bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 56faee27cdd..a55315ddd1d 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -129,33 +129,33 @@ 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="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="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 +<a href="http://hgdownload.gi.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/" +a blat/ directory for your machine type <a href="http://hgdownload.gi.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.* 129.70.40.99 134.160.84.67 128.114.198.32</code></pre> <p> This will allow connections with the U.S.-based genome.ucsc.edu site, the Europe-based mirror, @@ -182,31 +182,31 @@ <p> <strong>STEP 4.</strong> You now have all the required files on your local machine and can load this plant assembly hub by using this URL and selecting it under the "group" category where "Plant araTha1" displays:</p> <pre><code><a href="http://127.0.0.1:1234/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://127.0.0.1:1234/folders/hubExamples/hubAssembly/plantAraTha1/hub.txt" target="_blank">http://127.0.0.1:1234/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://127.0.0.1:1234/folders/hubExamples/hubAssembly/plantAraTha1/hub.txt</a></code></pre> <p> <strong>STEP 5.</strong> To enable blat you must acquire the gfServer utility. The UCSC Genome Browser and Blat software are free for academic, nonprofit, and personal use. Commercial download and installation of the Blat and In-Silico PCR software may be licensed through <a href="http://www.kentinformatics.com">Kent Informatics</a>.</p> <p> You can obtain just the gfServer utility on your GBiB with either of the following commands that 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.gi.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 isPcr yourLab.yourInstitution.edu 17779 </code></pre> <p>