198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/hubQuickStart.html src/hg/htdocs/goldenPath/help/hubQuickStart.html index 9b630ff7bc0..7a2e405832e 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStart.html +++ src/hg/htdocs/goldenPath/help/hubQuickStart.html @@ -105,31 +105,31 @@ <li> <strong><a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable Track Hubs</a></strong></li> </ul> <!-- ========== hub.txt ============================== --> <a name="hub.txt"></a> <h2>Understanding hub.txt</h2> <pre><code><strong>hub</strong> <em>MyHubsNameWithoutSpaces</em> <strong>shortLabel</strong> <em>My Hub's Name</em> <strong>longLabel</strong> <em>Name up to 80 characters versus shortLabel limited to 17 characters</em> <strong>genomesFile</strong> <em>genomes.txt</em> <strong>email</strong> <em>myEmail@address</em> <strong>descriptionUrl</strong> <em>aboutMyHub.html</em> </code></pre> <p> -A hub starts with a few short lines in hubs.txt. The hub.txt file informs the UCSC Browser where to +A hub starts with a few short lines in hub.txt. The hub.txt file informs the UCSC Browser where to find the underlying assemblies via the <code><strong> genomesFile</strong>genomes.txt</code> parameter, which in turn will direct the Browser to each assembly's related binary indexed track data outlined in the trackDb.txt. The optional <code><strong>descriptionUrl</strong></code> field allows you to add an HTML page describing your hub. See an example of a basic hub.txt file <a href="../help/examples/hubDirectory/hub.txt" target="_blank">here</a>.</p> <!-- ========== genomes.txt ============================== --> <a name="genomes.txt"></a> <h2>Understanding genomes.txt</h2> <pre><code><strong>genome</strong> <em>assembly_database_1</em> <strong>trackDb</strong> <em>assembly_1_path/trackDb.txt</em> <strong>genome</strong> <em>assembly_database_2</em> <strong>trackDb</strong> <em>assembly_2_path/trackDb.txt</em> </code></pre> @@ -151,31 +151,31 @@ <strong>bigDataUrl</strong> <em>track_data_url</em> <strong>shortLabel</strong> <em>label 17 chars</em> <strong>longLabel</strong> <em>long label up to 80 chars</em><br></code></pre> <p> The trackDb.txt file uses stanzas for each track to inform the Browser of the name, type, location, and description of each binary file to display. The <a href="trackDb/trackDbHub.html" target="_blank">trackDb settings</a> allow further display control such as by adding the line <code><strong>color</strong>255,0,0</code> to define a track's color. Each track <code><strong>type</strong></code> (<code><a href="trackDb/trackDbHub.html#bigBed_-_Item_or_Region_Track_Settings" target="_blank">bigBed</a>, <a href="trackDb/trackDbHub.html#bigWig_-_Signal_Graphing_Track_Settings" target="_blank">bigWig</a>, <a href="trackDb/trackDbHub.html#bam" target="_blank">bam</a>, </code>and<code> <a href="trackDb/trackDbHub.html#vcfTabix" target="_blank">vcfTabix</a></code>) has further customizable trackDb settings. The <code><strong>bigDataUrl</strong></code> can be a -relative path to a local file or a publicly-accessibly URL that accepts byte-ranges. The trackDb.txt +relative path to a local file or a publicly-accessible URL that accepts byte-ranges. The trackDb.txt also allows for advanced <a href="trackDb/trackDbHub.html#groupingTracks" target="_blank">track grouping</a> known as composites, superTracks and multiWigs. See a basic <a href="../help/examples/hubDirectory/hg19/trackDb.txt" target="_blank">example trackDb.txt</a>.</p> <p> When type is set to <b>bigBed</b>, the track hub assumes that the bigBed track is BED3 by default. To allow track hubs to use all fields in the bigBed file, one must define how many columns to expect. For example, if a bigBed file has nine columns, which would include an itemRgb field to display a R,G,B color value (e.g. 255,0,0), specify the type as <code>type bigBed 9</code>. If the file contains the first 9 <a href="../../FAQ/FAQformat.html#format1" target="_blank"> standard BED columns</a>, one could use <code>type bigBed 9 +</code> to denote the additional non-standard columns as defined in AutoSql format (.as) file, <code>-as=bedExample1.as</code>. </p>