subdirectories under kent/src/hg: </p> <p> <pre>cgilib das encode hgApi hgCollection hgFileSearch hgFileUi hgGateway hgGene hgGenome hgIntegrator hgPal hgPcr hgPhyloPlace hgPublicSessions hgSession hgSuggest hgTables hgTrackUi hgTracks hgVai hgc hubApi near visiGene liftOver</pre> </p> <p> -See the LICENSE file in the top level of our source code for a listing of licenses and directories that they apply to: +See the LICENSE file in the top level of our source code for a listing of +licenses and directories that they apply to: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE">https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE</a>. -</p> +Directories under non-commercial licenses have LICENSE files in them that start +with the "LicenseRef-proprietary" SPDX tag. </p> <p>When you use the UCSC Genome Browser in your work, please cite one of our <a href="../goldenPath/pubs.html">publications</a>.</p> +<br> <h1>Software: download and local installation of the graphical Genome Browser software and access to the source code is free for non-commercial uses but not commercial usage</h1> <p>Non-commercial usage for the Genome Browser graphical interface (primarily the "hgTracks" program), including download and local installation, aka setting up a <a href="../goldenPath/help/mirror.html">"mirror"</a>, is free. When you use the UCSC Genome Browser in your work, please cite one of our <a href="../goldenPath/pubs.html">publications</a>. </p> <p> For commercial use, a license is required for download and local installation of -certain Genome Browser webserver CGI binaries and source code. -As specified above, this applies to the following subdirectories and programs under kent/src/hg, these are the -programs that produce the graphical images and the graphical user interface for the UCSC Genome Browser: +certain Genome Browser webserver CGI binaries and source code. In the source +code repository, the respective directories are marked by special LICENSE +files in them. +As specified above, this applies to kent/src/blat, kent/src/jkOwnLib and the +following subdirectories and programs under kent/src/hg, the majority are the programs +that produce the graphical images and the graphical user interface for the UCSC +Genome Browser: <br> <p> <pre>cgilib das encode hgApi hgCollection hgFileSearch hgFileUi hgGateway hgGene hgGenome hgIntegrator hgPal hgPcr hgPhyloPlace hgPublicSessions hgSession hgSuggest hgTables hgTrackUi hgTracks hgVai hgc hubApi near visiGene liftOver</pre> </p> <p> Also, BLAT and isPCR, if needed, are covered by a separate license (see below). This concerns the source code directories src/blat and src/jkOwnLib. </p> <p> To purchase a commercial license for Genome Browser source code, LiftOver, GBiB, or GBiC, please visit the <a href="https://genome-store.ucsc.edu">Genome Browser store</a>. </p> We also have an <a href="../FAQ/FAQlicense.html">FAQ on licensing questions</a> which may help to clarify questions on how to license the code. We also have documentation on how to choose the best way to install a local installation of the Genome Browser, also called a <a target=_blank href="../goldenPath/help/mirror.html">"mirror"</a>. <p> If you would like to purchase more than 20 copies of the Genome Browser source code, please follow these instructions: <ol> <li> Read and sign the <A HREF="gbLicense2020.pdf" target=_blank>licensing agreement</a>.</li> <li> Email a signed copy of the license agreement to the UCSC Office for IP Management (<A HREF="mailto:genomebrowser@ucsc.edu" >genomebrowser@ucsc.edu</A>). <!-- above address is genomebrowser at ucsc.edu --> <li> Follow the instructions in the license agreement for submitting the signed original copy and payment.</li> <li> After your license application has been processed, you will receive instructions for downloading the browser software and data.</li> </ol></p> <p> Genome Browser licensing questions should be directed to <a href="mailto:genome-www@soe.ucsc.edu">genome-www@soe.ucsc.edu</a>. <!-- above address is genome-www at soe.ucsc.edu --> For information about commercial licensing of the Blat and In-Silico PCR tools, see the <a href="http://www.kentinformatics.com" target=_blank>Kent Informatics</a> website or contact <a href="mailto:kent@soe.ucsc.edu">kent@soe.ucsc.edu</a>.</p> <!-- above address is kent at soe.ucsc.edu --> <p> See the LICENSE file in the top level of our source code for a listing of licenses and directories that they apply to: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE">https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE</a>. <p> <br> <h1>Acknowledgements</h1> <p> This software includes software made by open-source projects: <ul> <li> htslib, see <a href="https://doi.org/10.1093/gigascience/giab007" target=_blank>Bonfield et al, 2021</a>: Copyright (C) 2012-2020 Genome Research Ltd., see kent/src/htslib <li> optimalLeaf, see <a href="https://www.ncbi.nlm.nih.gov/pubmed/12801867" target=_blank>Bar-Joseph et al. 2003</a>: released into the public domain by Ziv Bar-Joseph, see kent/src/optimalLeaf. <li> Portions of this software are copyright 2020 The FreeType Project (www.freetype.org). All rights reserved. <li> This software uses the (URW)++ fonts, Copyright 1999 by (URW)++ Design & Development. The files are not in git but can be obtained via rsync or ftp from hgdownload.soe.ucsc.edu/htdocs. </ul> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->