a74c645505a135d5c1e923afe477cdeb9c15bded markd Wed Jul 8 22:27:42 2020 -0700 added including multiple container directoies in genome dir path to gfServer diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 772400a..140d7c3 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -106,37 +106,82 @@ <!-- ========= assembly blat ============================== --> <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> +<pre> + transBlat yourLab.yourInstitution.edu 17777 + blat yourLab.yourInstitution.edu 17779 +</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 directory contain the +<code>2bit</code> and <code>gfidx</code> files. The final genome +directory and base name of the data files must be the same as the +genome name. +<p> +For example: +<pre> + transBlat yourLab.yourInstitution.edu 4096 dynamic myGenome + blat yourLab.yourInstitution.edu 4096 dynamic myGenome +</pre> +</p> +<p> +for files store in the form: +<pre> + $rootdir/myGenome/myGenome.2bit + $rootdir/myGenome/myGenome.untrans.gfidx + $rootdir/myGenome/myGenome.trans.gfidx +</pre> +</p> + <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. +For for more deeply nest directory, for instance, for instance following the 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>