f1900dde9063ea0a4887c3f2d96fd8c29c9a1d6a jnavarr5 Tue Feb 24 15:49:58 2026 -0800 Adding information about Hub Space to the NAR help documentation. Changing relative links to CGIs to absolute when possible. Adding a missing <p> tag on the track hub help page, and adding information about hub space, refs #36893 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index d1959956fc9..7143f37fd71 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -1249,32 +1249,34 @@ you will first need to create a single-column file that lists each non-UCSC setting and then use the "-extra=" option to specify this file when running hubCheck. For example, if you knew that a setting called "ensemblAssemblyName" was supported for use in track hubs by Ensembl, you could create a single line file that included the setting "ensemblAssemblyName". Then, when you want to check a hub that includes these extra trackDb settings, you would then specify this extra settings file on the command line:</p> <pre><code>$ hubCheck -checkSettings -extra=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubCheckUnsupportedSettings/myExtraSettings.txt http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubCheckUnsupportedSettings/hub.txt </code></pre> <p> (Note: The settings listed here in the "extra" file are just examples and do not represent real trackDb variables for hubs at Ensembl.)</p> <!-- ========== Where to host your data ============================== --> <a name="Hosting"></a> <h2>Where to host your data?</h2> +<p> As stated in <a href="#Intro">What Are Track Hubs?</a>, track hubs files must be located in web-accessible locations that support byte-range requests. Four options for hosting include: +</p> <ul> <li>Your institution's Information Technology services <li>Commercial webspace providers <li>Commercial cloud providers <li>Free webspace providers </ul> <p> <b>Your Institution:</b> Many universities provide a location for researchers to place shareable data on the web and contacting your institution's system administrators will help discover a location to store your data. For example, if you work at the NIH, there is an internal data sharing <a href="https://hpc.nih.gov/nih/datashare.html" target="_blank">NIH network</a> site. Sometimes institution firewall rules can change, and you may need to inform your system administrators to add browser IP addresses as exceptions, listed @@ -1313,30 +1315,35 @@ typically do work. As of 2020, they cost around 2-3 US cents/GB/month to store the hub data and 12-18 US cents per GB transferred, when the hub is used. For optimal performance, select a San Francisco / San Jose data center for the main UCSC site genome.ucsc.edu, a Frankfurt/Germany data center for genome-euro.ucsc.edu and a Tokyo data center for genome-asia.ucsc.edu. You may also want to review this discussion about issues with <a href="http://genomewiki.ucsc.edu/index.php/Cloud-storage_providers_and_byte-range_requests_of_UCSC_big*_files" target="_blank">distributed storage servers</a>. <b>These services are external to UCSC and may change.</b></p> <p><b>Free webspace:</b> If you do not want to pay for web space, and your institution does not provide a data location supporting byte-range requests, we know of at least the following sites where you can host research data and configuration files for free: <ul> + <li><a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect?#hubUpload" target="_blank">Hub + Space</a> - + UCSC's own hosting service which provides 10 GB of free storage per user. Please + <a href="/contacts.html" target="_blank">contact us</a> + if you need to increase the storage limit.</li> <li><a href="https://usegalaxy.org/" target="_blank">Galaxy</a> - Maximum size limit is 50 GB (uncompressed). 250 GB of storage is available per Galaxy account.</li> <li><a href="https://de.cyverse.org/de/" target="_blank">CyVerse Discovery Environment</a> - 5 GB of space for free, but can be relatively slow to display. Offers a paid subscription service to expand space.</li> <li><a href="https://github.com/" target="_blank">Github</a> - files limited to 100MB, but very fast.</li> <li><a href="https://figshare.com/" target="_blank">Figshare</a> - not limited and fast, but every file needs to be uploaded individually and cannot be changed. Optimal for very stable links, e.g. in publications.</li> <li><a href="https://dropbox.com/" target="_blank">DropBox</a> - 2 GB free on their BasicFree plan. Many other paid dropbox plans are available with much more space. </li> </ul> <p>