f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f gperez2 Fri Sep 26 17:46:49 2025 -0700 Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740 diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 9d68a920404..56faee27cdd 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -3,31 +3,31 @@ <!--#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. 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>. +<a href="assemblyHubHelp.html" target="_blank">Assembly Hub User Guide</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> <p> @@ -46,64 +46,63 @@ <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> <strong>STEP 3:</strong> Congratulations! Your assembly hub should display!</p> <p> If you are having problems, be sure all your files and the directories are publicly accessible. You may also wish to <a href="../../cgi-bin/cartReset" target="_blank">reset</a> the browser occasionally to clear all existing data. For hubs to work, your server must also accept byte-ranges. You can check using the following command to verify "Accept-Ranges: bytes" displays: <pre><code>curl -I http://yourURL/hub.txt</code></pre></p> <p> Now that you have the assembly hub copied from above, you can copy the directory and start to edit some of the documents such as genomes.txt, groups.txt, and trackDb.txt to understand how they work. -Refer to the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly -Hub Wiki</a> to understand how to build a <a href="twoBit.html" target="_blank">twoBit</a> file for +Refer to the <a href="assemblyHubHelp.html" target="_blank">Assembly Hub User Guide</a> to +understand how to build a <a href="twoBit.html" target="_blank">twoBit</a> file for your own original fasta files. Read more about <a href="trackDb/trackDbHub.html" target="_blank">trackDb settings</a> in the definition document.</p> <p> This assembly hub is a an abbreviated version of a larger plant assembly Public Hub. You can explore the larger hub structure <a href="http://genome-test.soe.ucsc.edu/~hiram/hubs/Plants/" target="_blank">here</a>.</p> <p> Please note that the Browser waits 5 minutes before checking for any changes to these files. <strong>When editing hub.txt, genomes.txt, trackDb.txt, and related hub files, shorten this delay by adding <code>udcTimeout=1</code> to your URL.</strong> For more information, please see the <a href="hgTrackHubHelp.html#Debug" target="_blank">Debugging and Updating Track Hubs</a> section of the <a href="hgTrackHubHelp.html" target="_blank">Track Hub User Guide</a>. Also, for more detailed instructions on setting up a regular hub, please see the <a href="hgTrackHubHelp.html#Setup" target="_blank">Setting Up Your Own Track Hub</a> section of the Track Hub User Guide.</p> <h2>Setting up Blat and In-Silico PCR for an Assembly Hub</h2> <p> By running gfServers from your institution, you can enable blat on your assembly hubs. See <a href="#blat">Starting Blat and In-Silico PCR for an Assembly Hub</a> for details.</p> <h2>Setting up an Assembly Hub on GBiB with Blat and In-Silico PCR included</h2> <p> With an operational installation of Genome Browser in a Box (GBiB), you can quickly and easily acquire an example assembly hub and run gfServers locally on the GBiB to enable Blat and In-Silico PCR. See the section <a href="#blatGbib">Starting a Blat and In-Silico PCR enabled Assembly Hub on GBiB</a> for more information.</p> <h2>Resources</h2> <ul> <li> - <strong><a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hubs - Wiki</a></strong></li> + <strong><a href="assemblyHubHelp.html" target="_blank">Assembly Hub User Guide</a></strong></li> <li> <strong><a href="hgTrackHubHelp.html" target="_blank">Track Hub User Guide</a></strong></li> <li> <strong><a href="trackDb/trackDbHub.html" target="_blank">Track Database (trackDb) Definition Document</a></strong></li> <li> <strong><a href="publicHubGuidelines.html" target="_blank">Public Hub Guidelines</a></strong></li> <li> <strong><a href="hubQuickStart.html" target="_blank">Quick Start Guide to a Basic Hub</a></strong></li> <li> <strong><a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Hubs</a></strong></li> </ul> @@ -121,39 +120,39 @@ <p> Then you can edit the genomes.txt file of your assembly hub to include three lines in the stanza referring to yourAssembly, that would have matching port numbers:</p> <pre> transBlat yourLab.yourInstitution.edu 17777 blat yourLab.yourInstitution.edu 17779 isPcr yourLab.yourInstitution.edu 17779 </code></pre> </pre> <p> The assembly hub can be configured to talk to a dynamic BLAT server that loads a pre-built index when started by an <code>xinetd</code> super-server. This allows genomes to have a blat server without needing it to be resident in memory at all times. See <a href="http://genomewiki.ucsc.edu/index.php/Running_your_own_gfServer">Running your own gfServer</a> and -<a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Adding_BLAT_servers">Adding BLAT servers</a> +<a href="assemblyHubHelp.html#addingBlatServers">Adding BLAT servers</a> for details on how to setup dynamic BLAT servers <p> See an example genomes.txt with commented out lines <a href="http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/genomes.txt" target="_blank">here</a>, and please note the uppercase "B" in transBlat. For more information, see the "Adding BLAT servers" section of the -<a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Adding_BLAT_servers" -target="_blank">Assembly Hub Wiki</a>. The +<a href="assemblyHubHelp.html#addingBlatServers" +target="_blank">Assembly Hub User Guide</a>. The <a href="http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads" target="_blank">Source Downloads</a> page offers access to utilities with pre-compiled binaries such as gfServer found in a blat/ directory for your machine type <a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">here</a> and further <a href="blatSpec.html" target="_blank">blat documentation here</a>. Please note that because the <code>-mask</code> option in the above <code>17777 -trans</code> gfServer option will mask all lower-case sequence from being matched, you may not wish to include it. See the above blat links and gfServer usage statement for more information.</p> <p> If you have trouble connecting your blat servers with the browser or if the browser cannot access your files, check if your institution has a firewall that prevents the browser from sending multiple inquiries. If this is the case, ask your systems administrator to add the following IP addresses as exceptions so that access is not limited. <pre><code>128.114.119.* 129.70.40.99 134.160.84.67