100924e5f5169717677039f59ab4fb85099d68d8
hiram
  Thu Aug 1 16:48:30 2019 -0700
add VGP outlink refs #23734

diff --git src/hg/utils/automation/asmHubGatewayPage.pl src/hg/utils/automation/asmHubGatewayPage.pl
index b10adda..6e3eed1 100755
--- src/hg/utils/automation/asmHubGatewayPage.pl
+++ src/hg/utils/automation/asmHubGatewayPage.pl
@@ -211,30 +211,31 @@
      $descrAsmType = $line;
   }
   if ($line =~ m/assembly\s+level:\s+/i) {
      next if ($asmLevel !~ m#\(n/a#);
      $line =~ s/.*assembly\s+level:\s+//i;
      $asmLevel = $line;
   }
   if ($line =~ m/assembly\s+name:\s+/i) {
      next if ($asmName !~ m#\(n/a#);
      $line =~ s/.*assembly\s+name:\s+//i;
      $asmName = $line;
   }
   if ($line =~ m/organism\s+name:\s+/i) {
      next if ($orgName !~ m#\(n/a#);
      $line =~ s/.*organism\s+name:\s+//i;
+     $line =~ s/\s+$//;
      $orgName = $line;
   }
   if ($line =~ m/submitter:\s+/i) {
      next if ($submitter !~ m#\(n/a#);
      $line =~ s/.*submitter:\s+//i;
      $submitter = $line;
   }
   if ($line =~ m/$asmType\s+assembly\s+accession:\s+/i) {
      next if ($asmAccession !~ m#\(n/a#);
      $line =~ s/.*$asmType\s+assembly\s+accession:\s+//i;
      $asmAccession = $line;
      $asmAccession =~ s/ .*//;
   }
   if ($line =~ m/taxid:\s+/i) {
      next if ($taxId !~ m#\(n/a#);
@@ -243,30 +244,31 @@
      if (exists($taxIdCommonName{$taxId})) {
        $commonName = $taxIdCommonName{$taxId};
      }
   }
 }
 close (FH);
 
 $commonName = $orgName if ($commonName =~ m#\(n/a#);
 if ($commonName =~ m/\(/) {
    $commonName =~ s/.*\(//;
    $commonName =~ s/\).*//;
 }
 if ($orgName =~ m/\(/) {
    $orgName =~ s/\(.*//;
 }
+$orgName =~ s/\s+$//;
 
 printf STDERR "#taxId\tcommonName\tsubmitter\tasmName\torgName\tbioSample\tasmType\tasmLevel\tasmDate\tasmAccession\n";
 printf STDERR "%s\t", $taxId;
 printf STDERR "%s\t", $commonName;
 printf STDERR "%s\t", $submitter;
 printf STDERR "%s\t", $asmName;
 printf STDERR "%s\t", $orgName;
 printf STDERR "%s\t", $bioSample;
 printf STDERR "%s\t", $descrAsmType;
 printf STDERR "%s\t", $asmLevel;
 printf STDERR "%s\t", $asmDate;
 printf STDERR "%s\n", $asmAccession;
 
 # printf "<script type='text/javascript'>var asmId='%s';</script>\n", $asmId;
 
@@ -276,41 +278,46 @@
   <tr><td align=RIGHT><a href=\"https://www.ncbi.nlm.nih.gov/assembly/%s\"
     target=_blank>
     <img src=\"../hubs/ncbiAssemblies/%s/html/%s\" width=%d height=%d alt=\"%s\"></a>
   </td></tr>
   <tr><td align=right>
     <font size=-1> <em>%s</em><BR>
     </font>
     <font size=-2> (Photo courtesy of
       <a href=\"%s\" target=_blank>%s</a>)
     </font>
   </td></tr>
 </table>
 \n", $imageWidth+$imageWidthBorder, $imageHeight, $asmAccession, $ftpName, $imageName, $imageWidth, $imageHeight, $commonName, $orgName, $photoCreditURL, $photoCreditName;
 }
 
+my $sciNameUnderscore = $orgName;
+$sciNameUnderscore =~ s/ /_/g;
+$sciNameUnderscore = "Strigops_habroptilus" if ($orgName =~ m/Strigops habroptila/);
+
 printf "<p>
 <b>Common name:</b>&nbsp;%s<br>
-<b>Taxonomic name: %s, taxonomy ID:</b> <a href=\"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%s\" target=_\"_blank\"> %s</a><br>
+<b>Taxonomic name: %s, taxonomy ID:</b> <a href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%s' target='_blank'> %s</a><br>
 <b>Sequencing/Assembly provider ID:</b> %s<br>
+<b>Vertebrate Genomes Project information:</b> <a href='https://vgp.github.io/genomeark/%s/' target=_blank>%s</a><br>
 <b>Assembly date:</b> %s<br>
 <b>Assembly type:</b> %s<br>
 <b>Assembly level:</b> %s<br>
 <b>Biosample:</b> <a href=\"https://www.ncbi.nlm.nih.gov/biosample/?term=%s\" target=\"_blank\">%s</a><br>
 <b>Assembly accession ID:</b> <a href=\"https://www.ncbi.nlm.nih.gov/assembly/%s\" target=\"_blank\">%s</a><br>
 <b>Assembly FTP location:</b> <a href=\"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/%s\" target=\"_blank\">%s</a><br>
-\n", $commonName, $orgName, $taxId, $taxId, $submitter, $asmDate, $descrAsmType,
+\n", $commonName, $orgName, $taxId, $taxId, $submitter, $sciNameUnderscore, $orgName, $asmDate, $descrAsmType,
   $asmLevel, $bioSample, $bioSample, $asmAccession, $asmAccession, $urlDirectory, $urlDirectory;
 
 chromSizes($chromSizes);
 
 printf "</p>\n<hr>
 <p>
 <b>Download files for this assembly hub:</b><br>
 To use the data from this assembly for a local hub instance at your
 institution, download these data as indicated by these instructions.<br>
 See also: <a href='/goldenPath/help/hgTrackHubHelp.html' target=_blank>track hub help</a> documentation.<br>
 <br>
 To download this assembly data, use this <em>rsync</em> command:
 <pre>
   rsync -a -P rsync://$sourceServer/hubs/VGP/genomes/$asmId/ ./$asmId/