d0ddd717713f275dc2f567c9b6d733fd3f55bd90 markd Fri Oct 2 21:27:25 2026 -0700 Put PRO-cap and ProCapNet inside a Transcription Initiation folder. refs #35528 The two data sources were top-level superTracks because a superTrack could not be a member of another one. #38460 fixes that, so they now sit inside a transcriptionStart superTrack, which is what the collection was meant to be. The container is written before either of its children, and both children before any of their members: tdbQuery -strict rejects a file in which another track comes between a superTrack and one of its children. This depends on the #38460 build. A plain make here with the installed binaries produces a half-built state, since hgTrackDb drops the container from the table and trackDbToTxt then writes an hs1 curated hub whose member names a parent stanza that is not there. Both makedocs say so. diff --git src/hg/makeDb/doc/hg38/transcriptionStart.txt src/hg/makeDb/doc/hg38/transcriptionStart.txt index f731063c44b..8e8bfc5f548 100644 --- src/hg/makeDb/doc/hg38/transcriptionStart.txt +++ src/hg/makeDb/doc/hg38/transcriptionStart.txt @@ -1,32 +1,35 @@ # 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. +# The two data-source superTracks sit inside a transcriptionStart superTrack. +# That needs the nesting fix in #38460: before it, a superTrack given a parent +# passed tdbQuery -check -strict and was then silently dropped at load. Until +# that fix is released, a plain make here produces a half-built state, because +# the trackDb make calls two installed binaries that predate it: hgTrackDb drops +# the container from the table, and trackDbToTxt then writes an hs1 curated hub +# whose member names a parent stanza that is not there. Load with a build that +# has the fix, and rebuild the hub, until it ships. # 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 \