f0cf6c47c691584bbc41d6b83dea263183727b8a brianlee Tue Dec 8 13:23:55 2020 -0800 Changing example isPcr in GBiB to be localhost fitting the rest of the example refs #21446 diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 67ac06e..09ca31f 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -183,31 +183,31 @@ 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 -isPcr yourLab.yourInstitution.edu 17779 </code></pre> +isPcr localhost 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