8b6ee6734404f7ab681577f5044559dd2ce8bc08 hiram Fri Sep 3 12:24:45 2021 -0700 print heredoc need to have ; on the print line refs #23891 diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index 46f1ad0..dfefd04 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -73,65 +73,65 @@ my $subSetMessage = "subset of $asmHubName only"; if ($asmHubName eq "vertebrate") { $subSetMessage = "subset of other ${asmHubName}s only"; } if ($vgpIndex) { my $vgpSubset = "(set of primary assemblies)"; if ($orderList =~ m/vgp.alternate/) { $vgpSubset = "(set of alternate/haplotype assemblies)"; } elsif ($orderList =~ m/vgp.trio/) { $vgpSubset = "(set of trio assemblies, maternal/paternal)"; } elsif ($orderList =~ m/vgp.legacy/) { $vgpSubset = "(set of legacy/superseded assemblies)"; } - print <<"END" + print <<"END"; <!DOCTYPE HTML 4.01 Transitional> <!--#set var="TITLE" value="VGP - Vertebrate Genomes Project assembly hub" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>VGP - Vertebrate Genomes Project assembly hub</h1> <p> <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> $vgpSubset </p> END } else { - print <<"END" + print <<"END"; <!DOCTYPE HTML 4.01 Transitional> <!--#set var="TITLE" value="$Name genomes assembly hubs" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>$Name Genomes assembly hubs</h1> <p> Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage. </p> END } -print <<"END" +print <<"END"; <h3>How to view the hub</h3> <p> Options: <ol> <li>The links to the genome browser in the table below will attach that one specific assembly to the genome browser. This is most likely what you want. Alternatively, the entire set of assemblies can be attached as one group to the genome browser with the following links depending upon which of our mirror site browsers you prefer to use: <table border="1"> <tr> <th>attach all assemblies to selected site:</th> <th> </th> <th><a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" target="_blank">genome.ucsc.edu</a></th> @@ -162,61 +162,71 @@ <p> After adding the hub, you will be redirected to the gateway page. The genome assemblies can be selected from the <em>${Name} Hub Assembly</em> dropdown menu. Instead of adding all the assemblies in one collected group, use the individual <em>view in browser</em> in the table below. </p> <h3>See also: <a href='asmStats.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a> <== additional information for these assemblies.</h3><br> <h3>Data resource links</h3> NOTE: <em>Click on the column headers to sort the table by that column</em><br> <br> The <em>common name and view in browser</em> will attach only that single assembly to the genome browser.<br> The <em>scientific name and data download</em> link provides access to the files for that one assembly hub.<br> +END + + if ($vgpIndex) { + print <<"END"; The <em>class VGP link</em> provides access to the VGP GenomeArk page for that genome.<br> +END + + } + +print <<"END"; The other links provide access to NCBI resources for these assemblies. END + } # sub startHtml() ############################################################################## ### start the table output ############################################################################## sub startTable() { print ' <table class="sortable" border="1"> <thead><tr><th>count</th> <th>common name and<br>view in browser</th> <th>scientific name<br>and data download</th> <th>NCBI assembly</th> <th>BioSample</th><th>BioProject</th> <th>assembly date,<br>source link</th> '; if ($vgpIndex) { printf "<th>class<br>VGP link</th>\n"; } print "</tr></thead><tbody>\n"; } # sub startTable() ############################################################################## ### end the table output ############################################################################## sub endTable() { -print <<"END" +print <<"END"; </tbody> </table> END } # sub endTable() ############################################################################## ### end the HTML output ############################################################################## sub endHtml() { &commonHtml::otherHubLinks($vgpIndex, $asmHubName); &commonHtml::htmlFooter($vgpIndex, $asmHubName); } # sub endHtml()