31e95f0d1dd4ca08feba9b081a356527bd4b45e6
markd
  Sat Sep 26 20:36:20 2026 -0700
Drop the hand-built Files column from the TSS faceted tables. refs #35528

UCSC will generate the download links in the faceted table, so the Files column
each composite built for itself is redundant. Remove downloadCell, the Files
header and cell, the Files entry in subtrackUrls, and the DOWNLOAD constant that
only fed them. The table is now Tissue, Sample class, Experiment, Cell line on
all three composites. writeMetadata no longer needs db or track; the metadata
files it writes are byte-identical.

Lead each Data Access section with the link to the hgdownload directory, since
that is now the way to a single file, and keep the naming convention beside it.
Drop the paragraph describing the Files column.

diff --git src/hg/makeDb/trackDb/human/proCapNet.html src/hg/makeDb/trackDb/human/proCapNet.html
index b6e37bcc9ea..4dc96db59b2 100644
--- src/hg/makeDb/trackDb/human/proCapNet.html
+++ src/hg/makeDb/trackDb/human/proCapNet.html
@@ -105,60 +105,57 @@
 
 <p>
 The ProCapNet model implementation is at
 <a href="https://github.com/kundajelab/ProCapNet" target="_blank">kundajelab/ProCapNet</a>.
 The steps that turned the published files into these tracks are recorded in
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/$db/transcriptionStart.txt"
 target="_blank">doc/$db/transcriptionStart.txt</a>, the scripts they run are in
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/outside/proCapNet"
 target="_blank">makeDb/outside/proCapNet</a>, and the track configuration is in
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/$db/transcriptionStart.ra"
 target="_blank">trackDb/human/$db/transcriptionStart.ra</a>.
 </p>
 
 <h2>Data Access</h2>
 
+<p>
+The bigWig files are on our
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/proCapNet/" target="_blank">download
+server</a>. Predictions are under <tt>pred/</tt> and are named for the cell line,
+the model and the strand, for example <tt>K562.proCapNet.pos.bw</tt> and
+<tt>K562.proCapNet.neg.bw</tt>. Contribution scores, which exist for GRCh38 only,
+are under <tt>contrib/</tt>, for example <tt>K562.proCapNet-contrib.bw</tt>.
+</p>
+
 <p>
 The data can be explored interactively in table format with the
 <a href="../cgi-bin/hgTables">Table Browser</a> or the
 <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to
 spreadsheet or tab-sep tables. From scripts, the data can be accessed through our
 <a href="https://api.genome.ucsc.edu" target="_blank">API</a>. The API returns one
 bigWig at a time, so name a single strand of one cell line rather than the
 container, for example track=<i>proCapNet_K562_pred_pos</i>.
 </p>
 
 <p>
-The Files column of the table on this page links each cell line's bigWigs
-directly, so a single file can be fetched without working out its path.
-</p>
-
-<p>
-For automated download and analysis, the genome annotation is stored in bigWig
-files that can be downloaded from
-<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/proCapNet/" target="_blank">our
-download server</a>. Predictions are under <tt>pred/</tt> and are named for the
-cell line, the model and the strand, for example
-<tt>K562.proCapNet.pos.bw</tt> and <tt>K562.proCapNet.neg.bw</tt>. Contribution
-scores, which exist for GRCh38 only, are under <tt>contrib/</tt>, for example
-<tt>K562.proCapNet-contrib.bw</tt>. Individual regions or the whole genome annotation
-can be obtained using our tool <tt>bigWigToBedGraph</tt>, which can be compiled
-from the source code or downloaded as a precompiled binary for your system.
-Instructions for downloading source code and binaries are on the
+Individual regions or the whole genome annotation can be obtained using our tool
+<tt>bigWigToBedGraph</tt>, which can be compiled from the source code or
+downloaded as a precompiled binary for your system. Instructions for downloading
+source code and binaries are on the
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads"
-target="_blank">utilities download page</a>.
-The tool can also be used to obtain features within a given range, e.g.
+target="_blank">utilities download page</a>. The tool can also be used to obtain
+features within a given range, e.g.
 <tt>bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/$db/proCapNet/pred/K562.proCapNet.pos.bw
 -chrom=chr21 -start=0 -end=100000000 stdout</tt>
 </p>
 
 <p>
 The ProCapNet models are on the
 <a href="https://www.encodeproject.org" target="_blank">ENCODE portal</a> as
 BPNet-model annotations, one per cell line, linked from the Experiment column of
 the table on this page. Each annotation also holds the trained model, sequence
 contribution scores and predicted signal over a selected set of regions. The
 genome-wide predictions shown here are not part of that ENCODE release.
 </p>
 
 <h2>Credits</h2>