a7e37b9dfa1c8e2c3e135d08a8ee873a2e855d47 mspeir Mon Nov 3 16:47:06 2025 -0800 removing references to hgdownload-euro, refs #35031 diff --git src/hg/htdocs/goldenPath/help/gbib.html src/hg/htdocs/goldenPath/help/gbib.html index d9cbca8a9e3..5a20dee0963 100755 --- src/hg/htdocs/goldenPath/help/gbib.html +++ src/hg/htdocs/goldenPath/help/gbib.html @@ -112,43 +112,40 @@ <li> A compatible version of the <a href="https://www.virtualbox.org/" target="_blank">VirtualBox</a> software (version 4.3.6 or higher) must be installed. This software is free to use in many situations. See the VirtualBox wiki for <a href="https://www.virtualbox.org/wiki/Licensing_FAQ" target="_blank">licensing terms and conditions</a> and <a href="https://www.virtualbox.org/wiki/Downloads" target="_blank">installation</a> instructions. You must have administrator privileges to install VirtualBox on your computer.</li> <li> The computer hard disk must have at least 20 GB of free space (more if you plan to mirror many tracks).</li> <li> Your network firewall must allow outgoing connections to the following servers and ports: <ul> <li>MariaDB connections, used to load tracks not local to your computer: <ul> - <li>US server: Port 3306 on genome-mysql.gi.ucsc.edu (128.114.119.174)</li> - <li>European server: Port 3306 on genome-euro-mysql.soe.ucsc.edu (129.70.40.120)</li> + <li>Port 3306 on genome-mysql.gi.ucsc.edu (128.114.119.174)</li> </ul> </li> <li>Rsync, used to download track data: <ul> - <li>US server: TCP port 873 on hgdownload.gi.ucsc.edu (128.114.119.163)</li> - <li>European server: TCP port 873 on hgdownload-euro.soe.ucsc.edu (129.70.40.99)</li> + <li>TCP port 873 on hgdownload.gi.ucsc.edu (128.114.119.163)</li> </ul></li> <li>Download HTML descriptions on the fly: <ul> - <li>US server: TCP port 80 on hgdownload.gi.ucsc.edu (128.114.119.163)</li> - <li>European server: TCP port 80 on hgdownload-euro.soe.ucsc.edu (129.70.40.99)</li> + <li>TCP port 80 on hgdownload.gi.ucsc.edu (128.114.119.163)</li> </ul> </li> </ul> </ul> <h3>Installation</h3> <ol> <li> Confirm that your system meets the above requirements.</li> <li> Download GBiB from the <a href="https://genome-store.ucsc.edu/" target="_blank">Genome Browser store</a> (see <a href="#License">Licensing Information</a>). Due to the large size of the <em>gbib.zip</em> product file, the download time may range from 30 minutes to a few hours depending on your Internet connection speed and distance from UCSC.</li> @@ -270,62 +267,55 @@ <p> In addition to downloading entire track sets, you can also download individual subtracks. The file size of each track is listed next to the track name. If you are unsure of which tracks to select, we recommend the option <em>Default tracks with conservation tables, but no alignments</em>. When downloading large tracks, keep in mind that you cannot delete these tracks and the related data from GBiB once you have downloaded them. If you find that you've started downloading the wrong track or a track that is too large for your machine, you can cancel the download at any point by clicking <em>Cancel Download Now</em>.</p> <p> Depending on your network bandwidth, the download can take several minutes or up to a few hours over a DSL line. <strong>During the download</strong>, the file <em>gbib-data.vdi</em> will grow in size, and <strong>you will not be able to use GBiB</strong>. Once the download is complete, the default tracks should load in less than three seconds for a typical genomic position.</p> <p> If you are in your GBiB on the command-line you can use a direct rsync command for files of -interest. For example, if you knew you wanted all the GENCODE tracks on hg19 you could run either -of the two rsync commands for the North American or European hgdownload servers: +interest. For example, if you knew you wanted all the GENCODE tracks on hg19 you could run +this rsync command: <pre> <code>sudo rsync hgdownload.gi.ucsc.edu::mysql/hg19/wgEncodeGencode* /data/mysql/hg19/.</code> </pre> -<pre> -<code>sudo rsync hgdownload-euro.soe.ucsc.edu::mysql/hg19/wgEncodeGencode* /data/mysql/hg19/.</code> -</pre> <p> The above commands will rsync all of the files at the UCSC hgdownload server in the hg19 assembly that start with wgEncodeGencode to your GBiB into the hg19 directory. There are some supporting files in a hgFixed directory, such as for the publication tracks, that could be mirrored with such commands.</p> <p> Here is another example for hg38 where the following commands would download all the supporting encRegTfbs and factorbook tables for the Transcription Factor ChIP-seq Clusters track: <pre> <code>sudo rsync hgdownload.gi.ucsc.edu::mysql/hg38/encRegTfbs* /data/mysql/hg38/.</code> </pre> <pre> <code>sudo rsync hgdownload.gi.ucsc.edu::mysql/hg38/factor* /data/mysql/hg38/.</code> </pre> <p> You can also download gbdb files in this manner. <pre> <code>sudo rsync hgdownload.gi.ucsc.edu::gbdb/hg19/multiz100way/phyloP100way.wib /data/gbdb/hg19/multiz100way/.</code> </pre> -<pre> -<code>sudo rsync hgdownload-euro.soe.ucsc.edu::gbdb/hg19/multiz100way/phyloP100way.wib /data/gbdb/hg19/multiz100way/.</code> -</pre> - <p>The above command would copy the phyloP100way track to display in the GBiB from a local file.</p> <h3>Offline mode</h3> <p> GBiB has an offline mode that is particularly useful when you want to ensure that GBiB no longer connects to the Internet once the initial download and setup are complete (for instance, to comply with corporate IT policy). Before going offline, first mirror all the tracks that you will want to access. Then, in the GBiB terminal window type the command: <code>gbibOffline</code>. This command will remove GBiB's network access to the UCSC MariaDB server and download servers.</p> <p> Once GBiB is in offline mode, the Genome Browser will display an error message if you attempt to access a data file not located on your local disk; therefore, we do not recommend this option for general use. To reactivate Internet access, click on the GBiB terminal window and type the command: <code>gbibOnline</code>.</p> @@ -864,31 +854,30 @@ <pre><code>noProxy=ucsc.edu,mit.edu,localhost,127.0.0.1</code></pre> <p> The file /usr/local/apache/cgi-bin/hg.conf should already include a line like <code>include hg.conf.local</code> to incorporate the changes in hg.conf.local.</p> <p> <strong>Problem:</strong> "No space left on device" error when running gbibAddTools.</p> <p> In older GBiB's, there is an error in the <code>gbibAddTools</code> command. To fix this command, edit the <code>/home/browser/.bashrc</code> file and change the following line: <pre><code>alias gbibAddTools='mkdir ~/bin -p; rsync -avP hgdownload.gi.ucsc.edu::genome/admin/exe/linux.x86_64/ ~/bin/'</code></pre> </p> <p> to either of the follwing lines: <pre><code>alias gbibAddTools='sudo mkdir -p /data/tools; sudo rsync -avP hgdownload.gi.ucsc.edu::genome/admin/exe/linux.x86_64/ /data/tools/ && ln -s /data/tools ~/bin'</code></pre> -<pre><code>alias gbibAddTools='sudo mkdir -p /data/tools; sudo rsync -avP hgdownload-euro.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ /data/tools/ && ln -s /data/tools ~/bin'</code></pre> </p> <p> The updated commands will install the tools to a location with more disk space available using either the North American or European hgdownload servers. </p> <a name="Commands"></a> <h2>Genome Browser in a Box commands</h2> <!-- Explanation here --> <p> In addition to normal Linux commands, GBiB defines some special commands you may use while inside the GBiB terminal's window. These additional commands are documented in the README.txt file on the GBiB terminal's home directory, which can also be accessed via <a href="#Connectwithssh">ssh</a>.</p>