df57ecff435188eeafe1d9505fb7a49c5941f764 hiram Tue Jan 20 11:50:25 2026 -0800 correctly appear and dismiss the liftExisting box and clean up the text documentation refs #31811 diff --git src/hg/htdocs/liftRequest.html src/hg/htdocs/liftRequest.html index 2c2c0458413..822307541a4 100755 --- src/hg/htdocs/liftRequest.html +++ src/hg/htdocs/liftRequest.html @@ -1,99 +1,112 @@ <!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. + 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 + The alignment here will be generated on the <a href='https://usegalaxy.org/' +target=_blank>Galaxy</a> platform, using a + workflow that uses the <a href='https://tacc.utexas.edu/' +target=_blank>TACC</a></a> 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, your 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. - + Once complete, your 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 also: <a href='https://genome.ucsc.edu/FAQ/FAQdownloads.html#download28' +target=_blank>Converting coordinates</a>. + Once these tracks are available, you can also use our Quicklift feature + to lift annotations on-the-fly, as you use the browser, + see also: <a href='https://docs.google.com/document/d/1wecESHUpgTlE6U_Mj0OnfHeSZBrTX9hkZRN5jlJS8ZQ/edit?usp=sharing' +target=_blank>Quick Lift guide</a> 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>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" +target=_blank>Assembly Request Page</a>, then come back here when the + assembly has been added to the browser. </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 id="liftExists" class="form-group" style="display: none;"> + <button id="dismissLiftExists" style="float: right; cursor: pointer;">×</button> <div class="description"> <p><strong>LiftOver chain files already exist for these assemblies:</strong></p> <p> <strong>Assembly 1:</strong> - <a id="genome1Link" href="" target="_blank"></a> browser link<br> - Download: <a id="genome1LiftOver" href="" download>Download chain file</a> over.chain.gz file + <a id="genome1Link" href="#" target="_blank"></a> browser link<br> + Download: <a id="genome1LiftOver" href="#" download>Download chain file</a> over.chain.gz file </p> <p> <strong>Assembly 2:</strong> - <a id="genome2Link" href="" target="_blank"></a> browser link<br> - Download: <a id="genome2LiftOver" href="" download>Download chain file</a> over.chain.gz file + <a id="genome2Link" href="#" target="_blank"></a> browser link<br> + Download: <a id="genome2LiftOver" href="#" download>Download chain file</a> over.chain.gz file </p> </div> </div> - <div class="form-group"> + <div id="emailForm" 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"> + <div id="commentsForm" 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"> + <div id="submitButton" class="form-group"> <input id="submitBtn" type="button" value="Submit Request" onclick="submitForm()"> </div> </div> <!-- end of formContainer --> <div id="successMessage"> <h2>Your request has been submitted, you will receive an email when the alignment is complete.</h2> <a href="<!--#echo var='ROOT' -->/cgi-bin/hgGateway">Back to the genome browser gateway page</a> </div> <div id="errorMessage"> <h3>Error</h3> <p id="errorText"></p> </div> <hr />