1e0b1b2cbd35e8c79caff322317c93365c8cc5a8 brianlee Tue Dec 17 08:18:58 2019 -0800 Removing td from htmlCheck and a section about rsync on gbib.html diff --git src/hg/htdocs/goldenPath/help/gbib.html src/hg/htdocs/goldenPath/help/gbib.html index 4d25100..65816a2 100755 --- src/hg/htdocs/goldenPath/help/gbib.html +++ src/hg/htdocs/goldenPath/help/gbib.html @@ -11,31 +11,30 @@ <h6><a href="#What">What is Genome Browser in a Box (GBiB)?</a></h6> <h6><a href="#GetStarted">Getting Started: Setting up Genome Browser in a Box</a></h6> <h6><a href="#UsingGbib">Using Genome Browser in a Box</a></h6> <h6><a href="#GbibMirroring">Improving speed and performance</a></h6> <h6><a href="#UpdatingGbib">Updating Genome Browser in a Box</a></h6> <h6><a href="#YourTracks">Viewing your own data</a></h6> <h6><a href="#SharingGBIB">Sharing Genome Browser in a Box with others</a></h6> <h6><a href="#UsrAcct">User accounts and sessions</a></h6> <h6><a href="#Trouble">Troubleshooting common problems</a></h6> <h6><a href="#Commands">Genome Browser in a Box commands</a></h6> <h6><a href="#License">Licensing information</a></h6> <hr> <p> <strong>Other resources:</strong> -<td> <ul><strong> <li><a class="toc" href="http://genome.ucsc.edu/blog/genome-browser-in-a-box-gbib-origins/" target="_blank">UCSC blog post about GBiB</a></li> <li><a class="toc" href="https://www.youtube.com/watch?v=1DzZZgB1gvQ" target="_blank">GBiB introductory video</a></li> </strong></ul> <a name="What"></a> <h2>What is Genome Browser in a Box?</h2> <p> Genome Browser in a Box (GBiB) is a "virtual machine" of the entire UCSC Genome Browser website that is designed to run on most PCs (Windows, Mac OSX or Linux). GBiB allows you to access much of the UCSC Genome Browser's functionality from the comfort of your own computer. It is particularly directed at individuals who want to use the Genome Browser toolset to view protected data. If it is not human sequencing reads, it usually does not fall under @@ -271,30 +270,39 @@ 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: <pre> <code>sudo rsync hgdownload.soe.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.soe.ucsc.edu::mysql/hg38/encRegTfbs* /data/mysql/hg38/.</code> +</pre> +<pre> +<code>sudo rsync hgdownload.soe.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.soe.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