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&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&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&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&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&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&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> -> <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&genome=%s&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&genome=%s&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); } ##############################################################################