dbbf12ecd3916a4105cd9191f328a5318ad30a40 hiram Mon Jan 26 13:12:12 2026 -0800 move the text to after the entry form refs #31811 diff --git src/hg/htdocs/liftRequest.html src/hg/htdocs/liftRequest.html index 2d243b8f76d..37dcc05a4f9 100755 --- src/hg/htdocs/liftRequest.html +++ src/hg/htdocs/liftRequest.html @@ -1,62 +1,28 @@ <!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 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, you 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" -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> @@ -85,30 +51,65 @@ <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 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 id="submitButton" class="form-group"> <input id="submitBtn" type="button" value="Submit Request" onclick="submitForm()"> </div> + + <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 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, you 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" +target=_blank>Assembly Request Page</a>, then come back here when the + assembly has been added to the browser. + </p> + </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 /> </div><!-- closing gbsPage from gbPageStartHardcoded.html --> </div><!-- closing container-fluid from gbPageStartHardcoded.html -->