65189b08b3a2b7efe27670b30379feb200187541
lrnassar
  Fri Apr 17 09:14:07 2026 -0700
Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923

Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10
bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting
(refs #36320 note 157) replaces $$ with the value from the primaryKey column,
making each accession in the configuration table a clickable link to the
corresponding file details page on the ENCODE portal. Also added a note in the
Data Access section of each composite's HTML, and updated both makedocs.

diff --git src/hg/makeDb/doc/hg38/encode4.regulation.txt src/hg/makeDb/doc/hg38/encode4.regulation.txt
index f7eb3e10839..1ab4b5e8688 100644
--- src/hg/makeDb/doc/hg38/encode4.regulation.txt
+++ src/hg/makeDb/doc/hg38/encode4.regulation.txt
@@ -307,30 +307,48 @@
 ##############################################################################
 
 # The Epigenetics and TF ChIP bigComposite tracks each contain both peak and
 # signal subtracks for the same experiments. To group these pairs adjacent in
 # the configure page, added an _Experiment column to the metadata TSVs
 # containing the ENCSR experiment accession (extracted from shortLabel in the
 # .ra stanzas). The underscore prefix hides it from facet filters.
 # Added defaultSortField _Experiment to the 2 composite stanzas.
 # Also fixed pre-existing CRLF line endings in the Epigenetics metadata TSV.
 #
 # Composites updated:
 #   wgEncodeReg4Epigenetics: 3,152 peak/signal pairs + 49 singletons
 #   wgEncodeReg4TfChip:      2,461 peak/signal pairs + 42 singletons
 # RNA-seq not changed (signal only, no peak/signal pairing).
 
+##############################################################################
+# Step 11: Link accession column to ENCODE portal (2026-04-17)
+##############################################################################
+
+# Jonathan added a new trackDb setting 'subtrackUrl' for faceted composites
+# (refs #36320, note 157). The setting takes a URL pattern where '$$' is
+# replaced with the value from the primaryKey column of the metadata TSV.
+# When set, the primary-key column on the track configuration page becomes
+# a clickable hyperlink.
+#
+# Since our primaryKey is 'accession' (an ENCFF file accession), added:
+#   subtrackUrl https://www.encodeproject.org/files/$$/
+# to all 3 hg38 bigComposites (Epigenetics, RnaSeq, TfChip).
+#
+# Also appended a sentence in the Data Access section of each composite's
+# HTML noting that clicking any accession leads to the corresponding file
+# details page on the ENCODE portal.
+
 ##############################################################################
 # Track hierarchy and disk usage summary
 ##############################################################################
 
 # Regulation group priority order: cCREs (0.8) > wgEncodeReg4 (0.9) > wgEncodeReg (1)
 #
 # wgEncodeReg4 (superTrack, priority 0.9, group=regulation)
 # ├── wgEncodeReg4MarkH3k27ac (multiWig, full)                     priority 1.4
 # ├── wgEncodeReg4Dnase       (multiWig, hide)                     priority 1.1
 # ├── wgEncodeReg4Atac        (multiWig, hide)                     priority 1.2
 # ├── wgEncodeReg4MarkH3k4me3 (multiWig, hide)                     priority 1.3
 # ├── wgEncodeReg4MarkCtcf    (multiWig, hide)                     priority 1.5
 # ├── wgEncodeReg4Txn         (multiWig, hide)                     priority 1.6
 # ├── wgEncodeReg4TfPeaks     (bigBed 12+ with decorator, hide)    priority 1.7
 # ├── wgEncodeReg4Epigenetics (bigComposite faceted, 6,353, 28 ON) priority 2.0