08320469134fa85d4162a1927ed3659af7e2fbe3 mspeir Mon Apr 28 18:57:20 2025 -0700 adding note about update command being compatible with db names and add lines about GBiC+Docker that were not in the .md file, refs #25120 diff --git src/hg/htdocs/goldenPath/help/gbic.html src/hg/htdocs/goldenPath/help/gbic.html index ad77eb578a2..035d3a89d52 100755 --- src/hg/htdocs/goldenPath/help/gbic.html +++ src/hg/htdocs/goldenPath/help/gbic.html @@ -17,32 +17,32 @@ <h6><a href='#how-does-the-gbic-program-work'>How does the GBiC program work?</a></h6> <h6><a href='#gbic-commands'>GBiC Commands</a></h6> <h6><a href='#all-gbic-options'>All GBiC options</a></h6> <h6><a href='#credits'>Credits</a></h6> <a name='what-is-genome-browser-in-the-cloud'></a> <h2>What is Genome Browser in the Cloud?</h2> <p> The Genome Browser in the Cloud (GBiC) program is a convenient tool that automates the setup of a UCSC Genome Browser mirror. The GBiC program is for users who want to set up a full mirror of the UCSC Genome Browser on their server/cloud instance, rather than using <a href='gbib.html' title=''>Genome Browser in a Box</a> (GBIB) or our public website. Please see the <a href='mirror.html#considerations-before-installing-a-genome-browser' title=''>Installation of a UCSC Genome Browser on a local machine (mirror)</a> page for a summary of installation options, including the pros and cons of using a mirror -installation via the GBiC program vs. using GBiB. GBiC can also be used as a Docker container. See -the <a href='docker.html' title=''>Docker help page</a> for more information. +installation via the GBiC program vs. using GBiB. GBiC can also be used as a Docker container. +See our <a href='docker.html' title=''>Docker help page</a> for more information. </p> <p> The program works by setting up MySQL (MariaDB), Apache, and Ghostscript, and then copying the Genome Browser CGIs onto the machine under <code>/usr/local/apache/</code>. Because it also deactivates the default Apache htdocs/cgi folders, it is best run on a new machine, or at least a host that is not already used as a web server. The tool can also download full or partial assembly databases, update the Genome Browser CGIs, and remove temporary files (aka “trash cleaning”). </p> <p> The GBiC program has been tested and confirmed to work with Ubuntu 18/20/22/24 LTS, Rocky 9.5, and Fedora 30/35/41. </p> @@ -75,50 +75,41 @@ <pre><code>sudo bash browserSetup.sh install</code></pre> <p> The <code>install</code> command downloads and configures Apache, MySQL (MariaDB) and Ghostscript, copies the Genome Browser CGIs, and configures the mirror to load data remotely from UCSC. The <code>install</code> command must be run before any other command is used. </p> <p> For mirror-specific help, please contact the Mirror Forum as listed on our <a href='https://genome.ucsc.edu/contacts.html' title=''>contact page</a>. </p> <p> For an installation demonstration, see the <a href='https://www.youtube.com/watch?v=dcJERBVnjio' title=''>Genome Browser in the Cloud (GBiC) Introduction</a> -video:<br> - -<!--#if expr="${SERVER_NAME} = /-china/" --> - <a href='../../../videos/dcJERBVnjio.mp4'> - <img src=../../images/videoIcon.png></a> - - Visit our <a href="/videos/" target="_blank">Video Page</a>. -<!--#else --> -<iframe width="560" height="350" src="https://www.youtube.com/embed/dcJERBVnjio?rel=0" -frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" -allowfullscreen></iframe> </p> - -<p> Visit our <a href="https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" -target="_blank">YouTube channel</a> for more videos. -</p> -<!--#endif --> +video: </p> <p> +<iframe width="560" height="315" src="https://www.youtube.com/embed/dcJERBVnjio?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> + +</iframe> + +</p> + <a name='how-does-the-gbic-program-work'></a> <h2>How does the GBiC program work?</h2> <p> The GBiC program downloads the Genome Browser CGIs and sets up the central MySQL (MariaDB) database. All potentially destructive steps require confirmation by the user (unless the <code>-b</code> batch mode option is specified). </p> <p> In particular, MySQL (MariaDB) and Apache are installed and set up with the right package manager (yum or apt-get). A default random password is set for the MySQL (MariaDB) root user and added to the <code>~/.my.cnf</code> file of the Unix root account. If you have already set up MySQL (MariaDB), you must create the <code>~/.my.cnf</code> file. The program will detect this and create a template file for you. The program also performs some minor tasks such as placing symlinks, detecting MariaDB, deactivating @@ -247,30 +238,37 @@ <pre><code>sudo bash browserSetup.sh -t noEncode mirror hg19</code></pre> <p> For a full list of <code>-t</code> options, see the <a href='#all-gbic-options' title=''>All GBiC options</a> section or run the program with no arguments. </p> <p> To update all CGIs and fully mirrored assemblies, call the tool with the <code>update</code> parameter like this: </p> <pre><code>sudo bash browserSetup.sh update</code></pre> +<p> +The <code>update</code> parameter can also be used to update the data for a single assembly by providing the +UCSC assembly name (e.g. rn6, bosTau6, equCab3): +</p> + +<pre><code>sudo bash browserSetup.sh update bosTau9</code></pre> + <p> Minimal mirror sites (those that have partially mirrored an assembly) should not use the <code>update</code> command, but rather just rerun the <code>minimal</code> command, so that only the minimal tables are updated. For instance, if you have partially mirrored the hg19 and hg38 databases, you may want to add this command to your crontab, perhaps running it every day, to keep your local tables in sync with those at UCSC: </p> <pre><code>sudo bash browserSetup.sh minimal hg19 hg38</code></pre> <p> To update only the Genome Browser software and not the data, use the <code>cgiUpdate</code> command: </p>