e5759993329b6e609e9ab825991a90283e714088 mspeir Wed Sep 9 11:17:57 2026 -0700 Help pages: fix broken internal links and restore anchors people still cite, refs #38062 Three groups of anchor problems on the help and FAQ pages. Broken internal links, five pages: posters.html listed a 2022 section that does not exist (no 2022 posters), api.html listed REST and JSON separately after the two sections were merged, docker.html pointed at a #UsrAcct section that is not on that page, FAQgenes.html had a capitalized #ncbiRefSeq where the anchor is #ncbiRefseq, and the genomes.txt settings rows in trackDbHub.v3.html carried no anchors so its own "genome" link missed. Retired anchors that are still cited in twenty years of answers on the genome list. Content moved to its own page and the old anchor was deleted rather than left behind, so the citations land at the top of the page. Reattached seven numeric FAQformat anchors to the Topics entry linking to each format's page. BED, PSL, GFF and GTF were removed from the custom track page in 2012 and never added back to its list of supported formats; added them with the old anchors, which fixes customTrack.html and hgTracksHelp.html together since both include customTrackText.html. Also restored #lines there, and #Session on hgTrackHubHelp.html and #link4 on FAQlink.html. Section anchors on six pages that had none, so a support answer can link to one part of them: bam.html, hic.html, bedgraph.html, ftp.html, net.html and trackDbIndexBb.html. Skipped quickLiftChain.html, oligoMatch.html and cutters.html, which are track description fragments included into the details page rather than standalone pages. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index efc6312604c..fa4772ef803 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -79,37 +79,41 @@ <li><a href="interact.html">interact</a> <li><a href="interact.html">bigInteract</a> </ul> </div> <div class="col-xs-12 col-sm-6 col-md-2"> <ul> <li><a href="bigWig.html">bigWig</a> <li><a href="bam.html">BAM</a> <li><a href="cram.html">CRAM</a> <li><a href="vcf.html">VCF</a> <li><a href="/FAQ/FAQformat.html#format5">MAF</a> </ul> </div> <div class="col-xs-12 col-sm-6 col-md-2"> <ul> + <li><a name="BED"></a><a href="../../FAQ/FAQformat.html#format1">BED</a> <li><a href="../../FAQ/FAQformat.html#format1.7">BED detail</a> <li><a href="../../FAQ/FAQformat.html#format10">Personal Genome SNP</a> <li><a href="../../FAQ/FAQformat.html#format13">broadPeak</a> </ul> </div> <div class="col-xs-12 col-sm-6 col-md-2"> <ul> + <li><a name="PSL"></a><a href="../../FAQ/FAQformat.html#format2">PSL</a> + <li><a name="GFF"></a><a href="../../FAQ/FAQformat.html#format3">GFF</a> + <li><a name="GTF"></a><a href="../../FAQ/FAQformat.html#format4">GTF</a> <li><a href="../../FAQ/FAQformat.html#format12">narrowPeak</a> <li><a href="../../FAQ/FAQformat.html#format6.5">microarray</a> (BED15) <li><a href="bedMethyl.html">bedMethyl</a> </ul> </div> </div> </div> <p> <em> NOTE: Some annotations need to be hosted remotely in a web-accessible location that support byte-range requests to be visualized on the UCSC Genome Browser, such as: bigBed, bigWig, BAM, VCF, etc. For examples of how to host your custom track data remotely, please refer to the track hub user guide, "<a href="/goldenPath/help/hgTrackHubHelp.html#Hosting" target="_blank">Where to host your data?</a>".</em> </p> @@ -362,30 +366,31 @@ configuration" text box. In the current implementation of this utility, the existing annotation data is not displayed. Because of this, the data cannot be incrementally edited through this interface, but instead must be fully replaced using one of the data entry methods described in <a href="#ADD_CT">Loading a Custom Track into the Genome Browser</a>. If description text has been uploaded for the track, it will be displayed in the track documentation edit box, where it may be edited or completely replaced. Once you have completed your updates, click the Submit button to upload the new data into the Genome Browser.</p> <p> If the data or description text for your custom track was originally loaded from a file on your hard disk or server, you should first edit the file, then reload it from the Update Custom Track page using the "Choose File" button. Note that edits made on this page to description text uploaded from a file will not be saved to the original file on your computer or server. Because of this, we recommend that you use the documentation edit box only for changes made to text that was typed or pasted in.</p> +<a name="lines"></a> <a name="BROWSER"></a> <h3>Creating browser lines for annotations</h3> <p> Browser lines are optional, but they give you control of many aspects of the overall display of the Genome Browser window when your annotation file is uploaded. Each line defines one display attribute. Browser lines are in the format:</p> <p> <pre><code>browser attribute_name attribute_value(s)</code></pre> <p> For example, if the browser line <code>browser position chr22:1-20000</code> is included in the annotation file, the Genome Browser window will initially display the first 20000 bases of chr 22.</p>