27228c7e494674469a64cdeb61d7c4e433102f24 hiram Thu Jan 2 13:16:14 2020 -0800 updated text to global reference wording refs #24534 diff --git src/hg/makeDb/doc/globalReference/mkHubIndex.pl src/hg/makeDb/doc/globalReference/mkHubIndex.pl index 52db04b..60b8cc4 100755 --- src/hg/makeDb/doc/globalReference/mkHubIndex.pl +++ src/hg/makeDb/doc/globalReference/mkHubIndex.pl @@ -27,78 +27,80 @@ return scalar reverse $text } ############################################################################## ### start the HTML output ############################################################################## sub startHtml() { my $timeStamp = `date "+%F"`; chomp $timeStamp; # <html xmlns="http://www.w3.org/1999/xhtml"> print <<"END" <!DOCTYPE HTML 4.01 Transitional> -<!--#set var="TITLE" value="Platinum Genomes Project assembly hub" --> +<!--#set var="TITLE" value="Global Reference Genomes assembly hubs" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> -<h1>Platinum Genomes Project assembly hub</h1> +<h1>Global Reference Genomes assembly hubs</h1> <p> -This assembly hub contains assemblies released -by the <a href='https://genome.cshlp.org/content/27/1/157' target=_blank> -Platinum Genomes Project.</a> +This assembly hub contains ten high-quality, population-identified assemblies released +by the <a href='https://www.genome.wustl.edu/items/reference-genome-improvement/' target=_blank> +Reference Genome Improvement</a> project. This population list is not conclusive and +represents reference genomes from 10 different human populations. Thank you to +Washington University in Saint Louis for consolidating these open source reference genomes. </p> <h3>How to view the hub</h3> <p> You can load this hub from our <a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> -page or by clicking these links to any of our official websites: +page or by clicking these assembly links to any of our official websites: <ul> <li> <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubWorkDir/hub.txt&genome=$defaultAssembly" target="_blank">genome.ucsc.edu</a></li> <li> <a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubWorkDir/hub.txt&genome=$defaultAssembly" target="_blank">genome-euro.ucsc.edu</a></li> <li> <a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubWorkDir/hub.txt&genome=$defaultAssembly" target="_blank">genome-asia.ucsc.edu</a></li> </ul> </p> <p> To manually attach this hub to other genome browsers: <ol> <li> From the blue navigation bar, go to <em><strong>My Data</strong> -> <strong>Track Hubs</strong></em></li> <li> Then select the <strong>My Hubs</strong> tab and enter this URL into the textbox: <br><code>https://hgdownload.soe.ucsc.edu/hubs/$asmHubWorkDir/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>Platinum Genomes Hub Assembly</em> dropdown menu. +genome assemblies can be selected from the <em>Reference Genome Improvement Hub Assembly</em> dropdown menu. </p> <p> <h3>See also: <a href='asmStats$Name.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> END } ############################################################################## ### start the table output ############################################################################## sub startTable() { print <<"END" <table class="sortable" border="1">