26becc145e422e03b2b441380aec31c1fa30e564 gperez2 Tue Apr 23 17:04:50 2024 -0700 Removing the hgHubConnect.remakeTrackHub=on setting from the hgTrackHubHelp page since it is an internal flag, refs #2110 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 30fb62e..429be55 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -282,32 +282,30 @@ <a href="/cgi-bin/hgTracks?db=hg38&hubUrl=https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hub.txt&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&hubUrl=https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt" target="_blank">https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hub.txt&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&hubUrl=https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt</a></pre> <h3>Creating a URL for an Assembly Hub</h3> <p> The following example links to an assembly hub using the <code>hubUrl=</code> and <code>genome=</code> parameters where in the example, <code>genome=araTha1</code>, is the assembly name set for <code>genome</code> in the genomes.txt file. URL parameters can be combined by using <code>&</code>.</p> <pre><a href=../cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt>https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</a></pre> </p> <h6>Additional hub connection parameters</h6> <ul> <li id="hubClear"><code>hubClear=</code>connects the hub and disconnects other hubs that are in the same directory</li> <li id=hgHubConnect><code>hgHubConnect</code>Replacing <code>hgTracks</code> with this parameter connects the hub and redirects the link to the <a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#unlistedHubs" target="_blank">Track Data Hubs</a> page</li> -<li id="hgHubConnect.remakeTrackHub"><code>hgHubConnect.remakeTrackHub=on</code> -acts to connect when pointed to /hgHubConnect</li> <li id="hgHub_do_firstDb"><code>hgHub_do_firstDb=1</code> uses the first database in genomes.txt</li> <li id="hgHub_do_redirect"><code>hgHub_do_redirect=on</code> redirects the attached hub to the Gateway page</li> </ul> <h6>Redirecting the URL to the Gateway page</h6> <p> The following example link connects the hub and redirects the link to the Gateway page to display the hub's description html page, which is defined in the genomes.txt by the <code>htmlPath</code> setting, by using <code>hgHubConnect</code>, <code>hgHub_do_redirect=on</code>, <code>hgHubConnect.remakeTrackHub=on</code>, <code>hgHub_do_firstDb=1</code>, and <code>hubUrl</code>. </ul> <pre><code><a href="http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt" target="_blank">http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&<strong>hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</strong></a></code>