6efc703aec6bbfaeb2c1550f1cb45b3771629f86 lrnassar Mon Oct 24 17:05:08 2022 -0700 Updating documentation from 'My Hubs' to the new name 'Connected Hubs' refs #29870 diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 7622c8a0..692ac64 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -20,31 +20,31 @@ <p> <strong>STEP 1:</strong> In a publicly accessible directory, copy this <em>Arabidopsis thaliana</em> plant assembly hub, which includes an araTha1.2bit file, using the following wget command:</p> <pre><code>wget -r --no-parent --reject "index.html*" -nH --cut-dirs=3 http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/</code></pre> <p> Alternatively, <strong>if you do not have wget installed,</strong> you can curl these files individually. Perform the curl -O option in the location you wish to copy the files:</p> <pre><code>curl -O http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</code></pre> <p> <em>If you use curl</eM>, be sure to recreate the structure with matching araTha1 and araTha1/bbi directories. Double check you have all the files by looking here: <pre><code><a href="http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/" target="_blank">http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/</a> </code></pre> <p> <strong>STEP 2:</strong> Paste your hub.txt link (<code>http://yourURL/hub.txt</code>) into the -<a href="../../cgi-bin/hgHubConnect" target="_blank">My Hubs</a> tab of the Track Data Hubs page, +<a href="../../cgi-bin/hgHubConnect" target="_blank">Connected Hubs</a> tab of the Track Data Hubs page, click the "Add Hub" button, and then click the "Genome Browser" link from the top bar.</p> <p> Alternatively build a URL that will directly load your assembly hub and display it on hgGateway. Then click the "Genome Browser" link from the top bar to view your assembly hub:</p> <p> <code> http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&<strong>hubUrl=http://yourURL/hub.txt</strong> </code> <p> This URL should work the same as using the original data just copied:</p> <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></pre> <p>