d937f06fd5b42ae4621cd7d6bf0d048ab2863a41
hiram
  Wed Aug 12 16:14:10 2026 -0700
fixups per code review refs #38005

diff --git src/hg/utils/automation/doNcbiGene.pl src/hg/utils/automation/doNcbiGene.pl
index 03884e5e025..f73bae4924a 100755
--- src/hg/utils/automation/doNcbiGene.pl
+++ src/hg/utils/automation/doNcbiGene.pl
@@ -21,31 +21,30 @@
     $opt_buildDir
     $opt_assemblySource
     $opt_chromSizes
     $opt_namesFile
     $opt_liftFile
     /;
 
 # Specify the steps supported with -continue / -stop:
 my $stepper = new HgStepManager(
     [ { name => 'ncbiGene', func => \&doNcbiGene },
       { name => 'cleanup',  func => \&doCleanup },
     ]
 				);
 
 # Option defaults:
-my $dbHost = 'hgwdev';
 my $workhorse = 'hgwdev';
 my $defaultWorkhorse = 'hgwdev';
 my $defaultFileServer = 'hgwdev';
 my $fileServer = 'hgwdev';
 
 my $base = $0;
 $base =~ s/^(.*\/)?//;
 
 sub usage {
   my ($status, $detailed) = @_;
   print STDERR "
 usage: $base [options] asmId db
 required arguments:
     asmId              - assembly identifier at NCBI, e.g.
                           GCF_000001405.32_GRCh38.p6 -- used to locate the
@@ -60,32 +59,31 @@
   print STDERR <<_EOF_
     -buildDir dir         Use dir instead of default (current directory).
                           This *is* the runDir -- typically the hub's
                           trackData/ncbiGene -- no further nesting is added.
     -assemblySource dir   Directory holding \${asmId}_genomic.gff.gz.
     -chromSizes path      Path to the assembly's chrom.sizes file.
     -namesFile path       Path to the hub's \$db.names.tab (built by the
                           gatewayPage step), e.g.
                           \$buildDir/../../html/\$db.names.tab -- used
                           for the archived-version description page.
     -liftFile path        Optional lift file translating NCBI names to
                           UCSC names, e.g.
                           \$buildDir/../../sequence/\$asmId.ncbiToUcsc.lift
 _EOF_
   ;
-  print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
-					'workhorse' => $defaultWorkhorse,
+  print STDERR &HgAutomate::getCommonOptionHelp('workhorse' => $defaultWorkhorse,
 					'fileServer' => $defaultFileServer);
   print STDERR "
 Automates construction of the 'ncbiGene' track from an assembly's own
 NCBI GFF3 gene predictions, for assembly hub (GenArk) builds. Steps:
     ncbiGene: if a previous \$db.ncbiGene.bb exists and the source gff
               is newer, translate the current gff3 into a bigGenePred track,
               building it entirely under *.new file names so the existing
               live track is never touched while the build might still fail.
               Only once that build has fully succeeded is the previous
               version archived under archive/<date>/ (keyed by the previous
               build's own gff-derived mtime) and the new *.new files
               promoted into place.
     cleanup:  compress intermediate files
 ";
   print "\n";
@@ -99,31 +97,30 @@
 
 sub checkOptions {
   my $ok = GetOptions(@HgStepManager::optionSpec,
 		      'buildDir=s',
 		      'assemblySource=s',
 		      'chromSizes=s',
 		      'namesFile=s',
 		      'liftFile=s',
 		      @HgAutomate::commonOptionSpec,
 		      );
   &usage(1) if (!$ok);
   &usage(0, 1) if ($opt_help);
   &HgAutomate::processCommonOptions();
   my $err = $stepper->processOptions();
   usage(1) if ($err);
-  $dbHost = $opt_dbHost if ($opt_dbHost);
   $workhorse = $opt_workhorse if ($opt_workhorse);
   $fileServer = $opt_fileServer if ($opt_fileServer);
 }
 
 # same mtime-compare doAssemblyHub.pl has used all along
 sub needsUpdate($$) {
   my ($source, $result) = @_;
   if (-s $result) {
     return (stat($source)->mtime > stat($result)->mtime) ? 1 : 0;
   }
   return 1;
 }
 
 #########################################################################
 # archive whatever the previous build left behind, keyed by the date