3227ff50033faf22cb1199ad40610f9042c7fd10 hiram Fri Mar 17 16:19:21 2023 -0700 add special section for the VGP index page to point to the special listings of files no redmine diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index b2d3fc7..4b341b4 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -180,30 +180,48 @@ <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>${Name} Hub Assembly</em> dropdown menu. Instead of adding all the assemblies in one collected group, use the individual <em>view in browser</em> in the table below. </p> <h3>See also: <a href='asmStats.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a> <== additional information for these assemblies.</h3><br> +END + +if ($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> +END +} + +print <<"END"; <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 }