631a7882f8c689b66f3d81fc8f25fbf98f73499a hiram Mon Oct 2 16:55:41 2023 -0700 remove the all genomes at once attachment option refs #29545 diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index 4414bf6..e72a403 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -156,76 +156,38 @@ <!--#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, $subSetMessage. </p> END } } print <<"END"; -<h3>How to view the hub</h3> +<h3>How to view the assembly of interest</h3> <p> -Options: -<ol> - <li>The links to the genome browser in the table below will attach that - one specific assembly to the genome browser. This is most likely what - you want. Alternatively, the entire set of assemblies can be attached - as one group to the genome browser with the following links depending - upon which of our mirror site browsers you prefer to use: -<table border="1"> -<tr> - <th>attach all assemblies to selected site:</th> - <th> </th> - <th><a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" - target="_blank">genome.ucsc.edu</a></th> - <th> </th> - <th><a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$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> +The links to the genome browser in the table below will attach that +one specific assembly to the genome browser. Use the links in +the column labeled <b>common name and view in browser</b> to view that +assembly in the genome browser. </p> -<p> -After adding the hub, you will be redirected to the gateway page. The -genome assemblies can be selected from the -<em>${Name} Hub Assembly</em> dropdown menu. -Instead of adding all the assemblies in one collected group, use the individual -<em>view in browser</em> in the table below. -</p> <h3>See also: <a href='asmStats.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a> <== additional information for these assemblies.</h3><br> END if ($vgpIndex) { print <<"END"; <h3>Listings:</h3> <b>(from RepeatModeler masking)</b> <p> <ul> <li><a href='modeler.families.urls.txt' target=_blank>families fasta.gz</a> list of URLs for the custom library created by the RepeatModeler run</li> <li><a href='modeler.2bit.urls.txt' target=_blank>assembly 2bit file list</a> of URLs as masked with the RepeatModeler + <b>TRF/simpleRepeats</b> with period of 12 or less</li> <li><a href='rmod.log.file.list.txt' target=_blank>the rmod.log files from each RepeatModeler run</a></li> <li><a href='default.twoBit.file.list.txt' target=_blank>default GenArk 2bit file list</a> of URLs as masked with the ordinary RepeatMasker + <b>TRF/simpleRepeats</b> with period of 12 or less</li> <li><a href='modeler.table.txt' target=_blank>this data table in tab-separated</a> file text format (including TBD not working yet, or in VGP collection but not on the alignment list)</li> </ul> </p>