22a67b8eddff877e9265906cfbc4df5a41c3e0db
lrnassar
  Mon Aug 5 12:01:54 2019 -0700
Pointing hard-coded links to hgdownload refs #23734

diff --git src/hg/makeDb/doc/VGP/mkHubIndex.pl src/hg/makeDb/doc/VGP/mkHubIndex.pl
index 8e61706..1ff0fff 100755
--- src/hg/makeDb/doc/VGP/mkHubIndex.pl
+++ src/hg/makeDb/doc/VGP/mkHubIndex.pl
@@ -42,50 +42,50 @@
 <a href='https://vertebrategenomesproject.org/' target=_blank>
 <img src='VGPlogo.png' width=280 alt='VGP logo'></a></p>
 <p>
 This assembly hub contains assemblies released
 by the <a href='https://vertebrategenomesproject.org/' target=_blank>
 Vertebrate Genomes Project.</a>
 </p>
 
 <h3>How to view the hub</h3>
 <p>
 You can load this hub from our
 <a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> 
 page or by clicking these links to any of our official websites:
 <ul>
   <li>
-    <a href="http://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&amp;genome=GCF_004126475.1_mPhyDis1_v1.p"
+    <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&amp;genome=GCF_004126475.1_mPhyDis1_v1.p"
     target="_blank">genome.ucsc.edu</a></li>
   <li> 
-    <a href="http://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&amp;genome=GCF_004126475.1_mPhyDis1_v1.p"
+    <a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&amp;genome=GCF_004126475.1_mPhyDis1_v1.p"
     target="_blank">genome-euro.ucsc.edu</a></li>
   <li>
-    <a href="http://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&amp;genome=GCF_004126475.1_mPhyDis1_v1.p"
+    <a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&amp;genome=GCF_004126475.1_mPhyDis1_v1.p"
     target="_blank">genome-asia.ucsc.edu</a></li>
 </ul>
 </p>
 
 <p>
 To manually attach this hub to other genome browsers:
 <ol>
   <li>
     From the blue navigation bar, go to
     <em><strong>My Data</strong> -&gt; <strong>Track Hubs</strong></em></li>
   <li>
     Then select the <strong>My Hubs</strong> tab and enter this URL into the textbox:
-    <br><code>http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt</code></li>
+    <br><code>https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt</code></li>
   <li>
     Once you have added the URL to the entry form, press the <em><strong>Add Hub</strong></em>
     button to add the hub.</li>
 </ol>
 </p>
 
 <p>
 After adding the hub, you will be redirected to the gateway page.  The
 genome assemblies can be selected from the <em>VGP Hub Assembly</em> dropdown menu.
 </p>
 <p>
 <h3>See also: <a href='asmStatsVGP.html' target=_blank>assembly statistics</a></h3>
 </p>
 <h3>Data resource links</h3>
 NOTE: <em>Click on the column headers to sort the table by that column</em>
@@ -185,32 +185,32 @@
            $commonName =~ s/\)//;
            $sciName =~ s/.*:\s+//;
            $sciName =~ s/\s+\(.*//;
         }
       } elsif ($line =~ m/Taxid:/) {
         if ($taxId =~ m/notFound/) {
            ++$itemsFound;
            $taxId = $line;
            $taxId =~ s/.*:\s+//;
         }
       }
     }
     close (FH);
     $commonName = $betterName{$asmId} if (exists($betterName{$asmId}));
     printf CN "%s\t%s\n", $commonName, $asmId;
-    printf "<tr><td align=center><a href='https://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&amp;genome=%s&amp;position=lastDbPos' target=_blank>%s</a></td>\n", $asmId, $commonName;
-    printf "    <td align=center><a href='https://genome-test.gi.ucsc.edu/hubs/VGP/genomes/%s/' target=_blank>%s</a></td>\n", $asmId, $sciName;
+    printf "<tr><td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&amp;genome=%s&amp;position=lastDbPos' target=_blank>%s</a></td>\n", $asmId, $commonName;
+    printf "    <td align=center><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/%s/' target=_blank>%s</a></td>\n", $asmId, $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;
     printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>\n", $bioSample, $bioSample;
     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=right><a href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%d' target=_blank>%s</a></td>\n", $taxId, $taxId;
     my $sciNameUnderscore = $sciName;
     $sciNameUnderscore =~ s/ /_/g;
     $sciNameUnderscore = "Strigops_habroptilus" if ($sciName =~ m/Strigops habroptila/);
     printf "    <td align=center><a href='https://vgp.github.io/genomeark/%s/' target=_blank>%s</a></td>\n", $sciNameUnderscore, $asmDate;
     printf "    <td align=right>%s</td>\n", $class{$asmId};
     printf "</tr>\n";
   }
   close(CN);
 }
 
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