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/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 23a4810a6e9..13871a795a6 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -987,31 +987,31 @@ and "Display load times" checked:</p> <p class='text-center'> <img class='text-center' src="../../images/hubDevelopment.png" alt="The Hub Development tool checks config setting" width="749" height="249"> <p class='gbsCaption text-center'>The Hub Development tool checks for proper configuration files and track hub settings, and allows access to debugging settings.</p> <h3>Check hub settings using hubCheck utility</h3> <p> It is a good practice to run the command-line utility <em>hubCheck</em> on your track hub when you first bring it online and whenever you make significant changes. This utility by default checks that the files in the hub are correctly formatted, but it can also be configured to check a few other things including that various trackDb settings are correctly spelled and that they are supported by the UCSC Genome Browser. You can read more about using hubCheck to check the -compatibility of your hub with other genome browsers <a href="#Compatibility"</a>below</a>.</p> +compatibility of your hub with other genome browsers <a href="#Compatibility">below</a>.</p> <p> Here is the usage statement for the hubCheck utility: <pre><code>hubCheck - Check a track data hub for integrity. usage: hubCheck http://yourHost/yourDir/hub.txt options: -checkSettings - check trackDb settings to spec -version=[v?|url] - version to validate settings against (defaults to version in hub.txt, or current standard) -extra=[file|url] - accept settings in this file (or url) -level=base|required - reject settings below this support level -settings - just list settings with support level Will create this directory if not existing -noTracks - don't check remote files for tracks, just trackDb (faster) @@ -1053,31 +1053,31 @@ -udcDir=/dir/to/udcCache Path to udc directory -download Download data files in addition to the hub configuration files </code></pre></p> <p> Note that you will have to use the -udcDir option if /tmp/udcCache is not writable on your machine.</p> <p> The hubClone program is available from the UCSC downloads server at <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">http://hgdownload.gi.ucsc.edu/admin/exe/</a>.</p> <!-- ========== Setting Up Track Item Search ============================== --> <a name="Search"></a> <h2>Setting up track item search</h2> <p> The Genome Browser supports searching for items within bigBed tracks in track data hubs. To support -this behavior you have to add an index to the bigBed file when you initially create the the bigBed +this behavior you have to add an index to the bigBed file when you initially create the bigBed file from the bed file input. Indices are usually created on the name field of the bed, but can be created on any field of the bed. Free-text searches can also be enabled by creating a <a href="trix.html">TRIX index file</a> that maps id's in the track to free-text metadata. Further instructions can be found in the <a href="hubQuickStartSearch.html">Searchable Hub Quick Start Guide</a>.</p> <p> See the searchIndex and searchTrix fields in the <a href="trackDb/trackDbHub.html">Hub Track Database Definition document</a> for information on how to set up your bigBed to enable searching. The searchIndex setting requires the input BED data to be case-sensitive sorted (<code>sort -k1,1 -k2,2n</code>), which can be done using the <code>-sort</code> option in the <a href="http://hgdownload.gi.ucsc.edu/admin/exe/" target="_blank">bedToBigBed utility</a>.</p> <p> When a bigBed file is used in a track hub, additional indices can be created to support searching on specific fields. For example, running <code>bedToBigBed</code> with <code>-extraIndex=name</code> @@ -1627,31 +1627,31 @@ One must first create a DropBox account, upload the <em>bigDataUrl</em> files, or drag-and-drop from local disk. DropBox also has an app. They provide support for MacOS and Android too. Copy the share URL provided. Edit your <em>hub.txt</em> appropriately. Use <code>useOneFile on</code> hub setting that allows the hub properties to be specified in a single file. More information about this setting can be found on the <a href="./hgTracksHelp.html#UseOneFile" target="_blank">Genome Browser User Guide</a>. If you would like to add metadata to your track hub, the following <a href="./metadata.html">metadata guide</a> contains examples of how to include the information in your tracks.</p> <p> Click share on each data file, choose copy link, Ctrl-C and paste the dropbox URL into the hub oneFile the bigDataUrl field in the trackDb section of your useOneFile hub txt. -It will look somehting like this: +It will look something like this: </p> <pre> bigDataUrl https://www.dropbox.com/scl/fi/8t785o3sqidp0tmar91bf/dnaseRep3.bw?rlkey=37wucbhdvwqntw4ejvig4kg7c&st=11v8l216&dl=0 </pre> <p> Click the share button over your hub .txt file and Copy Link, Ctrl-C. Paste that dropbox hub url into the hgHubConnect CGI tab. </p> <pre> https://www.dropbox.com/scl/fi/6wrobg6wqcgtm7khew4qo/hub1.txt?rlkey=vi32q9tb68kjpn2xhy0qjuqkf&st=nldzp2tw&dl=0 </pre> <p> Note that DropBox does not use pathnames as part of the URLs, therefore bigDataUrl files