06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index f3a79ce..f9d5a93 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -59,80 +59,81 @@ 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 for an Assembly Hub</h2> +<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 for an Assembly Hub</a> for details.</p> +<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 included</h2> +<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. See the -section <a href="#blatGbib">Starting a Blat enabled Assembly Hub on GBiB</a> for more +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> <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="http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines" target="_blank">Public Hub Guidelines Wiki</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> <!-- ========= assembly blat ============================== --> <a name="blat"></a> -<h2>Starting Blat for an Assembly Hub</h2> +<h2>Starting Blat and In-Silico PCR for an Assembly Hub</h2> <p> From the location of yourAssembly.2bit file, <code>http://yourURL/yourAssembly/yourAssembly.2bit</code>, you can start two gfServers, specifying a port for the assembly hub to access amino acid sequence, <code>17777 -trans</code>, or DNA sequence, <code>17779</code>, in this example:</p> <pre><code>gfServer start localhost 17777 -trans -mask yourAssembly.2bit & gfServer start localhost 17779 -stepSize=5 yourAssembly.2bit &</code></pre> <p> -Then you can edit the genomes.txt file of your assembly hub to include two lines in the stanza +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. <p> </p> A dynamic BLAT server is specified with the <code>dynamic</code> argument to the <code>blat</code> or <code>transBlat</code> specification, followed by the <code>gfServer</code> dynamic root-relative path of the directory containing the <code>2bit</code> and <code>gfidx</code> files, named in the form <ul> <li><code><em>myGenome</em>.2bit</code> - two-bit format genomic sequence <li><code><em>myGenome</em>.untrans.gfidx</code> - untranslated index, built by <code>gfServer index</code> @@ -191,31 +192,31 @@ 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.* 129.70.40.99 134.160.84.67 128.114.198.32</code></pre> <p> This will allow connections with the U.S.-based genome.ucsc.edu site, the Europe-based mirror, the Asia-based mirror, and the UCSC development server.</p> <!-- ========== blat assembly hub GBiB ============================== --> <a name="blatGbib"></a> -<h2>Starting a Blat enabled Assembly Hub on GBiB</h2> +<h2>Starting a Blat and In-Silico PCR enabled Assembly Hub on GBiB</h2> <p> <strong>STEP 1.</strong> Acquire and install Genome Browser in a Box: <a href="gbib.html" target="_blank">http://genome.ucsc.edu/goldenPath/help/gbib.html</a>. You may also wish to read this UCSC <a href="../../blog/genome-browser-in-a-box-gbib-origins/" target="_blank">blog post</a>.</p> <p> <strong>STEP 2.</strong> With your GBiB operational, use your computer's terminal program to ssh into your GBiB: <code>ssh browser@localhost -p 1235</code>, using <code>browser</code> for the password.</p> <p> <strong>STEP 3.</strong> Navigate to the GBiB's <code>/folders</code> directory and use sudo to wget this assembly hub:</p> <pre><code>cd /folders sudo wget -r --no-parent --reject "index.html*" -nH --cut-dirs=3 http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/</code></pre> <p> @@ -234,31 +235,32 @@ will create a bin directory and install the tool. The commands use the North American and the European download servers respectively.</p> <pre><code>mkdir ~/bin -p; rsync -avP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/blat/gfServer ~/bin/</code></pre> <pre><code>mkdir ~/bin -p; rsync -avP hgdownload-euro.soe.ucsc.edu::genome/admin/exe/linux.x86_64/blat/gfServer ~/bin/</code></pre> <p> The GBiB also includes a tool you can run on the command line to download an entire suite of tools including gfServer: <code>gbibAddTools</code></p> <p> <strong>STEP 6.</strong> Navigate to the genomes.txt file of this assembly hub:</p> <pre><code>cd /folders/hubExamples/hubAssembly/plantAraTha1/</code></pre> <p> Edit the currently commented-out blat lines with <code>sudo vi genomes.txt</code> and use "x" when the cursor is over the <code>#</code> at the start of the line to remove it and <code>:w!</code> to save the changes and <code>:q</code> to quit. </p> <pre><code>blat localhost 17779 -transBlat localhost 17777</code></pre> +transBlat localhost 17777 +isPcr yourLab.yourInstitution.edu 17779 </code></pre> <p> Please note that if you loaded your hub earlier, it will take five minutes (300 seconds) for the browser to check for any changes to genomes.txt, and that this delay can be shortened temporarily by adding <code>&udcTimeout=10</code> to the URL. See more information in the <a href="hgTrackHubHelp.html#Debug" target="_blank">Debugging and Updating</a> section of the Track Hub User Guide.</p> <p> <strong>STEP 7.</strong> Change directories to the 2bit file:</p> <pre><code>cd /folders/hubExamples/hubAssembly/plantAraTha1/araTha1</code></pre> <p> Run the two gfServer commands to start the blat servers:</p> <pre><code>gfServer start localhost 17777 -trans -mask araTha1.2bit & gfServer start localhost 17779 -stepSize=5 araTha1.2bit & </code></pre> <p> <strong>STEP 8.</strong> Load this plant assembly hub by using this URL and selecting it under the