569c126e603831fc2fb997b54f98391f42d33a8d brianlee Wed Jun 15 07:15:23 2022 -0700 Adding note about GenArkon Quickstart Assembly Hub page, no RM diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 816710e..7622c8a0 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -1,28 +1,32 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Assembly Hub Quick Start" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Quick Start Guide to Assembly Hubs</h1> <p> Assembly Hubs allow researchers to create Track Data Hubs on assemblies that are not in the UCSC Browser. By including the underlying reference sequence in UCSC <a href="twoBit.html" target="_blank">twoBit</a> format, as well as data tracks, researchers can browse and annotate any -genome. For more information please refer to the +genome. We may have a <a href="../../FAQ/FAQreleases.html#release13" target="_blank">GenArk Hub</a> of +your genome, or you can visit our <a href="../../assemblyRequest.html" target="_blank">assembly +request page</a> and we can build an assembly hub for you.</p> +<p> +For more information please refer to the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hub Wiki</a>. Below is also a section about starting <a href="#blatGbib">GBiB Assembly Hubs</a>.</p> <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>