6db91c5823e6f55265fc2e2a06343110786ccd66
gperez2
  Tue May 26 13:41:50 2026 -0700
Removed the 2026-05-26 mouseDevTimecourse bigBed and categories reorder per team feedback in #36998 notes 54-56. Restored the original bigBed files from the Wold Lab hub, kept the new colors, and removed the reorder steps from the mm10 and mm39 makedocs. refs #37001

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index f9bb8250dcb..63f927b4cd2 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -19963,52 +19963,16 @@
     with open(cats) as f:
         lines = f.readlines()
     out = []
     for line in lines:
         if not line.strip():
             out.append(line)
             continue
         cols = line.rstrip("\n").split("\t")
         cols[1] = label_color[cols[0]]
         out.append("\t".join(cols) + "\n")
     with open(cats, "w") as f:
         f.writelines(out)
     print("updated .categories: " + cats)
 EOF
 
-# 2026-05-26 (Gerardo): Reorder the bars shown on the Genome Browser image so
-# they follow the biological tissue order Peng requested (matching the .facets
-# row order set on 2026-05-13). Redmine #36998 note-46, #37001 note-29,
-# #37619 note-4.
-#
-# The bar order shown on the Genome Browser image is set by the column order
-# of expScores inside the .bb file at build time, so the .bb files have to be
-# rebuilt with the per-tissue expScores values reordered in every row, and a
-# matching .categories file in the same new order. The barChartReorder.py
-# script handles this: it reorders the expScores values in every bed row
-# dumped from the input .bb, writes a matching .categories file, and rebuilds
-# the .bb with bedToBigBed. Run `barChartReorder.py --help` for argument
-# descriptions.
-
-cd /hive/data/outside/woldlab/mouseDevTimecourse/mm10
-
-SCRIPT=~/kent/src/hg/makeDb/scripts/barChartReorder/barChartReorder.py
-
-# Reorder all four mm10 .bb files (TPM/FPKM x M4/M21) using the matching
-# .facets per GENCODE version. Two unique .categories files (M4 and M21);
-# each gets rewritten on its first run and overwritten with identical content
-# on its second.
-for v in M4 M21; do
-    for variant in TPM FPKM; do
-        "$SCRIPT" \
-            --bb            mouse_development_${variant}_${v}_mm10.bb \
-            --categories    mouse_development_${v}.categories \
-            --facets        mouse_development_${v}.facets \
-            --chromSizes    /hive/data/genomes/mm10/chrom.sizes \
-            --outBb         mouse_development_${variant}_${v}_mm10.bb.new \
-            --outCategories mouse_development_${v}.categories.new
-        mv mouse_development_${variant}_${v}_mm10.bb.new mouse_development_${variant}_${v}_mm10.bb
-        mv mouse_development_${v}.categories.new        mouse_development_${v}.categories
-    done
-done
-
 ##############################################################################