22a9ec8b34dd60a14257bdef408f21c03db601b4
hiram
  Mon Feb 17 16:06:38 2020 -0800
now using the shorter assembly name for genome identifier and fix some common names refs #23891

diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
index 4b22d5c..2fe5b20 100755
--- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
+++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
@@ -226,48 +226,50 @@
            $commonName = $betterName{$asmId} if (exists($betterName{$asmId}));
            $sciName =~ s/.*:\s+//;
            $sciName =~ s/\s+\(.*//;
         }
       } elsif ($line =~ m/Taxid:/) {
         if ($taxId =~ m/notFound/) {
            ++$itemsFound;
            $taxId = $line;
            $taxId =~ s/.*:\s+//;
         }
       }
     }
     close (FH);
     my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$accessionDir/$accessionId";
     printf "<tr><td align=right>%d</td>\n", ++$rowCount;
-    printf "<td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=%s/hub.txt&amp;genome=%s&amp;position=lastDbPos' target=_blank>%s</a></td>\n", $hubUrl, $asmId, $commonName;
+###    printf "<td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=%s/hub.txt&amp;genome=%s&amp;position=lastDbPos' target=_blank>%s</a></td>\n", $hubUrl, $accessionId, $commonName;
+    printf "<td align=center><a href='https://hgwdev-hiram.gi.ucsc.edu/h/%s' target=_blank>%s</a></td>\n", $accessionId, $commonName;
     printf "    <td align=center><a href='%s/' target=_blank>%s</a></td>\n", $hubUrl, $sciName;
     printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s</a></td>\n", $gcPrefix, $asmAcc, $asmId;
     if ( $bioSample ne "notFound" ) {
     printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>\n", $bioSample, $bioSample;
     } else {
     printf "    <td align=left>n/a</td>\n";
     }
     printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/bioproject/?term=%s' target=_blank>%s</a></td>\n", $bioProject, $bioProject;
     printf "    <td align=center><a href='%s' target=_blank>%s</a></td>\n", $ncbiFtpLink, $asmDate;
     printf "</tr>\n";
   }
 }	#	sub tableContents()
 
 ##############################################################################
 ### main()
 ##############################################################################
 
 open (FH, "<$toolsDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
 while (my $line = <FH>) {
+  next if ($line =~ m/^#/);
   chomp $line;
   my ($commonName, $asmId) = split('\t', $line);
   push @orderList, $asmId;
   $betterName{$asmId} = $commonName;
   ++$assemblyCount;
 }
 close (FH);
 
 startHtml();
 startTable();
 tableContents();
 endTable();
 endHtml();