87f551dfb14925f9e7e1d6f23d798fef313fd73c
hiram
  Mon Sep 1 23:25:33 2025 -0700
new chain net construction and update genePred names

diff --git src/hg/utils/automation/makeGenomeDb.pl src/hg/utils/automation/makeGenomeDb.pl
index 2d338609872..f56714fe42d 100755
--- src/hg/utils/automation/makeGenomeDb.pl
+++ src/hg/utils/automation/makeGenomeDb.pl
@@ -1372,31 +1372,32 @@
   &HgAutomate::mustMkdir("$topDir/html");
   &makeDescription();
   my $localFiles = &makeLocalTrackDbRa();
   my $whatItDoes =<<_EOF_
 It makes a local checkout of kent/src/hg/makeDb/trackDb/
 and makes *suggested* modifications.  Checking in modified files, and adding
 new files, is left up to the user in case this script has made some wrong
 guesses about proper names and locations.
 _EOF_
   ;
   my $bossScript = new HgRemoteScript("$scriptDir/makeTrackDb.csh", $dbHost,
 				      $runDir, $whatItDoes, $CONFIG);
 
   $bossScript->add(<<_EOF_
 # These directories are necessary for running make in trackDb:
-$HgAutomate::git archive --remote=git://genome-source.soe.ucsc.edu/kent.git \\
+https://raw.githubusercontent.com/ucscGenomeBrowser/kent.git
+$HgAutomate::git archive --remote=git://raw.githubusercontent.com/ucscGenomeBrowser/kent.git \\
   --prefix=kent/ HEAD src/hg/makeDb/trackDb/loadTracks \\
 src/hg/makeDb/trackDb/$dbDbSpeciesDir \\
 src/hg/makeDb/trackDb/trackDb.transMap.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.ra \\
 src/hg/makeDb/trackDb/trackDb.encode3.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra \\
 src/hg/makeDb/trackDb/crisprAll.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.other.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.afrotheria.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.birds.ra \\
 src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra \\