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/hgSessionHelp.html src/hg/htdocs/goldenPath/help/hgSessionHelp.html index 65b6220f107..53eb4d9cf11 100755 --- src/hg/htdocs/goldenPath/help/hgSessionHelp.html +++ src/hg/htdocs/goldenPath/help/hgSessionHelp.html @@ -56,31 +56,31 @@ target="_blank">create an account</a> and <a href="../../cgi-bin/hgSession" target="_blank">log in</a> before using the session manager.</p> <p> Individual sessions may be designated as either <a href="#ShareOrNot"><em>shared</em> or <em>non-shared</em></a> to protect the privacy of confidential data. To avoid having a new shared session from someone else override your existing Genome Browser settings, you are encouraged to open a new web-browser instance or to save existing settings in a session before <a href="#Open">loading</a> a new shared session.</p> <p> Note that not all of the Genome Browser <a href="../../mirror.html">mirror sites</a> have all of the session features enabled.</p> <p> This User's Guide provides a few examples that introduce the features of the Session tool, followed by detailed directions on creating, saving, modifying and sharing sessions.</p> <p> -You may also wish to reivew two blog posts, +You may also wish to review two blog posts, <a href="https://genome-blog.gi.ucsc.edu/blog/how-to-share-your-ucsc-screenthoughts/" target="_blank">How to share your UCSC screenthoughts</a> and <a href="https://genome-blog.gi.ucsc.edu/blog/sharing-data-with-sessions-and-urls/" target="_blank">Sharing Data with Sessions and URLs</a> for more discussions about sessions.</p> <!-- ====Example======================== --> <a name="Example"></a> <h2>Some simple examples</h2> <p> This section contains some example sessions that demonstrate the use of the Session tool. To enable you to view these sessions, we have <a href="../../cgi-bin/hgSession" target="_blank">created a user account</a> with the name <em>Example</em>. </P> <!-- =====Example 1======================= --> <a name="Example1"></a> @@ -200,31 +200,31 @@ then be listed by name under <em>My Sessions</em>.</li> <li> <strong>Save session settings to a file.</strong> Alternatively, you can create a file from your session settings that can be saved to your local machine or posted to a URL for <a href="#Open">access or sharing</a>. To do this, go to the <code>Save Settings</code> section. Type a name into the <code>Save current settings to a local file</code> box. Click the <button>submit</button> button to save or display the file. The session will be saved in plain text (ascii) format by default. To select a compressed format, select one of the options from the <code>file type returned</code> menu before clicking <button>submit</button>. If you simply wish to preview the contents of the file in your browser window, leave the file name blank and click <button>submit</button>.</li> </ul> <h3>How to back up text-based Custom Track data to a file</h3> <ul> <li> - <strong>Save Custom Tracks.</strong> Save a backup of your current browser sessions's custom + <strong>Save Custom Tracks.</strong> Save a backup of your current browser session's custom tracks to your local machine. This backup is intended to be used to restore uploaded text-based custom tracks that would otherwise be lost in case of an unexpected system failure at UCSC. Saving your data is easy and ensures that your hard work is safe and recoverable. To download your custom track data, navigate to the <code>Save Settings</code> section. Click the <button>submit</button> button to the right of "back up custom tracks archive .tar.gz". For each genome assembly, the custom track names will be shown along with individual and total file size. To proceed, click the <button>create custom track backup archive</button> button. All of the custom track data for the active session will be archived and compressed. Large custom tracks may take several minutes to finish. To download the archive to your computer, type in a name for the downloaded archive file and click the <button>download backup archive</button> button. The file will have a ".tar.gz" extension. Note that Safari browsers will unzip the archive leaving you with a .tar file in your Downloads directory. Click the <button>return</button> button to return to the Session Management page. To save viewing settings like track visibilities, highlighting, and sequence positions, use the "Save session settings to a local file" feature mentioned above.</li> @@ -347,31 +347,31 @@ <em>non-shared</em>. By default, new sessions are created as shared and must be explicitly changed to non-shared status.</p> <p> Shared sessions can be opened by other Genome Browser users to whom you've provided one of the following:</p> <ul> <li> the user name and session name of the saved session</li> <li> access privileges to a local file that contains the saved session information</li> <li> the URL of a web-accessible session settings file</li> </ul> <p> Sessions which you've added to the list of <a href="../../../cgi-bin/hgPublicSessions">Public -Sessions</a> will available to the world. Note that unless you've added them to this list of Public +Sessions</a> will be available to the world. Note that unless you've added them to this list of Public Sessions, your shared sessions will not be available in a general way to other Genome Browser users; they will need at least one of these access methods.</p> <p> If you choose to keep your session private, other users of the Genome Browser will not be able to access your data or browser configuration. Any confidential data or locations of interest that you are working with will be safe from viewing by others.</p> <p> The most secure way to control your session is to save the settings to a local file, then deny access to that file by others.</p> <!-- =====Sharing a Session with Others======================= --> <a name="HowToShare"></a> <h3>Sharing your session with others</h3> <p> There are five ways to let others know about your saved sessions: @@ -408,47 +408,47 @@ them to load it using the Session tool.</li> <li> <strong>Share a web URL.</strong> If you have saved your settings to a file on a web server, you can provide a link like this to others: <pre><code>http://genome.ucsc.edu/cgi-bin/hgSession?hgS_doLoadUrl=submit&hgS_loadUrlName=<em>MyUrl</em></code></pre> <p> where <code><em>MyUrl</em></code> is the URL of your settings file, e.g., <code>http://www.mysite.edu/~me/mySession.txt</code>. In this type of link, you may replace "<code>hgSession</code>" with "<code>hgTracks</code>" to proceed directly to the Genome Browser.</li> <li> <strong>List it on the Public Sessions page.</strong> The "<a href="../../../cgi-bin/hgPublicSessions">Public Sessions</a>" tool allows you to post and share your exciting and interesting Browser snapshots with the world. After having saved your session, you can add it to this public listing by checking the box in the column under - "post in public listing?". People can then find your sesssion by entering a search term. + "post in public listing?". People can then find your session by entering a search term. You can even create a <a href="sessions.html#lab" target="_blank">gallery of Public Sessions</a> related to your search by using a unique string in your descriptions.</li> </ul> <!-- =====Opening a Shared Session======================= --> <a name="Open"></a> <h3>Opening a shared session</h3> <p> If you open a shared session while viewing the Genome Browser, it is possible to lose all of your own browser settings. That is, the settings for the newly-opened session will take precedence over your existing settings and will replace them. If you wish to preserve your original settings, you should first save your own settings as a session before opening a new session, or open a new tab or window in your internet browser before loading the new session.</p> <p> There are four ways to open a shared session, depending on what information you have about the -session. The instructions below assume that you want to replace your current session the new +session. The instructions below assume that you want to replace your current session with the new session. Be sure to preserve your original session first if you don't want to overwrite it.</p> <ul> <li> <strong>Open a session from an email link.</strong> If you receive an email message with a link to a colleague's shared session, simply click on the link to view the Genome Browser with the session settings.</li> <li> <strong>Open another user's session.</strong> If you know the name of another user's shared session you can type in the user and session name in the "Restore Settings" section and click "submit" This will generate an "Updated Session" message and you can click on the Browser link to load the browser with the settings saved in this session.</li> <li> <strong>Open a session from a settings file.</strong> Open the Session tool, then scroll down to <em>Restore Settings</em> in the <em>Session Management</em> section. @@ -507,31 +507,31 @@ <button>delete</button> button next to the session name you would like to delete. This will permanently delete all details of the session from the UCSC server. Any saved links to that session will no longer work.</p> <p> No other user can delete your saved sessions, even if you have provided access to your sessions to them. Other users simply have a <em>copy</em> of your session.</p> <p> Unlike most other browser preferences, the session settings are not saved in your Genome Browser "cart". Therefore, if you choose to reset the Genome Browser, it will <em>not</em> delete your saved sessions.</p> <!-- =====Lifespan of a Session======================== --> <a name="Lifespan"></a> <h2>Lifespan of a session</h2> <p> -Your saved sessions will not be expired and will available you (and others if you +Your saved sessions will not be expired and will be available to you (and others if you <a href="#Share">share</a> them) until you <a href="#Delete">delete</a> them. We have discontinued our previous policy of removing saved sessions and associated custom track data after four months. However, note that the UCSC Genome Browser is not a data storage service; please keep a local backup of your session contents and custom track data.</p> <!-- =====Session Gallery======================== --> <a name="Gallery"></a> <h2>Session gallery</h2> <p> The <a href="sessions.html" target="_blank">Session Gallery</a> is a collection of track views that help highlight viewing different topics in the browser. The sessions in the Session Gallery were created in the browser and then saved to a local file, which was then uploaded to an online location. This allows creating a single link, such as http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=U, where <strong>U</strong> is the URL of the session file, e.g., http://www.mysite.edu/~me/mySession.txt, @@ -596,59 +596,59 @@ to: <a href="/FAQ/FAQformat.html#format5.1" target="_blank">BAM</a>, <a href="/FAQ/FAQformat.html#format1.5" target="_blank">bigBed</a>, <a href="/FAQ/FAQformat.html#format6" target="_blank">WIG</a>, <a href="/FAQ/FAQformat.html#format6.1" target="_blank">bigWig</a>, and <a href="/FAQ/FAQformat.html#format10.1" target="_blank">VCF</a> data types. The last attribute, <strong>bigDataUrl</strong>, is required for remotely hosted data types such as <a href="../help/bam.html" target="_blank">BAM</a>, <a href="../help/cram.html" target="_blank">CRAM</a>, <a href="../help/bigBed.html" target="_blank">bigBed</a>, <a href="../help/bigWig.html" target="_blank">bigWig</a>, and <a href="../help/vcf.html" target="_blank">VCF</a>.</p> <p> Adding more <a href="customTrack.html#TRACK">attribute=value</a> pairs can further customize the display. Here is a custom track that uses the <strong>visibility</strong> and -<strong>description</strong> atrributes: +<strong>description</strong> attributes: <pre><code>track type=bam visibility=dense name="My BAM" description="Example from the ENCODE RNA-seq CSHL track" bigDataUrl=http://hgdownload.gi.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqA549CellPapAlnRep1.bam</code></pre></p> <p> There are also options to <a href="hgBamTrackHelp.html">configure the display</a> of your BAM files, such as a <em>density plot feature</em> that will dynamically process the underlying BAM into a wiggle signal.</p> <hr> <h6>bigWig custom track</h6> <p> A bigWig file is useful when trying to display dense, continuous data. Read more on the <a href="bigWig.html">bigWig track format</a> help page. Here is an example bigWig track that is colored red, instead of the default black color, that can be pasted directly into the <a href="/cgi-bin/hgCustom">Custom Tracks Page</a>: <pre><code>track color=255,0,0 name="HeLa-S3 nucleus minus signal" description="RNA Subcellular CAGE Localization from ENCODE/RIKEN" type=bigWig visibility=full bigDataUrl=http://hgdownload.gi.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHelas3NucleusPapMinusSignalRep1.bigWig</code></pre></p> <p> There are also options to <a href="hgWiggleTrackHelp.html">configure the display</a> of your wiggle tracks, such as changing the track height or type of graph.</p> <!-- ====Creating a session====================== --> <a name="NAR_session"></a> <h3>Creating a session for NAR publications</h3> <p> After creating your custom tracks and viewing your data on the Genome Browser, you can save all of your tracks and settings to a snapshot of the Genome Browser called a <em>session</em>. You can - easily save a session by following these five steps:</p> + easily save a session by following these steps:</p> <ol> <li> <strong>Configure the Genome Browser to your preference</strong><br> Make sure the display of your custom tracks is to your liking on the Genome Browser.</li> <li> <strong>Navigate to the sessions page</strong><br> Once you are satisfied with the display, go to the <a href="/cgi-bin/hgSession">My Sessions</a> page by either: <ul> <li> Going to <em><strong>My Data</strong></em> -> <em><strong>My Sessions</strong></em> from the navigation bar.</li> <li> Using the "<em><strong>s</strong> then <strong>s</strong></em>" keyboard shortcut when viewing the main page of the <a href="/cgi-bin/hgTracks">Genome Browser</a>.</li>