c2e7dafc8f5c5d8a3500608a7c746e065813efc2 gperez2 Tue Nov 1 18:10:17 2022 -0700 Replacing the wiki page link with a UCSC page link, refs #28424 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index e2a834f..22604bc 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -26,32 +26,31 @@ <p> <strong>Additional resources</strong></p> <ul> <li>Raney BJ, et al. <a href="https://doi.org/10.1093/bioinformatics/btt637" target="_blank">Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser</a>. <em>Bioinformatics</em>. 2014 Apr 1;30(7):1003-5. <li> <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hubs Wiki</a></li> <li> <a href="trackDb/trackDbHub.html" target="_blank">Track Database Definition Document</a> (Reference guide for trackDb parameter definitions)</li> <li><a href="https://genome-blog.soe.ucsc.edu/blog/2022/06/28/track-hub-settings/" target= "_blank">Track hub settings blog post</a></li> <li> - <a href="http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines" target="_blank">Public Hub - Guidelines Wiki</a></li> + <a href="publicHubGuidelines.html" target="_blank">Public Hub Guidelines</a></li> <li> <a href="hubQuickStart.html" target="_blank">Quick Start Guide to Basic Hubs</a></li> <li> <a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into Groupings</a></li> <li> <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs with Blat</a></li> <li><a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable Track Hubs</a></li> <li><a href="hubQuickStartFilter.html" target="_blank">Quick Start Guide to adding Filters to Hubs</a></li> </ul> <div> <form name="googleForm1" method="GET" action="https://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+' site:genome.ucsc.edu/goldenPath/help';"> @@ -794,31 +793,31 @@ <p> For more information on the options available and examples on how to set up filters, see our <a href="hubQuickStartFilter.html" target="_blank">Track Hub Filters Quick Start Guide</a> and the filter entries in the <a href="trackDb/trackDbHub.html#filter" target="_blank"> Track Database Definition Document</a>.</p> <!-- ========== Registering a Track Hub with UCSC ==================== --> <a name="Register"></a> <h2>Registering a Track Hub with UCSC</h2> <p> If you would like to share your track hub with other Genome Browser users, you can register your hub with UCSC by contacting the Genome Browser technical support mailing list at <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. Please include the URL of your hub.txt file in the message. Once registered, your hub will appear as a link on the Public Hubs tab on the Track Hubs page. To assist developers of Public Hubs, there is a -<a href="http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines">Public Hubs Guidelines</a> +<a href="publicHubGuidelines.html" target="_blank">Public Hub Guidelines</a> page. The page shares pointers and preferred style approaches, such as the need for creating description html pages for your data that display any available references and an email contact for further data questions.</p> <p> Alternatively, you can share your track hub with selected colleagues by providing them with the URL needed to load your hub via the Connected Hubs tab.</p> <!--Note: Probably should add a blurb about (lack of) security here. Maybe just expand this section to be about sharing hub data.--> <!-- ======== Testing hub compatibility between genome browsers ============== --> <a name="Compatibility"></a> <h2>Checking Hub settings and Compatibility</h2> <p> Due to the growth in popularity of the track hub format, other genome browsers have begun supporting the UCSC track hub format. The hubCheck utility can be used to check