297c479ca3a30cff1b1669b231a8f76928f15d6e
jcasper
  Sun Sep 13 01:11:22 2026 -0700
Installing updated hg.conf files from UCSC servers

diff --git confs/hgwdev.hg.conf confs/hgwdev.hg.conf
index d608679f7c1..02181d19351 100644
--- confs/hgwdev.hg.conf
+++ confs/hgwdev.hg.conf
@@ -464,30 +464,33 @@
 tusdDataDir=/tusd
 tusdMountPoint=/data/tusd
 # The tusd endpoint files are uploaded to
 hubSpaceTusdEndpoint=https://hgwdev-hubspace.gi.ucsc.edu/files
 # The web accessible location after tusd moves the files
 # when an upload is completed
 hubSpaceUrl=https://hgwdev.gi.ucsc.edu/hubspace
 # let users create an api key on the hub development tab to use hubSpace from the command line
 showHubApiKey=true
 
 # Enables the QuickLift checkbox on hgConvert
 browser.quickLift=on
 # Lets QuickLift lift alignment tracks too: psl, bigPsl, chain, bigChain, maf,
 # bigMaf and wigMaf.  Refs #38249.
 browser.quickLiftAlignments=on
+# Enables the bigNet track type, a net of pairwise alignments in a bigBed, and
+# QuickLift support for it.  Refs #20824.
+bigNet=on
 # Additional settings for QuickLift
 quickLift.lengthLimit=100000
 quickLift.insColor=64,127,0,64
 quickLift.delColor=0,0,127,64
 quickLift.doubleColor=127,127,127,64
 quickLift.mismatchColor=255,0,0,64
 
 # Increases the number of items that can be queried from a BAM file
 BAMMaxItems=60000
 
 # new flag for testing rm32751 turn on automatic creation of custom tracks from hgBlat results.
 autoBlatBigPsl=on
 # you can also comment it out and test that it behaves the old way as expected.
 
 # BLAT shows locus name of the match #35993
@@ -563,15 +566,31 @@
 login.emailLink=on
 
 # Enable new BLAT UI, 37996
 blatNewForm=on
 
 # Enables the redesigned hgc alignment viewer, refs #37893
 modernAlignPage=on
 
 # Send the Content Security Policy as an http response header, so pages that
 # write their own http header block still carry a policy, refs #38151
 cspResponseHeader=on
 
 # Measure how long the track image takes to reach the reader, on one page
 # load in N. Left out, it is off. refs #38109
 pngTimingSampleRate=1
+
+# Copy a track collection's hub file when hgCollection is about to write it,
+# instead of on every session load, refs #38273
+collectionHubCopyOnWrite=on
+
+# Second codon number in the gene-track codon mouseover, counted on the
+# transcript, for transcripts that align with bases the assembly lacks, refs #38298
+showTxCodonNumbers=on
+
+# Step over a CGI or cookie pair that has no =value, instead of losing the pair
+# after it or aborting the request, refs #38340
+skipMalformedCgiPairs=on
+
+# Serve the request when the bottleneck server cannot be reached, instead of
+# failing the CGI.  Refs #37738
+bottleneck.serveOnFailure=on