0c42aea56b751a2b4a58feb225a9659819a90994
markd
  Sat Oct 3 06:22:01 2026 -0700
Nest the TSS tracks on alpha only, leaving the release as it is. refs #35528

PRO-cap and ProCapNet sit inside a transcriptionStart superTrack on alpha. That
needs #38460, which is on master but not in a release, and these tracks are
already released, so each source is written twice with complementary release
tags: the nested copy alpha, the flat copy beta,public. hgTrackDb takes the copy
whose release matches and rejects two whose releases overlap.

Verified that beta and public are untouched: a public build from this file is
byte-identical to a public build from the released flat tree, same md5 over
tableName, shortLabel, type, visibility, priority and settings. tdbQuery -check
-strict passes on all three releases, and an alpha build has the container with
both members parented while beta and public have neither.

Drop the release tags and the flat copies once #38460 ships.

The makedocs also record that the alpha build needs hgTrackDb and trackDbToTxt
in /cluster/bin/x86_64 to carry the #38460 fix. make alpha does not install
there, BINDIR defaults to ~/bin/$MACHTYPE, so they were put in by hand and the
weekly utils build will overwrite them.

diff --git src/hg/makeDb/doc/hg38/transcriptionStart.txt src/hg/makeDb/doc/hg38/transcriptionStart.txt
index 5174803edd9..83b1a762bdf 100644
--- src/hg/makeDb/doc/hg38/transcriptionStart.txt
+++ src/hg/makeDb/doc/hg38/transcriptionStart.txt
@@ -1,32 +1,42 @@
 # Transcription start sites: ENCODE 4 PRO-cap and ProCapNet, #35528, Claude
 Thu Sep 17 2026 (Claude/markd)
 
 # Layout: one superTrack per data source, each holding its multiWig overlays
 # directly, the way fantom5 does.  Not a composite: under a composite hgTrackUi
 # lists descendant leaves rather than containers, so an overlay gets no
 # configuration block of its own and hiding both strands of a cell line leaves an
 # empty row where the overlay was (#38441).  As a superTrack member each overlay
 # is a track in its own right, with a full configuration page, and hiding it
 # hides the whole overlay.  The cost is the subtrack matrix and the sample class
 # filter, neither of which a superTrack offers.
 #
-# These two superTracks are top level rather than sitting inside a single
-# transcriptionStart folder, because superTracks do not nest: a superTrack given
-# a parent passes tdbQuery -check -strict and is then silently dropped at load
-# (#38460).  transcriptionStart.html is left in the tree unused against that
-# being fixed.
+# On alpha the two data-source superTracks sit inside a transcriptionStart
+# superTrack; on beta and public they stand on their own.  Nesting a superTrack
+# inside a superTrack needs the fix in #38460, which is on master but not in a
+# release, and these tracks are already released, so each source is written
+# twice with complementary release tags: the nested copy alpha, the flat copy
+# beta,public.  hgTrackDb takes the copy whose release matches and rejects two
+# whose releases overlap, so the tags have to stay complementary.  The public
+# build is byte-identical to what was released.  Drop the release tags and the
+# flat copies once #38460 ships.
+#
+# The alpha build here also needs hgTrackDb and trackDbToTxt in
+# /cluster/bin/x86_64 to carry the #38460 fix.  make alpha does not put anything
+# there: BINDIR defaults to ~/bin/$MACHTYPE, and that directory is updated by
+# the weekly utils build.  They were installed by hand on 2026-10-03 and the
+# next weekly build will overwrite them with whatever is in the branch then.
 
 # Scripts are in ~/kent/src/hg/makeDb/outside/proCapNet.  The cell lines, their
 # ENCODE accessions and their colors are in proCapNetExperiments.tsv there.
 
 ##############################################################################
 # ProCapNet predictions and sequence-contribution scores
 ##############################################################################
 
 # The predictions are 24 GB per file and are re-encoded, so they are fetched to
 # a working area outside the track directory.  The contribution scores are used
 # unaltered and go straight to their final home.
 
 mkdir -p /hive/data/outside/proCapNet/hg38 /hive/data/genomes/hg38/bed/proCapNet
 cd /hive/data/genomes/hg38/bed/proCapNet
 ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetDownload hg38 \