70ac948e82b41ef316523635c04e5e2c4a89c417
mspeir
  Fri Sep 4 16:57:54 2026 -0700
trackLists: give the variant frequency projects their own table, move the page
to goldenPath/help/mirrorTracks.html, add the otto cron line, refs #37781

Half the restricted list was national sequencing cohorts sitting under varFreqs
and phasedVars, and in one alphabetical table they buried the tracks people
actually write in about, OMIM, HGMD and DECIPHER. Those cohorts now get a table
of their own below the rest. The split is read off the trackDb parent chain, so
the next cohort added under varFreqs lands in the right table with no edit here.

The page moves off the htdocs root to goldenPath/help/mirrorTracks.html, beside
mirror.html, which now links to it. That link goes in src/product/README.txt,
the pandoc source mirror.html is generated from. The licensing page link follows
the move, and the page title changes with the file name.

Also adds the weekly otto line, placed above the HGDB_CONF that would otherwise
apply to it, and keeps the job from listing itself as a self-updating track.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/product/README.txt src/product/README.txt
index 09dc1c6667b..52ca725a331 100644
--- src/product/README.txt
+++ src/product/README.txt
@@ -93,30 +93,39 @@
         * Not easy to setup, even for experienced Unix administrators.
         * Will probably require some support via the [genome-mirror](mailto:genome-mirror@soe.ucsc.edu) mailing list.
         * To keep up with changes in the Genome Browser, you will have to 
           install linux packages and update the linux distribution yourself in 
           the future and apply UCSC data updates yourself using rsync or MariaDB table loads
         * Configuration changes on our side may break your setup.
         * For maximum browsing speed, can require up to 2-6TB to store all genome annotation tracks.
         * For commercial users: license agreements take longer to negotiate, no click-through license.
 
 A license is required for commercial download and/or installation of the Genome
 Browser binaries and source code. No license is needed for academic, nonprofit,
 and personal use. To purchase a
 license, see our [license Instructions](https://genome.ucsc.edu/license/index.html)
 or visit the [Genome Browser store](https://genome-store.ucsc.edu/). 
 
+Not every track on our site can be part of a mirror. Some data reaches us under terms
+that let us show it but not pass it on, so it is absent from our download server and
+will be missing from your copy. Other tracks are rebuilt here on a schedule and will
+drift away from your copy between updates, and some annotation was contributed by
+outside groups rather than built at UCSC. All three sets are named on the
+[track lists for mirror sites](https://genome.ucsc.edu/goldenPath/help/mirrorTracks.html)
+page, which is
+regenerated from our servers rather than kept by hand.
+
 # Installing a Genome Browser locally with the GBiC installer
 
 If you do not want to use our prepared virtual machine Genome-Browser-in-a-Box, we provide a
 Genome Browser in the Cloud (GBiC)
 [installation program](https://genome.ucsc.edu/goldenPath/help/gbic.html) 
 that sets up a fully functional mirror on all major Linux
 distributions.  
 
 The GBiC program has been tested and confirmed to work with Ubuntu 18/20/22/24 LTS,
 Rocky 9.5, and Fedora 30/35/41.
 
 Preferably, the installation should be performed on a fresh Linux
 installation, as it deactivates the default site config file in Apache
 and fills the MariaDB directory with numerous databases. The easiest way to accomplish this is to
 run the Genome Browser in the Cloud program in a new virtual machine. The program also works on