b066b38ccaff9d15f82a8888ecec6c7267a8c067 jnavarr5 Fri May 3 14:45:27 2019 -0700 Using definition lists instead of <strong> tags, refs #20551 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index d0d38bc..1bbf031 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -1216,56 +1216,58 @@ conversion file is not listed, send a request to the <a href="../../contacts.html">genome mailing list</a> and we may be able to generate one for you.</p> <a name="Download"></a> <h2>Downloading genome data</h2> <p> Most of the underlying tables containing the genomic sequence and annotation data displayed in the Genome Browser can be downloaded. All of the tables are freely usable for any purpose except as indicated in the README.txt file in the download directories. This data was contributed by many researchers, as listed on the Genome Browser <a href="../credits.html" target="_blank">Credits</a> page. Please acknowledge the contributor(s) of the data you use. <h3>Downloading the data</h3> <p> Genome data can be downloaded in different ways:</p> -<p> -<ul class="gbsNoBullet"> - <li> - <strong>Via rsync:</strong> The UCSC Genome Browser hgdownload server contains download +<dl> + <dt>Via rsync:</dt> + <dd> + The UCSC Genome Browser hgdownload server contains download directories for all genome versions currently accessible in the Genome Browser. The rsync command <code>rsync -a -P rsync://hgdownload.soe.ucsc.edu/path/file ./</code> can quickly and efficiently download large files to your current directory (./). To download an entire directory (note the trailing slash), you would use an expression such as <code>rsync -a -P rsync://hgdownload.soe.ucsc.edu/directory/ ./</code> For more information please - click <a href="../help/ftp.html" target="_blank">here</a>.</li> - <li> - <strong>Via ftp:</strong> The UCSC Genome Browser ftp server contains download directories + click <a href="../help/ftp.html" target="_blank">here</a>.</dd> + <dt>Via ftp:</dt> + <dd> + The UCSC Genome Browser ftp server contains download directories for all genome versions currently accessible in the Genome Browser. The ftp command <code>ftp://hgdownload.soe.ucsc.edu/goldenPath/</code> will take you to a directory that contains the genome download directories. This download method is not recommended if you plan to download a large file or multiple files from a single directory compared to rsync (see above). You can, however, use the <em>mget</em> command to download multiple files: mget <em>filename1 - filename2</em>, or mget -a (to download all the files in the directory).</li> - <li> - <strong>Via the Downloads link:</strong> Click the + filename2</em>, or mget -a (to download all the files in the directory).</dd> + <dt>Via the Downloads link:</dt> + <dd> + Click the <a href="http://hgdownload.soe.ucsc.edu/downloads.html" target="_blank">Downloads</a> link on the left side bar on the UCSC Genome Browser home page to display a list of all database directories available for download. If the data you wish to download pre-dates the assembly versions listed, look for the data on our <a href="http://hgdownload.soe.ucsc.edu/downloads.html" - target="_blank">Downloads</a> page.</li> -</ul> + target="_blank">Downloads</a> page.</dd> +</dl> <h3>Types of data available</h3> <p> There may be several download directories associated with each version of a genome assembly: the full data set <em>(bigZips)</em>, the full data set by chromosome <em>(chromosome)</em>, the annotation database tables <em>(database)</em>, and one or more sets of comparative cross-species alignments.</p> <p> <em>BigZips</em> contains the entire draft of the genome in chromosome and/or contig form. Depending on the genome, this directory may contain some or all of the following files:</p> <ul> <li> <strong>chromAgp.zip:</strong> Description of how the assembly was generated, unpacking to one file per chromosome.</li> <li>