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/ftp.html src/hg/htdocs/goldenPath/help/ftp.html index 23d5af7ded3..5789bcf3c19 100755 --- src/hg/htdocs/goldenPath/help/ftp.html +++ src/hg/htdocs/goldenPath/help/ftp.html @@ -1,63 +1,66 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Data Downloads" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Downloading data</h1> +<a id="rsync"></a> <h2>Rsync (recommended method)</h2> <p> We recommend that you download data via rsync using the command line, especially for large files using the North American or European download servers.</p> <p> For example, when downloading files to your present directory (./), use an expression such as:</p> <pre><code>rsync -a -P rsync://hgdownload.gi.ucsc.edu/gbdb/hg38/uniprot/unipAliTrembl.bb ./</code></pre> <p> To download the entire directory (note the trailing slash), use an expression such as:</p> <pre><code>rsync -a -P rsync://hgdownload.gi.ucsc.edu/gbdb/hg38/uniprot/ ./</code></pre> <p> To obtain a file's location (URL) to use with rsync (<em>rsync://hgdownload.gi.ucsc.edu/...</em>), navigate in your browser to our FTP site at <a href="ftp://hgdownload.gi.ucsc.edu/" target="_blank">ftp://hgdownload.gi.ucsc.edu/</a> or our downloads page at <a href="http://hgdownload.gi.ucsc.edu/" target="_blank">http://hgdownload.gi.ucsc.edu/downloads.html</a>, and look for your file of interest. To learn more about rsync's options, type "man rsync" on the command line.</p> +<a id="webBrowser"></a> <h2>Downloading from a web browser</h2> <p> If you are not comfortable using the command line, you can download your file via FTP in your browser at <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath" target="_blank">ftp://hgdownload.gi.ucsc.edu/goldenPath</a>, or from our downloads page at <a href="http://hgdownload.gi.ucsc.edu/" target="_blank">http://hgdownload.gi.ucsc.edu/downloads.html</a>.</p> <p> However, downloading via your browser will be very slow or may even time out for large files (i.e., bigBed, bigWig, BAM, VCF, etc.). Also, Safari does not support FTP inside the browser. When you enter a FTP URL in Safari, you may have to select "Guest" and click submit to log in before a FTP file system will open in a window on your desktop.</p> +<a id="ftp"></a> <h2>FTP from the command line</h2> <p> <em><strong>We do not encourage the use of FTP for downloading large data files</strong></em>. Rsync is a more efficient and convenient transport mechanism, and is therefore quicker and easier to use for downloading our data files. However, here are the command line steps for FTP, should you choose to use it: </p><pre><code>$ ftp hgdownload.gi.ucsc.edu Name: anonymous Password: <your email address> ftp> cd goldenPath ftp> cd <assembly name> (e.g., hg19) ftp> cd <data directory> (e.g., liftOver)</code></pre> <p> To download multiple files from the UNIX ftp command line, use the "mget" command. You may want to use the <code>prompt</code> command to toggle the interactive mode if you do not want to be prompted for each file that you download.</p> <pre><code>ftp> mget [filename1] [filename2] ...</code></pre> <p> Or to download all the files in the directory:</p> <pre><code>ftp> mget -a</code></pre> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->