bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index eb2934761c6..4f97eabb88d 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -23,31 +23,31 @@ <h6><a href="#Hosting">Where to host your data</a></h6> <h6><a href="https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html" target = _blank>Track Hub Database Definition Document</a></h6> <hr> <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="assemblyHubHelp.html" target="_blank">Assembly Hub User Guide</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= + <li><a href="https://genome-blog.gi.ucsc.edu/blog/2022/06/28/track-hub-settings/" target= "_blank">Track hub settings blog post</a></li> <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> @@ -196,37 +196,37 @@ <a name="hubUrl"></a> <h3>Creating a URL for a Track Hub</h3> <p>Hubs can be loaded into the URL using the <code>hubUrl=</code> parameter. This parameter takes input similar to the <a href="/cgi-bin/hgHubConnect#unlistedHubs">track hub input box</a>. Native UCSC supported genomes can be loaded into the URL using the <code>db=</code> parameter while non-natively supported genomes such as assembly hubs or GenArk hubs use the <code>genome=</code> parameter. URL parameters can be combined by using <code>&</code>. </p> <p>The following example links to the hg19 genome database and an example track hub using the <code>db=</code> and the <code>hubUrl=</code> parameters:</p> <pre><a href=../../cgi-bin/hgTracks?db=hg19&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt</a></pre> <p>Track hubs' track visibility can also be changed from the URL parameters. As an example, the following link specifies: <ul> <li> the genome database (db=hg38)</li> -<li> loads a track hub (hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt)</li> +<li> loads a track hub (hubUrl=http://hgdownload.gi.ucsc.edu/hubs/gtex/hub.txt)</li> <li> hides all tracks (hideTracks=1)</li> <li> hides the subtrack kids of a particular track (gtexRnaSignalMaleYoung_hideKids=1)</li> <li> sets a specific subtrack to be displayed (gtexRnaSignalSRR1311243=full)</li> <li> ignores user settings (ignoreCookie=1).</p></li> </ul> -<pre><a href="../../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1">https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1&gtexRnaSignalMaleYoung_hideKids=1&gtexRnaSignalMaleYoung=full&gtexRnaSignalSRR1311243=full&ignoreCookie=1</a></pre> +<pre><a href="../../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.gi.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1">https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.gi.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1&gtexRnaSignalMaleYoung_hideKids=1&gtexRnaSignalMaleYoung=full&gtexRnaSignalSRR1311243=full&ignoreCookie=1</a></pre> <h6>Optional parameters that can be added to the URL:</h6> <ul> <li><code>guidelines=on/off</code> - activate or deactivate the blue guidelines</li> <li><code>hgFind.matches=<listOfNames></code> - highlight features given their names</li> <li><code>hgt.reset=1</code> - show only the default tracks</li> <li><code>hgt.toggleRevCmplDisp=1</code> - show the reverse-complement</li> <li><code>hgt.labelWidth=<number></code> - set the size of the left-side label area</li> <li><code>hideTracks=1</code> - hide all tracks</li> <li><code>hideTracks=1&<trackName>=full|dense|pack|hide</code> - hide all tracks and show other tracks</li> <li><code>highlight=<db>.<chrom>:<chromStart>-<chromEnd>#<color>|...</code></li> - highlight one or more regions in a given color on the image. Note that the arguments have to be @@ -881,31 +881,31 @@ <li>The <b>label</b> setting specifies the title of the group in the genome browser. By default, groups are sorted alphabetically based on the label.</li> <li>The <b>priority</b> setting dictates the display order of the track groups, with lower numbers shown first.</li> <li>The <b>defaultIsClosed</b> setting controls whether the group is initially expanded or collapsed (0 for expanded, 1 for collapsed).</li> </ul> <p> After defining the "groups.txt" file, tracks can be assigned to a specific group within the "trackDb.txt" file using the <b>group</b> setting. For example, to assign the "bigBed1" track to the "category1" group, you could use the following stanza: </p> <pre><code>track bigBed1 -bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb +bigDataUrl https://hgdownload.gi.ucsc.edu/gbdb/hg38/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb shortLabel bigBed example 1 longLabel This bigBed file is an example from the NCBI RefSeq Diffs Track type bigBed <strong>group</strong> category1 visibility dense</code></pre> <p> The full "trackDb.txt" file, which includes the "bigBed1" track and additional examples, can be viewed here: <a href="/goldenPath/help/examples/hubExamples/hubGroupings/groupsExample/hg38/trackDb.txt" target="_blank">trackDb.txt</a>.</p> <p> Next, incorporate the "groups.txt" file with the <b>groups</b> setting into the genome stanza. This can be for a UCSC genome, a GenArk assembly, or an assembly hub. Below is an example using the hg38 genome:</p> @@ -953,31 +953,31 @@ <p> Browser software attempts to speed performance by reading the trackDb architecture into a separate cache. This software assumes that the timestamp on a file like a hub's trackDb.txt should always be increasing in time and never decreasing (i.e., a new update to the file should not have an earlier timestamp). We did discover that if someone were to copy an older file (say with <code>cp -p</code> to preserve file timestamp), for example to restore a trackDb.txt to an earlier version, they might get stuck with a hub that is not updating. To resolve this specific problem the person would only need to edit or touch the file and give it a new timestamp.</p> <a name="validate"></a> <h3>Check hub settings using Hub Development tool</h3> <p> Hubs can be checked for valid file configuration, trackDb keywords, and composite or super track settings with the Hub Development tool. This tool can be accessed from the Track Hub page under <a href="../../cgi-bin/hgHubConnect?#hubDeveloper">the Hub Development tab</a>. After entering your URL in the search box, -the tool runs the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" +the tool runs the <a href="http://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads" target="_blank">hubCheck utility</a> program equivalent to:</p> <pre>hubCheck -noTracks http://url.to.hub.txt</pre> <p> The noTracks setting speeds up the validation process but does not check for the presence or validity of your remotely hosted data track files. This tool checks your hub.txt, genome.txt, and trackDb.txt settings and displays warnings and errors in bright red font, such as "<font color="red">Missing required setting...</font>" and "<font color="red">Cannot open...</font>". The "Display load times" and "Enable hub refresh" optional settings show the load timing at the bottom of the Genome Browser page and allow instant hub refresh instead of 5 minute refresh. These options can be checked and activated by clicking "View Hub on Genome Browser". The following picture shows <a href="examples/hubExamples/hubGroupings/hub.txt">the example track grouping hub</a> with the warning that the hub has no hub description page, no configuration errors, and "Display load times" checked:</p> @@ -1003,31 +1003,31 @@ hubCheck http://yourHost/yourDir/hub.txt options: -checkSettings - check trackDb settings to spec -version=[v?|url] - version to validate settings against (defaults to version in hub.txt, or current standard) -extra=[file|url] - accept settings in this file (or url) -level=base|required - reject settings below this support level -settings - just list settings with support level Will create this directory if not existing -noTracks - don't check remote files for tracks, just trackDb (faster) -udcDir=/dir/to/cache - place to put cache for remote bigBeds and bigWigs </code></pre></p> <p> Note that you will have to use the -udcDir option if /tmp/udcCache is not writable on your machine.</p> <p> The hubCheck program is available from the UCSC downloads server at -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">http://hgdownload.soe.ucsc.edu/admin/exe/</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">http://hgdownload.gi.ucsc.edu/admin/exe/</a>.</p> <a name="troubleConnecting"></a> <h3>Troubleshooting Track Hub connections</h3> <p> If the browser is unable to load a track hub, it will display an error message. Some common causes for an import to fail include typos in the URL, a hub server that is offline, or errors in the track hub configuration files. Occasionally, remote track hubs may be missing, off-line, or otherwise unavailable. If a user is already browsing data from the remote hub when it disconnects, a yellow error message will be displayed instead of the expected data.</p> <a name="hubClone"></a> <h3>Download all files in a hub using hubClone utility</h3> <p> You can use the command-line utility <em>hubClone</em> to download all of the @@ -1041,50 +1041,50 @@ <p> Here is the usage message for the hubClone utility: <pre><code>hubClone - Clone the remote hub text files to a local copy in newDirectoryName, fixing up bigDataUrls to remote location if necessary usage: hubClone http://url/to/hub.txt options: -udcDir=/dir/to/udcCache Path to udc directory -download Download data files in addition to the hub configuration files </code></pre></p> <p> Note that you will have to use the -udcDir option if /tmp/udcCache is not writable on your machine.</p> <p> The hubClone program is available from the UCSC downloads server at -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">http://hgdownload.soe.ucsc.edu/admin/exe/</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">http://hgdownload.gi.ucsc.edu/admin/exe/</a>.</p> <!-- ========== Setting Up Track Item Search ============================== --> <a name="Search"></a> <h2>Setting up track item search</h2> <p> The Genome Browser supports searching for items within bigBed tracks in track data hubs. To support this behavior you have to add an index to the bigBed file when you initially create the the bigBed file from the bed file input. Indices are usually created on the name field of the bed, but can be created on any field of the bed. Free-text searches can also be enabled by creating a <a href="trix.html">TRIX index file</a> that maps id's in the track to free-text metadata. Further instructions can be found in the <a href="hubQuickStartSearch.html">Searchable Hub Quick Start Guide</a>.</p> <p> See the searchIndex and searchTrix fields in the <a href="trackDb/trackDbHub.html">Hub Track Database Definition document</a> for information on how to set up your bigBed to enable searching. The searchIndex setting requires the input BED data to be case-senstive sorted (<code>sort -k1,1 -k2,2n</code>). You can use either the example UNIX <code>sort</code> command or the <code>bedSort</code> utility available -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">here</a>. See an example +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/" target="_blank">here</a>. See an example <a href="examples/hubExamples/hubIndexedBigBedSearchable/" target="_blank">searchable hub</a>.</p> <!-- ========== Adding Filters to Track Hub ============================== --> <a name="Filters"></a> <h2>Adding Filters to your Track Hub</h2> <p> The Genome Browser supports three varieties of data filter options for bigBed data. These can improve data usability in many ways, such as displaying specific data by default (e.g. only items that pass certain quality scores), allow for filtering based on pre-specified categories (e.g designate only LINE repetitive elements from a list of options) and more.</p> <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">