242be79fd8f99be5b645add0d0a275c1fd58e052 brianlee Mon May 30 06:34:08 2022 -0700 Closing ticket on trix examples, added resources section and link to gpToIx.pl script refs #24091 diff --git src/hg/htdocs/goldenPath/help/trix.html src/hg/htdocs/goldenPath/help/trix.html index 60915ac..464d4c7 100755 --- src/hg/htdocs/goldenPath/help/trix.html +++ src/hg/htdocs/goldenPath/help/trix.html @@ -1,38 +1,44 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Trix Indices" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Trix Indices</h1> <p> A Trix index consists of a pair of files that allow for fast look-up of free text associated with a list of identifiers. The index is created from a single line-oriented text file using the program <code>ixIxx</code>. Each line in the text file starts with an identifier, followed by free text associated with the ID. For a more complete description of how to make a searchable track hub (or custom track), please visit the <a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable track hubs</a>.</p> <p> To complete the steps below you must first download the <code>ixIxx</code> utility. For more information on downloading our command line utilities, see these <a href="http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads">instructions</a>.</p> <p> To create a Trix index, follow these steps: <ol> <li> Prepare a text file that associates your IDs with free text:<br> <pre><code> id1 this is text for id1 id2 this is text for id2 id3 this is text for id3</code></pre></li> <li> Run the <code>ixIxx</code> program on your text file.<br> <pre><code> ixIxx input.txt myTrix.ix myTrix.ixx</code></pre></li> </ol> +<h3 id="resources">Resources and examples</h3> <p> If you want to use your Trix index in a track hub, see the <code>searchTrix</code> setting in the -<a href="trackDb/trackDbHub.html#searchTrix">Track Database Definition Document</a> or the -<a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable track hubs</a> -for more information.</p> +<a href="trackDb/trackDbHub.html#searchTrix">Track Database Definition Document</a>.</p> +<p> +Review our <a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable track hubs</a> +for illustrated steps building a track hub.</p> +<p> +There are also tools available for taking genePred format to trix format, such as +this <a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/utils/automation/gpToIx.pl" +target="_blank">gpToIx.pl</a> perl script.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->