c99b62d7865a828f8f41c6e82dd36cbd2dd26780 markd Wed Jul 1 21:45:43 2020 -0700 hgBlat mostly works diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 90d84a9..772400a 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -109,30 +109,35 @@ <a name="blat"></a> <h2>Starting Blat 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 referring to yourAssembly, that would have matching port numbers:</p> <pre><code>transBlat yourLab.yourInstitution.edu 17777 blat yourLab.yourInstitution.edu 17779 </code></pre> <p> +An addition argument of the string <code>dynamic</code> to the <code>blat</code> +or <code>transBlat</code> specification indicates that the BLAT server is dynamic and +started by <code>xinetd</code>. See <code>gfServer</code> documentation for the details +of configuring a dynamic BLAT server. + 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