5b211c300c02e8db4a5b4daedb1711122d9321d3 hiram Fri Jan 16 11:47:18 2026 -0800 initial content for the liftRequest function refs #31811 diff --git src/hg/htdocs/liftRequest.html src/hg/htdocs/liftRequest.html new file mode 100755 index 00000000000..6c9fbbfb9ad --- /dev/null +++ src/hg/htdocs/liftRequest.html @@ -0,0 +1,91 @@ +<!DOCTYPE HTML> +<!--#set var="TITLE" value="Genome Assembly Alignment Request" --> +<!--#set var="ROOT" value="" --> + +<!--#include virtual='$ROOT/inc/gbPageStartHardcoded.html' --> + +<link rel='stylesheet' type='text/css' href='<!--#echo var='ROOT' -->/style/jquery-ui.css'> +<link rel='stylesheet' type='text/css' href='<!--#echo var='ROOT' -->/style/HGStyle.css'> +<link rel='stylesheet' type='text/css' href='<!--#echo var='ROOT' -->/style/liftRequest.css'> + +<div id="formContainer" class="form-container"> + <h1>Genome Assembly Alignment Request</h1> + + <p> + On this page you can request a whole-genome alignment between two genomes that are on the UCSC Genome Browser. + Such alignments can take thousands of compute hours to produce. + The alignment here will be produced on the Galaxy platform, using a + workflow that uses TACC high performance compute GPU resources. The full + process may take up to a few days. You will receive an email when it is + complete. + </p> + </p> + Once complete, will find two new tracks on both assemblies, one with the full alignment results ("all chains"), and one + track with the best alignment (single coverage) for every basepair, which can be used for "liftOver". + Since these tracks are single-coverage on the current genome, the alignments are reciprocal so one is produced + per assembly. + For more information on how to download these chain files and use liftOver, see --here--. + Once these tracks are available, you can also use our Quicklift feature to lift annotations on-the-fly, as you browser, + see --here-- for more information. + + + </p> + <p>If one of the two genomes is not on the UCSC browser yet, please request it first on our <a href="https://genome.ucsc.edu/assemblySearch.html">Assembly Request Page</a>, then come back here later. + </p> + + <div class="form-group"> + <label for="genomeSearch1">Assembly 1</label> + <div class="assembly-input-wrapper"> + <input id="genomeSearch1" type="text" placeholder="Search any species, genome or assembly name" autocomplete="off"> + <input id="genomeSearchButton1" value="Search" type="button"> + </div> + <div id="genomeLabel1" class="selected-assembly">No assembly selected</div> + </div> + + <div class="form-group"> + <label for="genomeSearch2">Assembly 2</label> + <div class="assembly-input-wrapper"> + <input id="genomeSearch2" type="text" placeholder="Search any species, genome or assembly name" autocomplete="off"> + <input id="genomeSearchButton2" value="Search" type="button"> + </div> + <div id="genomeLabel2" class="selected-assembly">No assembly selected</div> + </div> + + <div class="form-group"> + <label for="emailInput">Email Address</label> + <div class="description">You will receive a notification at this address when the alignment is complete.</div> + <input id="emailInput" type="email" placeholder="your.email@example.com"> + </div> + + <div class="form-group"> + <label for="commentsInput">Comments (optional)</label> + <div class="description">Any additional information or notes about this alignment request.</div> + <textarea id="commentsInput" placeholder="Enter any additional information here..."></textarea> + </div> + + <div class="form-group"> + <input id="submitBtn" type="button" value="Submit Request" onclick="submitForm()"> + </div> +</div> + +<div id="successMessage"> + <h2>Your request has been submitted, you will receive an email when the alignment is complete.</h2> + <a href="../cgi-bin/hgGateway">Back to the genome browser gateway page</a> +</div> + +<div id="errorMessage"> + <h3>Error</h3> + <p id="errorText"></p> +</div> + +<hr /> +</div><!-- closing gbsPage from gbPageStartHardcoded.html --> +</div><!-- closing container-fluid from gbPageStartHardcoded.html --> +<!--#include virtual="$ROOT/inc/gbFooterHardcoded.html"--> +<script src="<!--#echo var='ROOT' -->/js/liftRequest.js"></script> +<script src="<!--#echo var='ROOT' -->/js/jquery.js"></script> +<script src="<!--#echo var='ROOT' -->/js/jquery.plugins.js"></script> +<script src="<!--#echo var='ROOT' -->/js/utils.js"></script> +<script src="<!--#echo var='ROOT' -->/js/jquery-ui.js"></script> +<script src="<!--#echo var='ROOT' -->/js/autocompleteCat.js"></script> +</body></html>