68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81 hiram Tue Mar 31 12:08:22 2020 -0700 correct hub.txt not testHub.txt refs #23891 diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index d21d570..9402773 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -49,73 +49,79 @@ 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, $subSetMessage. </p> <h3>How to view the hub</h3> <p> -You can load this hub from our -<a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> -page or by clicking these assembly links to any of our official websites: +Options: +<ol> + <li>The links to the genome browser in the table below will attach that + one specific assembly to the genome browser. This is most likely what + you want.</li> + <li>Instead, you can attach the entire set of assemblies as one group to + the genome browser with the following links depending upon which of + our mirror site browsers you prefer to use: <ul> - <li> - <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + <li><a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=GCF_000001405.39" 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" + <li><a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=GCF_000001405.39" target="_blank">genome-euro.ucsc.edu</a></li> - <li> - <a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + <li><a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=GCF_000001405.39" target="_blank">genome-asia.ucsc.edu</a></li> </ul> -</p> - -<p> -To manually attach all the assemblies in this hub to other genome browsers: + </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 + <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: + <li>Then select the <strong>My Hubs</strong> tab and enter this URL into + the textbox: <br><code>https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt</code></li> - <li> - Once you have added the URL to the entry form, press the <em><strong>Add Hub</strong></em> - button to add the hub.</li> + <li> Once you have added the URL to the entry form, + press the <em><strong>Add Hub</strong></em> button to add the hub.</li> + </ol> + </li> </ol> </p> <p> After adding the hub, you will be redirected to the gateway page. The genome assemblies can be selected from the <em>${Name} Hub Assembly</em> dropdown menu. Instead of adding all the assemblies in one collected group, use the individual <em>link to genome browser</em> in the table below. </p> -<h3>See also: <a href='asmStats${Name}.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a></h3><br> +<h3>See also: <a href='asmStats.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a> <== additional information for these assemblies.</h3><br> <h3>Data resource links</h3> +<p> NOTE: <em>Click on the column headers to sort the table by that column</em><br> -The <em>link to genome browser</em> will attach only that single assembly to -the genome browser. +The <em>common name/link to genome browser</em> will attach only that single assembly to +the genome browser.<br> +The <em>scientific name/and data download</em> link provides access to the files for that one +assembly hub.<br> +The other links provide access to NCBI resources for these assemblies. +</p> END } # sub startHtml() ############################################################################## ### start the table output ############################################################################## sub startTable() { print <<"END" <table class="sortable" border="1"> <thead><tr><th>count</th> <th>common name<br>link to genome browser</th> <th>scientific name<br>and data download</th> <th>NCBI assembly</th> <th>bioSample</th><th>bioProject</th> <th>assembly date,<br>source link</th> @@ -129,45 +135,46 @@ sub endTable() { print <<"END" </tbody> </table> END } # sub endTable() ############################################################################## ### end the HTML output ############################################################################## sub endHtml() { if ($asmHubName ne "viral") { - printf "<p>\n<table border='1'><thead>\n<tr>"; - printf "<th>Assembly hubs index pages: </th>\n"; + printf "<p>\n<table border='1'><thead>\n"; + printf "<tr><th colspan=6 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n"; + printf "<tr><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 "</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 "<th><a href='../primates/asmStats.html'>Primates</a></th>\n"; + printf "<th><a href='../mammals/asmStats.html'>Mammals</a></th>\n"; + printf "<th><a href='../birds/asmStats.html'>Birds</a></th>\n"; + printf "<th><a href='../fish/asmStats.html'>Fish</a></th>\n"; + printf "<th><a href='../vertebrate/asmStats.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 -->