982d69ac4a666c4ff32f7ed167f788b81d960285 hiram Wed Jun 17 12:30:05 2020 -0700 reduce the vertical space consumed by options and explanations refs #25555 diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index e2ee199..719c1a2 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -114,90 +114,93 @@ <h1>$Name Genomes assembly hubs</h1> <p> Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage. </p> END } print <<"END" <h3>How to view the hub</h3> <p> Options: <ol> <li>The links to the genome browser in the table below will attach that one specific assembly to the genome browser. This is most likely what - you want.</li> - <li>Instead, you can attach the entire set of assemblies as one group to - the genome browser with the following links depending upon which of - our mirror site browsers you prefer to use: - <ul> - <li><a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" - target="_blank">genome.ucsc.edu</a></li> - <li><a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" - target="_blank">genome-euro.ucsc.edu</a></li> - <li><a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" - target="_blank">genome-asia.ucsc.edu</a></li> - </ul> + you want. Alternatively, the entire set of assemblies can be attached + as one group to the genome browser with the following links depending + upon which of our mirror site browsers you prefer to use: +<table border="1"> +<tr> + <th>attach all assemblies to selected site:</th> + <th> </th> + <th><a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + target="_blank">genome.ucsc.edu</a></th> + <th> </th> + <th><a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + target="_blank">genome-euro.ucsc.edu</a></th> + <th> </th> + <th><a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + target="_blank">genome-asia.ucsc.edu</a></th> +</tr> +</table> </li> <li>To manually attach all the assemblies in this hub to genome browsers that are not one of the three UCSC mirror sites: <ol> <li>From the blue navigation bar, go to <em><strong>My Data</strong> -> <strong>Track Hubs</strong></em></li> <li>Then select the <strong>My Hubs</strong> tab and enter this URL into the textbox: <br><code>https://hgdownload.soe.ucsc.edu/hubs/$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> </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>${Name} Hub Assembly</em> dropdown menu. Instead of adding all the assemblies in one collected group, use the individual <em>view in browser</em> in the table below. </p> <h3>See also: <a href='asmStats.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a> <== additional information for these assemblies.</h3><br> <h3>Data resource links</h3> -<p> NOTE: <em>Click on the column headers to sort the table by that column</em><br> -The <em>common name/view in browser</em> will attach only that single assembly to +The <em>common name and view in browser</em> will attach only that single assembly to the genome browser.<br> -The <em>scientific name/and data download</em> link provides access to the files for that one +The <em>scientific name and data download</em> link provides access to the files for that one assembly hub.<br> -The <em>class/VGP link</em> provides access to the VGP GenomeArk page for that genome<br> +The <em>class VGP link</em> provides access to the VGP GenomeArk page for that genome.<br> The other links provide access to NCBI resources for these assemblies. -</p> END } # sub startHtml() ############################################################################## ### start the table output ############################################################################## sub startTable() { print ' <table class="sortable" border="1"> <thead><tr><th>count</th> <th>common name and<br>view in browser</th> <th>scientific name<br>and data download</th> <th>NCBI assembly</th> - <th>bioSample</th><th>bioProject</th> + <th>BioSample</th><th>BioProject</th> <th>assembly date,<br>source link</th> '; if ($vgpIndex) { printf "<th>class<br>VGP link</th>\n"; } print "</tr></thead><tbody>\n"; } # sub startTable() ############################################################################## ### end the table output ############################################################################## sub endTable() { print <<"END" @@ -289,30 +292,32 @@ } } } 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://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"; } + # one broken assembly_report + $bioProject= "PRJEB25768" if ($accessionId eq "GCA_900324465.2"); if ($bioProject eq "notFound") { printf " <td align=left>%s</td>\n", $bioProject; } else { 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, $asmDate; if ($vgpIndex) { my $sciNameUnderscore = $sciName; $sciNameUnderscore =~ s/ /_/g; $sciNameUnderscore = "Strigops_habroptilus" if ($sciName =~ m/Strigops habroptila/); if (! defined($vgpClass{$asmId})) { printf STDERR "# ERROR: no 'class' defined for VGP assembly %s\n", $asmId; exit 255; }