dff254260c6b5cb3ab0f2257775fce47bbbfa3ea hiram Wed Mar 25 11:56:34 2020 -0700 now staging on hgdownload.soe.ucsc.edu refs #24748 diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index 2fe5b20..d21d570 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -87,31 +87,31 @@ Then select the <strong>My Hubs</strong> tab and enter this URL into the textbox: <br><code>https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt</code></li> <li> Once you have added the URL to the entry form, press the <em><strong>Add Hub</strong></em> button to add the hub.</li> </ol> </p> <p> After adding the hub, you will be redirected to the gateway page. The genome assemblies can be selected from the <em>${Name} Hub Assembly</em> dropdown menu. Instead of adding all the assemblies in one collected group, use the individual <em>link to genome browser</em> in the table below. </p> -<h3>See also: <a href='asmStats${Name}.html'>assembly statistics</a></h3><br> +<h3>See also: <a href='asmStats${Name}.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a></h3><br> <h3>Data resource links</h3> NOTE: <em>Click on the column headers to sort the table by that column</em><br> The <em>link to genome browser</em> will attach only that single assembly to the genome browser. END } # sub startHtml() ############################################################################## ### start the table output ############################################################################## sub startTable() { print <<"END" <table class="sortable" border="1"> <thead><tr><th>count</th> <th>common name<br>link to genome browser</th> @@ -129,42 +129,53 @@ sub endTable() { print <<"END" </tbody> </table> END } # sub endTable() ############################################################################## ### end the HTML output ############################################################################## sub endHtml() { if ($asmHubName ne "viral") { - printf "<p>\nOther assembly hubs available:<br>\n<table border='1'><thead>\n<tr>"; + printf "<p>\n<table border='1'><thead>\n<tr>"; + printf "<th>Assembly hubs index pages: </th>\n"; + printf "<th><a href='../primates/index.html'>Primates</a></th>\n"; + printf "<th><a href='../mammals/index.html'>Mammals</a></th>\n"; + printf "<th><a href='../birds/index.html'>Birds</a></th>\n"; + printf "<th><a href='../fish/index.html'>Fish</a></th>\n"; + printf "<th><a href='../vertebrate/index.html'>other vertebrates</a></th>\n"; - printf "<th><a href='../primates/index.html'>Primates</a></th>\n" - if ($asmHubName ne "primates"); - printf "<th><a href='../mammals/index.html'>Mammals</a></th>\n" - if ($asmHubName ne "mammals"); - printf "<th><a href='../birds/index.html'>Birds</a></th>\n" - if ($asmHubName ne "birds"); - printf "<th><a href='../fish/index.html'>Fish</a></th>\n" - if ($asmHubName ne "fish"); - printf "<th><a href='../vertebrate/index.html'>other vertebrates</a></th>\n" - if ($asmHubName ne "vertebrate"); + printf "</tr><tr>\n"; + printf "<th>Hubs assembly statistics: </th>\n"; + printf "<th><a href='../primates/asmStatsPrimates.html'>Primates</a></th>\n"; + printf "<th><a href='../mammals/asmStatsMammals.html'>Mammals</a></th>\n"; + printf "<th><a href='../birds/asmStatsBirds.html'>Birds</a></th>\n"; + printf "<th><a href='../fish/asmStatsFish.html'>Fish</a></th>\n"; + printf "<th><a href='../vertebrate/asmStatsVertebrate.html'>other vertebrates</a></th>\n"; + + printf "</tr><tr>\n"; + printf "<th>Hubs track statistics: </th>\n"; + printf "<th><a href='../primates/trackData.html'>Primates</a></th>\n"; + printf "<th><a href='../mammals/trackData.html'>Mammals</a></th>\n"; + printf "<th><a href='../birds/trackData.html'>Birds</a></th>\n"; + printf "<th><a href='../fish/trackData.html'>Fish</a></th>\n"; + printf "<th><a href='../vertebrate/trackData.html'>other vertebrates</a></th>\n"; printf "</tr></thead>\n</table>\n</p>\n"; } print <<"END" </div><!-- closing gbsPage from gbPageStartHardcoded.html --> </div><!-- closing container-fluid from gbPageStartHardcoded.html --> <!--#include virtual="\$ROOT/inc/gbFooterHardcoded.html"--> <script type="text/javascript" src="/js/sorttable.js"></script> </body></html> END } # sub endHtml() ############################################################################## ### tableContents() @@ -227,31 +238,31 @@ $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&genome=%s&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='https://genome.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()