7038a4fdd383a996d3cd109bf46e1cb0274c58f5 brianlee Tue May 31 10:06:10 2022 -0700 Adding a new Assembly Hub overview section to trackDbHub page and linked to existing docs to provide anchors for groups, twoBitPath, defaultPos #1629 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 8784778..281d3e8 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -469,93 +469,94 @@ <em>trackDb</em> - the relative path of the trackDb file for the assembly designated by the <em>genome</em> tag. By convention, the trackDb file is located in a subdirectory of the hub directory. However, the trackDb tag may also specify a complete URL.</p> <p><em>metaDb</em> - the path to an optional tagStorm file that has the metadata for each track. Each track with metadata should have a "meta" tag specified in the trackDb stanza for that track and a "meta" tag in the tagStorm file.</p> <p><em>metaTab</em> - the path to an optional tab separated file that has the metadata for each track. Each track with metadata should have a "meta" tag specified in the trackDb stanza for that track and a "meta" tag in the tab separated file. The first line of the TSV file should start with a '#' and have the field names for each column, one of them being "meta".</p> <p> If this genomes.txt file is for an assembly that does not have native support in the browser, the following fields must also be present:</p> <p> -<em>twoBitPath</em> - refers to the .2bit file containing the sequence for this assembly. Typically +<em id="twoBitPath">twoBitPath</em> - refers to the .2bit file containing the sequence for this assembly. Typically this file is constructed from the original fasta files for the sequence using the kent program faToTwoBit. See <a href="twoBit.html">here</a> for instructions on how to build a 2bit file.</p> <p> -<em>groups</em> - a file which defines the track groups on this Genome Browser. Track groups are the +<em id="groups">groups</em> - a file which defines the track groups on this Genome Browser. Track groups are the sections of related tracks grouped together under the primary genome browser graphics display image. The groups.txt file defines the grouping of track controls under the primary Genome Browser image display. The example referenced here has the usual definitions as found in the UCSC Genome Browser. Each group is defined, for example the Mapping group:</p> <pre><code>name map label Mapping priority 2 defaultIsClosed 0 </code></pre> <p> The name is used in the trackDb.txt track definition group, to assign a particular track to this group. The label is displayed on the genome browser as the title of this group of track controls The priority orders this track group with the other track groups. The defaultIsClosed determines if this track group is expanded or closed by default. Values to use are 0 or 1.</p> <p> -<em>description</em> - will be displayed for user information on the gateway page and most title +<em id="description">description</em> - will be displayed for user information on the gateway page and most title pages of this genome assembly browser. It is the name displayed in the assembly pull-down menu on the browser gateway page.</p> <p> -<em>organism</em> - the string which is displayed along with the description on most title pages in the Genome Browser. Adjust your names in organism and description until they are appropriate. This +<em id="organism">organism</em> - the string which is displayed along with the description on most title pages +in the Genome Browser. Adjust your names in organism and description until they are appropriate. This organism name is the name that appears in the genome pull-down menu on the browser gateway page.</p> <p> -<em>defaultPos</em> - specifies the default position the genome browser will open when a user first +<em id="scientificName">scientificName</em> - specifies the scientific name for the assembly.</p> +<p> +<em id="defaultPos">defaultPos</em> - specifies the default position the genome browser will open when a user first views this assembly. This is usually selected to highlight a popular gene or region of interest in the genome assembly.</p> <p> <em>orderKey </em> - used with other genome definitions at this hub to order the pull-down menu ordering the genome pull-down menu.</p> <p> -<em>htmlPath</em> - refers to an html file that is used on the gateway page to display information -about the assembly.</p> -<p> -<strong><em>Example 3:</em></strong> Sample genomes.txt file defining attributes for the hub shown -in <em>Example 1</em>.</p> +<em id="htmlPath">htmlPath</em> - refers to an html file that is used on the gateway page to display +information for a novel assembly.</p> +<h6 id="example_genomes.txt">Example genomes.txt including a newOrg1 assembly</h6> <pre><code><strong>genome</strong> hg18 <strong>trackDb</strong> hg18/trackDb.txt <br> <strong>genome</strong> hg19 <strong>trackDb</strong> hg19/trackDb.txt <br> <strong>genome</strong> newOrg1 <strong>trackDb</strong> newOrg1/trackDb.txt <strong>twoBitPath</strong> newOrg1/newOrg1.2bit <strong>groups</strong> newOrg1/groups.txt <strong>description</strong> Big Foot V4 <strong>organism</strong> BigFoot <strong>defaultPos</strong> chr21:33031596-33033258 <strong>orderKey</strong> 4800 <strong>scientificName</strong> Biggus Footus <strong>htmlPath</strong> newOrg1/description.html </code></pre> <hr> <p> <strong>Step 6. Create the genome assembly subdirectories</strong><br> Within the track hub directory, create a subdirectory for each of the genome assemblies that have track data in the hub. The subdirectory names must have a 1:1 correspondence with the database names defined by the <em>genome</em> tags in the genomes.txt file.</p> <hr> <p> -<strong>Step 7. Create the trackDb.txt files</strong><br> +<strong id="trackDb.txt">Step 7. Create the trackDb.txt files</strong><br> The trackDb.txt file, which is based on the Genome Browser .ra format, is the most complicated of the text files in the hub directory. It contains a stanza for each of the data files for the given assembly that defines display and configuration properties for the track. If the tracks are grouped into larger entities, such as composite or super-tracks, the larger entities will have a stanza in the file as well.</p> <p> The <a href ="trackDb/trackDbHub.html">Track Database Definition Document</a> will help you understand how to create a trackDb.txt file. This document describes how to declare dataset display settings and values, and indicates the support level for each setting. While there are over 100 track settings supported at UCSC, other sites that display hubs have more limited settings support. To further portability of hubs, we have used input from other sites to identify a "base" subset of the "full" settings list, and the document has been assigned a version number. See the document introduction for a fuller explanation.</p> <p> At a minimum, each track in the trackDb.txt file must contain the "required" settings:</p>