ad8d6746d5d68ff4e893262d2ff28d9b2a71ac26
hiram
  Mon Sep 12 11:45:58 2022 -0700
no longer any need for asmHubName argument to gateway page no redmine

diff --git src/hg/utils/automation/asmHubGatewayPage.pl src/hg/utils/automation/asmHubGatewayPage.pl
index 40ff976..2ba5366 100755
--- src/hg/utils/automation/asmHubGatewayPage.pl
+++ src/hg/utils/automation/asmHubGatewayPage.pl
@@ -4,31 +4,31 @@
 use warnings;
 use FindBin qw($Bin);
 use lib "$Bin";
 use AsmHub;
 use File::Basename;
 
 ### XXX ### temporary hgdownload-test.gi
 ### my $sourceServer = "hgdownload-test.gi.ucsc.edu";
 
 my $sourceServer = "hgdownload.soe.ucsc.edu";
 my $genomeSize = 0;	# will be set below
 
 my @months = qw( 0 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec );
 
 sub usage() {
-  printf STDERR "usage: asmHubGatewayPage.pl <asmHubName> <pathTo>/*assembly_report.txt <pathTo>/asmId.chrom.sizes <pathTo>/image.jpg <pathTo>/photoCredits.txt\n";
+  printf STDERR "usage: asmHubGatewayPage.pl <pathTo>/*assembly_report.txt <pathTo>/asmId.chrom.sizes <pathTo>/image.jpg <pathTo>/photoCredits.txt\n";
   printf STDERR "output is to stdout, redirect to file: > description.html\n";
   printf STDERR "photoCredits.txt is a two line tag<tab>string file:\n";
   printf STDERR "tags: photoCreditURL and photoCreditName\n";
   printf STDERR "use string 'noPhoto' for image and credits when no photo\n";
   printf STDERR "stderr output is routed to a 'asmId.names.tab' file for use elsewhere\n";
   exit 255;
 }
 
 sub chromSizes($) {
   my ($sizeFile) = @_;
   if ( -s $sizeFile ) {
     printf STDERR "# reading chrom.sizes file:\n#\t'%s\'\n", $sizeFile;
     my $ix = 0;
     my $contigCount = 0;
 
@@ -86,35 +86,35 @@
     }
   } else {
     printf STDERR "# error: can not find chrom.sizes file:\n#\t'%s\'\n",
       $sizeFile;
   }
 }
 
 # typical reference:
 #   ${inside}/scripts/gatewayPage.pl ${outside}/${asmReport} \
 #       > "${inside}/${D}/${B}.description.html" \
 #       2> "${inside}/${D}/${B}.names.tab"
 
 
 my $argc = scalar(@ARGV);
 
-if ($argc != 5) {
+if ($argc != 4) {
   usage;
 }
 
-my ($asmHubName, $asmReport, $chromSizes, $jpgImage, $photoCredits) = @ARGV;
+my ($asmReport, $chromSizes, $jpgImage, $photoCredits) = @ARGV;
 if ( ! -s $asmReport ) {
   printf STDERR "ERROR: can not find '$asmReport'\n";
   usage;
 }
 if ( ! -s $chromSizes ) {
   printf STDERR "ERROR: can not find '$chromSizes'\n";
   usage;
 }
 if ($jpgImage ne "noPhoto") {
   if ( ! -s $jpgImage ) {
     printf STDERR "ERROR: can not find '$jpgImage'\n";
     usage;
   }
   if ( ! -s $photoCredits ) {
     printf STDERR "ERROR: can not find '$photoCredits'\n";
@@ -437,31 +437,31 @@
 </pre>
 For a protein fasta query with your protein sequence in the file: <b>someProtein.faa</b>
 with result in the file: <b>$accessionId.someProtein.psl</b>
 <pre>
 gfClient -t=dnax -q=prot  -genome=$accessionId -genomeDataDir=$accessionDir \
     dynablat-01.soe.ucsc.edu 4040 ./ someProtein.faa $accessionId.someProtein.psl
 </pre>
 </p>\n";
 
 } else {
   printf "<hr>
 <p>
 At this time, this genome size: %s, is too large (greater than 4294967296),
 to function with the UCSC blat system.  We hope to have improvements to
 that system in the future to allow blat service for the larger genome sizes.
-</p>\n", commify($genomeSize);
+</p>\n", &AsmHub::commify($genomeSize);
 }
 
 printf "<hr>
 <p>
 <b>Search the assembly:</b>
 <ul>
 <li>
 <b>By position or search term: </b> Use the &quot;position or search term&quot;
 box to find areas of the genome associated with many different attributes, such
 as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or
 keywords from the GenBank description of an mRNA.
 <a href=\"http://genome.ucsc.edu/goldenPath/help/query.html\">More information</a>, including sample queries.</li>
 <li>
 <b>By gene name: </b> Type a gene name into the &quot;search term&quot; box,
 choose your gene from the drop-down list, then press &quot;submit&quot; to go