7c934496e3650521dc129b65658326d542cbd20b
hiram
  Tue May 17 12:52:51 2022 -0700
trying out new rmsk format bigBed joined display no redmine

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index dfbcc0b..279603f 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -449,31 +449,31 @@
 }	# sub unlocalizedFasta($$$)
 
 #########################################################################
 # read alt_scaffold_placement file, return name correspondence in
 # given hash pointer
 sub readAltPlacement($$) {
   my ($altPlacementFile, $accToChr) = @_;
   open (AP, "<$altPlacementFile") or die "can not read $altPlacementFile";
   while (my $line = <AP>) {
     chomp $line;
     next if ($line =~ m/^#/);
     my ($alt_asm_name, $prim_asm_name, $alt_scaf_name, $alt_scaf_acc, $parent_type, $parent_name, $parent_acc, $region_name, $ori, $alt_scaf_start, $alt_scaf_stop, $parent_start, $parent_stop, $alt_start_tail, $alt_stop_tail) = split('\t', $line);
     my $acc = $alt_scaf_acc;
     $alt_scaf_acc = $acc;
     my $ucscName = $acc;
-    if ($ucscNames) {
+    if (1 == 1 || $ucscNames) {
       $alt_scaf_acc =~ s/\./v/;
       $ucscName = sprintf("chr%s_%s_alt", $parent_name, $alt_scaf_acc);
       if ( $prim_asm_name ne "Primary Assembly" ) {
         $ucscName = sprintf("%s_alt", $alt_scaf_acc);
       }
     }
     $accToChr->{$acc} = $ucscName;
     printf STDERR "# warning: name longer than 31 characters: '%s'\n# in: '%s'\n", $ucscName, $altPlacementFile if (length($ucscName) > 31);
   }
   close (AP);
 }	#	sub readAltPlacement($$)
 
 #########################################################################
 ### process one of the alternate AGP files, changing names via the nameHash
 ### and writing to the given fileHandle (fh)
@@ -1068,33 +1068,33 @@
     exit 255;
   }
   my $runDir = "$buildDir/html";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "construct html/$asmId.description.html";
   my $bossScript = newBash HgRemoteScript("$runDir/doGatewayPage.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   my $photoJpg = "noPhoto";
   my $photoCredit = "noPhoto";
   my $photoLink = "";
   my $speciesNoBlank = $species;
   $speciesNoBlank =~ s/ /_/g;
   if ( -s "$runDir/../photo/$speciesNoBlank.jpg" ) {
-     $photoJpg = "../photo/\${species}.jpg";
+     $photoJpg = "../photo/${speciesNoBlank}.jpg";
      $photoCredit = "../photo/photoCredits.txt";
-     $photoLink = "rm -f \${species}.jpg; ln -s ../photo/\${species}.jpg ."
+     $photoLink = "rm -f ${speciesNoBlank}.jpg; ln -s ../photo/${speciesNoBlank}.jpg ."
   } else {
      printf STDERR "# gatewayPage: warning: no photograph available\n";
   }
 
   $bossScript->add(<<_EOF_
 export asmId=$asmId
 
 \$HOME/kent/src/hg/utils/automation/asmHubGatewayPage.pl \\
      $asmHubName ../download/\${asmId}_assembly_report.txt \\
        ../\${asmId}.chrom.sizes \\
          $photoJpg $photoCredit \\
            > \$asmId.description.html 2> \$asmId.names.tab
 \$HOME/kent/src/hg/utils/automation/genbank/buildStats.pl \\
        ../\$asmId.chrom.sizes 2> \$asmId.build.stats.txt
 $photoLink