d8d9e8bc8fa214d169bc3011359fbe9bfd6b7c08 jnavarr5 Tue Jan 5 17:06:01 2021 -0800 Removing the escaped characters to clean up the markdown file (github README) refs #23297 diff --git src/hg/htdocs/goldenPath/help/gbic.html src/hg/htdocs/goldenPath/help/gbic.html index adcab99..41287d1 100755 --- src/hg/htdocs/goldenPath/help/gbic.html +++ src/hg/htdocs/goldenPath/help/gbic.html @@ -25,41 +25,41 @@ 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. </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"). +update the Genome Browser CGIs, and remove temporary files (aka “trash cleaning”). </p> <p> The GBiC program has been tested with Ubuntu 14/16 LTS, Centos 6/6.7/7.2, and Fedora 20. </p> <p> It has also been tested on virtual machines in Amazon EC2 (Centos 6 and Ubuntu 14) and Microsoft Azure (Ubuntu). If you want to load data on the fly from UCSC, you need to select the -data centers "US West (N. California)" (Amazon) or "West US" (Microsoft) for best performance. +data centers “US West (N. California)” (Amazon) or “West US” (Microsoft) for best performance. Other data centers (e.g. East Coast) will require a local copy of the genome assembly, which requires 2TB-7TB of storage for the hg19 assembly. Note that this exceeds the current maximum size of a single Amazon EBS volume. </p> <a name='quick-start-instructions'></a> <h2>Quick Start Instructions</h2> <p> Download the GBiC program from the <a href='https://genome-store.ucsc.edu/' title=''>UCSC Genome Browser store</a>. </p> <p> Run the program as root, like this: </p> @@ -139,42 +139,42 @@ <li>European server: TCP port 873 on hgdownload-euro.soe.ucsc.edu (129.70.40.99)</li> </ul></li> <li>Download HTML descriptions on the fly: <ul> <li>US server: TCP port 80 on hgdownload.soe.ucsc.edu (128.114.119.163)</li> <li>European server: TCP port 80 on hgdownload-euro.soe.ucsc.edu (129.70.40.99)</li> </ul></li> </ul> <h3 id="root-file-system-too-small-for-all-data">Root file system too small for all data</h3> <p> If you need to move data to another partition because the root file system is too small for all of the assembly's data, the following steps will help complete the installation. First, do a minimal -installation with the browserSetup.sh script as described below, using just the "install" -argument. Then make symlinks to the directory that will contain the data, e.g. if your biggest -filesystem is called "/big": +installation with the browserSetup.sh script as described below, using just the “install” +argument. Then make symlinks to the directory that will contain the data, e.g. if your +biggest filesystem is called “/big”: </p> <pre><code>sudo mv /var/lib/mysql /big/ sudo mv /gbdb /big/ sudo ln -s /big/mysql /var/lib/mysql sudo ln -s /big/gbdb /gbdb</code></pre> <p> -Then use the "mirror" or "minimal" arguments to browserSetup.sh to rsync over the majority of +Then use the “mirror” or “minimal” arguments to browserSetup.sh to rsync over the majority of the data. </p> <a name='gbic-commands'></a> <h2>GBiC Commands</h2> <p> The first argument of the program is called <code>command</code> in the following section of this document. The first command that you will need is <code>install</code>, which installs the Genome Browser dependencies, binary files and basic MySQL (MariaDB) infrastructure: </p> <pre><code>sudo bash browserSetup.sh install</code></pre> <p>