71a2c73633337ab11c6344fee8c077e13daf815b markd Tue Feb 2 12:03:42 2021 -0800 move most doc on setting up dynamic blat servers to the wiki diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 41c25c8..91f4c5f 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -115,88 +115,36 @@ 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 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. +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> +for details on how to setup dynamic BLAT servers <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> - <li><code><em>myGenome</em>.trans.gfidx</code> - translated index, built by <code>gfServer -trans index</code> -</ul> -<p> -For example: -<pre> - transBlat yourLab.yourInstitution.edu 4096 dynamic jillLab - blat yourLab.yourInstitution.edu 4096 dynamic jillLab - isPcr yourLab.yourInstitution.edu 4096 dynamic jillLab -</pre> -</p> - -<p> -The following commands are an example on how to make the gfidx files: -<pre> -gfServer index -stepSize=5 myGenome.untrans.gfidx myGenome.2bit -gfServer index -trans myGenome.trans.gfidx myGenome.2bit -</pre> -</p> - -<p> -The files names in the form: -<pre> - $rootdir/jillLab/myGenome.2bit - $rootdir/jillLab/myGenome.untrans.gfidx - $rootdir/jillLab/myGenome.trans.gfidx -</pre> -</p> - -<p> -For a more deeply nest directory, for instance, the following NCBI -convention: -<pre> - transBlat yourLab.yourInstitution.edu 4096 dynamic GCF/000/181/335/GCF_000181335.3 - blat yourLab.yourInstitution.edu 4096 dynamic GCF/000/181/335/GCF_000181335.3 -</pre> -</p> -<p> -will reference these genome files: -<pre> - $rootdir/GCF/000/181/335/GCF_000181335.3/GCF_000181335.3.2bit - $rootdir/GCF/000/181/335/GCF_000181335.3/GCF_000181335.3.untrans.gfidx - $rootdir/GCF/000/181/335/GCF_000181335.3/GCF_000181335.3.trans.gfidx -</pre> -</p> - -See <code>gfServer</code> documentation for the details -of configuring a dynamic BLAT server and generating indexes. - 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="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