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/mm10.encode4.regulation.txt src/hg/makeDb/doc/mm10.encode4.regulation.txt
index 7877b320ccb..e032deb1ea1 100644
--- src/hg/makeDb/doc/mm10.encode4.regulation.txt
+++ src/hg/makeDb/doc/mm10.encode4.regulation.txt
@@ -269,30 +269,48 @@
 
 # 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 and TF ChIP
 # metadata TSVs.
 #
 # Composites updated:
 #   encode4RegEpigenetics: 589 peak/signal pairs, 0 singletons
 #   encode4RegTfChip:      167 peak/signal pairs, 0 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 mm10 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 (0.4) > encode4Reg (0.5) > tabulaMuris (1)
 #
 # encode4Reg (superTrack, priority 0.5, group=regulation)
 # ├── encode4RegMarkH3k27ac (multiWig, full)                         priority 1.4
 # ├── encode4RegDnase       (multiWig, hide)                         priority 1.1
 # ├── encode4RegAtac        (multiWig, hide)                         priority 1.2
 # ├── encode4RegMarkH3k4me3 (multiWig, hide)                         priority 1.3
 # ├── encode4RegMarkCtcf    (multiWig, hide)                         priority 1.5
 # ├── encode4RegTxn         (multiWig, hide)                         priority 1.6
 # ├── encode4RegEpigenetics (bigComposite faceted, 1,178, 30 ON)     priority 2.0
 # ├── encode4RegRnaSeq      (bigComposite faceted, 1,054, 6 ON)      priority 2.1