extensions/net.sf.basedb.reggie/trunk/resources/analysis/hisat_start.jsp

Code
Comments
Other
Rev Date Author Line
4594 26 Sep 17 nicklas 1 <%@ page
4594 26 Sep 17 nicklas 2   pageEncoding="UTF-8"
4594 26 Sep 17 nicklas 3   session="false"
4594 26 Sep 17 nicklas 4   import="net.sf.basedb.core.User"
4594 26 Sep 17 nicklas 5   import="net.sf.basedb.core.DbControl"
4594 26 Sep 17 nicklas 6   import="net.sf.basedb.core.SessionControl"
4594 26 Sep 17 nicklas 7   import="net.sf.basedb.core.Application"
4594 26 Sep 17 nicklas 8   import="net.sf.basedb.clients.web.Base"  
4594 26 Sep 17 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
4594 26 Sep 17 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
4594 26 Sep 17 nicklas 11 %>
4594 26 Sep 17 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
4594 26 Sep 17 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
4594 26 Sep 17 nicklas 14 <%
4594 26 Sep 17 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
4594 26 Sep 17 nicklas 16 final String ID = sc.getId();
4594 26 Sep 17 nicklas 17 final float scale = Base.getScale(sc);
4594 26 Sep 17 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
4594 26 Sep 17 nicklas 19 DbControl dc = null;
4594 26 Sep 17 nicklas 20 try
4594 26 Sep 17 nicklas 21 {
4594 26 Sep 17 nicklas 22   dc = sc.newDbControl();
4594 26 Sep 17 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
4594 26 Sep 17 nicklas 24 %>
4594 26 Sep 17 nicklas 25 <base:page type="default" >
4594 26 Sep 17 nicklas 26 <base:head 
4594 26 Sep 17 nicklas 27   scripts="~../reggie-2.js,~hisat_start.js" 
4594 26 Sep 17 nicklas 28   styles="path.css,~../css/reggie-2.css"
4594 26 Sep 17 nicklas 29 />
4594 26 Sep 17 nicklas 30 <base:body>
4594 26 Sep 17 nicklas 31
4594 26 Sep 17 nicklas 32   <p:path><p:pathelement 
4594 26 Sep 17 nicklas 33     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
4594 26 Sep 17 nicklas 34     /><p:pathelement title="Start Hisat alignment" 
4594 26 Sep 17 nicklas 35     /></p:path>
4594 26 Sep 17 nicklas 36
4594 26 Sep 17 nicklas 37   <div class="content">
4594 26 Sep 17 nicklas 38   <form name="reggie" id="wizard" class="wizard">
4594 26 Sep 17 nicklas 39
4594 26 Sep 17 nicklas 40   <div class="step auto-hide" id="step-1">
4594 26 Sep 17 nicklas 41     <div class="step-no">1</div>
4594 26 Sep 17 nicklas 42     <div class="step-title">Select merged sequences</div>
4594 26 Sep 17 nicklas 43     <div class="step-content">
4594 26 Sep 17 nicklas 44     
4594 26 Sep 17 nicklas 45       <table class="step-form">
4594 26 Sep 17 nicklas 46       <tr class="align-top">
4594 26 Sep 17 nicklas 47         <td class="prompt">Merged sequences</td>
4594 26 Sep 17 nicklas 48         <td class="input">
4594 26 Sep 17 nicklas 49           <select class="required yellow-label-support" multiple size="30"
4594 26 Sep 17 nicklas 50             name="mergedSequences" id="mergedSequences"></select>
4594 26 Sep 17 nicklas 51             
4594 26 Sep 17 nicklas 52           <base:buttongroup style="margin-top: 0.5em;">
4594 26 Sep 17 nicklas 53             <base:button title="Select manually&hellip;" id="btnSelectMergedSequences" />
4594 26 Sep 17 nicklas 54           </base:buttongroup>
4594 26 Sep 17 nicklas 55         </td>
4594 26 Sep 17 nicklas 56         <td class="status" id="mergedSequences.status"></td>
4594 26 Sep 17 nicklas 57         <td class="help"><span id="mergedSequences.message" class="message"></span>
4596 27 Sep 17 nicklas 58           Select the sequences that should be aligned. The list contains merged sequences 
4596 27 Sep 17 nicklas 59           from the <b>Hisat pipeline</b> item list (max 250).<br><br>
4594 26 Sep 17 nicklas 60           Items marked with <b>[R]</b> have been marked for re-alignment due to a failure of
4594 26 Sep 17 nicklas 61           a previous alignment.
4594 26 Sep 17 nicklas 62         </td>
4594 26 Sep 17 nicklas 63       </tr>
4594 26 Sep 17 nicklas 64       </table>
4594 26 Sep 17 nicklas 65
4594 26 Sep 17 nicklas 66     </div>
4594 26 Sep 17 nicklas 67   </div>
4594 26 Sep 17 nicklas 68   
4594 26 Sep 17 nicklas 69   
4594 26 Sep 17 nicklas 70   <div class="step" id="step-2">
4594 26 Sep 17 nicklas 71     <div class="step-no">2</div>
4656 24 Jan 18 nicklas 72     <div class="step-title">Masking and alignment information</div>
4594 26 Sep 17 nicklas 73     <div class="step-content">
4594 26 Sep 17 nicklas 74
4594 26 Sep 17 nicklas 75       <table class="step-form">
4594 26 Sep 17 nicklas 76       <tbody>
4594 26 Sep 17 nicklas 77         <tr class="section-header">
4656 24 Jan 18 nicklas 78           <td colspan="4">Masking</td>
4656 24 Jan 18 nicklas 79         </tr>
4656 24 Jan 18 nicklas 80         <tr>
4656 24 Jan 18 nicklas 81           <td class="subprompt">Protocol</td>
4656 24 Jan 18 nicklas 82           <td class="input">
4656 24 Jan 18 nicklas 83             <select name="maskingProtocol" id="maskingProtocol"></select>
4656 24 Jan 18 nicklas 84           </td>
4656 24 Jan 18 nicklas 85           <td class="status" id="maskingProtocol.status"></td>
4656 24 Jan 18 nicklas 86           <td class="help">
4656 24 Jan 18 nicklas 87             <span id="maskingProtocol.message" class="message"></span>
4656 24 Jan 18 nicklas 88             Select the protocol used for filtering.
4656 24 Jan 18 nicklas 89           </td>
4656 24 Jan 18 nicklas 90         </tr>
4656 24 Jan 18 nicklas 91         <tr>
4656 24 Jan 18 nicklas 92           <td class="subprompt">Software</td>
4656 24 Jan 18 nicklas 93           <td class="input">
4656 24 Jan 18 nicklas 94             <select name="maskingSoftware" id="maskingSoftware"></select>
4656 24 Jan 18 nicklas 95           </td>
4656 24 Jan 18 nicklas 96           <td class="status" id="maskingSoftware.status"></td>
4656 24 Jan 18 nicklas 97           <td class="help">
4656 24 Jan 18 nicklas 98             <span id="maskingSoftware.message" class="message"></span>
4656 24 Jan 18 nicklas 99             Select the software to use for masking.
4656 24 Jan 18 nicklas 100           </td>
4656 24 Jan 18 nicklas 101         </tr>
4656 24 Jan 18 nicklas 102       </tbody>
4656 24 Jan 18 nicklas 103       <tbody class="info-section">
4656 24 Jan 18 nicklas 104         <tr>
4656 24 Jan 18 nicklas 105           <td class="subprompt">Parameter set</td>
4656 24 Jan 18 nicklas 106           <td class="info" colspan="2">
4656 24 Jan 18 nicklas 107             <span id="maskingSoftware.parameterSet"></span>
4656 24 Jan 18 nicklas 108             <div id="maskingSoftware.description" class="item-description"></div>
4656 24 Jan 18 nicklas 109           </td>
4656 24 Jan 18 nicklas 110           <td class="help">
4656 24 Jan 18 nicklas 111             This step uses Bowtie2 for masking unwanted sequences. Parameters are configured in 
6813 25 Aug 22 nicklas 112             &lt;align-hisat&gt; section in reggie-config.xml.
4656 24 Jan 18 nicklas 113           </td>
4656 24 Jan 18 nicklas 114         </tr>
4656 24 Jan 18 nicklas 115       </tbody>
4656 24 Jan 18 nicklas 116       <tbody>
4656 24 Jan 18 nicklas 117         <tr class="section-header">
4594 26 Sep 17 nicklas 118           <td colspan="4">Align</td>
4594 26 Sep 17 nicklas 119         </tr>
4594 26 Sep 17 nicklas 120         <tr valign="top">
4594 26 Sep 17 nicklas 121           <td class="subprompt">Protocol</td>
4594 26 Sep 17 nicklas 122           <td class="input">
4594 26 Sep 17 nicklas 123             <select name="alignProtocol" id="alignProtocol"></select>
4594 26 Sep 17 nicklas 124           </td>
4594 26 Sep 17 nicklas 125           <td class="status" id="alignProtocol.status"></td>
4594 26 Sep 17 nicklas 126           <td class="help">
4594 26 Sep 17 nicklas 127             <span id="alignProtocol.message" class="message"></span>
4594 26 Sep 17 nicklas 128             Select the protocol used for alignment.
4594 26 Sep 17 nicklas 129           </td>
4594 26 Sep 17 nicklas 130         </tr>
4594 26 Sep 17 nicklas 131         <tr>
4594 26 Sep 17 nicklas 132           <td class="subprompt">Software</td>
4594 26 Sep 17 nicklas 133           <td class="input">
4594 26 Sep 17 nicklas 134             <select name="alignSoftware" id="alignSoftware"></select>
4594 26 Sep 17 nicklas 135           </td>
4594 26 Sep 17 nicklas 136           <td class="status" id="alignSoftware.status"></td>
4594 26 Sep 17 nicklas 137           <td class="help">
4594 26 Sep 17 nicklas 138             <span id="alignSoftware.message" class="message"></span>
4594 26 Sep 17 nicklas 139             Select the software to use for alignment.
4594 26 Sep 17 nicklas 140           </td>
4594 26 Sep 17 nicklas 141         </tr>
4594 26 Sep 17 nicklas 142       </tbody>
4594 26 Sep 17 nicklas 143       <tbody class="info-section">
4594 26 Sep 17 nicklas 144         <tr>
4594 26 Sep 17 nicklas 145           <td class="subprompt">Parameter set</td>
4594 26 Sep 17 nicklas 146           <td class="info" colspan="2">
4594 26 Sep 17 nicklas 147             <span id="alignSoftware.parameterSet"></span>
4594 26 Sep 17 nicklas 148             <div id="alignSoftware.description" class="item-description"></div>
4594 26 Sep 17 nicklas 149           </td>
4594 26 Sep 17 nicklas 150           <td class="help">
4594 26 Sep 17 nicklas 151             This step uses Hisat for for aligning sequences. After the alignment
4594 26 Sep 17 nicklas 152             it will run Picard MarkDuplicates as well
4594 26 Sep 17 nicklas 153             as a few other tools for statistics. Parameters are configured in 
4594 26 Sep 17 nicklas 154             &lt;align-hisat&gt; section in reggie-config.xml.
4594 26 Sep 17 nicklas 155           </td>
4594 26 Sep 17 nicklas 156         </tr>
4594 26 Sep 17 nicklas 157       </tbody>
4594 26 Sep 17 nicklas 158       <tbody>
4594 26 Sep 17 nicklas 159         <tr class="section-header">
6735 09 May 22 nicklas 160           <td colspan="4">Job scheduler</td>
4594 26 Sep 17 nicklas 161         </tr>
4594 26 Sep 17 nicklas 162         <tr>
4594 26 Sep 17 nicklas 163           <td class="subprompt">Cluster</td>
4594 26 Sep 17 nicklas 164           <td class="input">
4594 26 Sep 17 nicklas 165             <select name="clusters" id="clusters" class="required"></select></td>
4594 26 Sep 17 nicklas 166           <td class="status" id="clusters.status"></td>
4594 26 Sep 17 nicklas 167           <td class="help">
4594 26 Sep 17 nicklas 168             <span id="clusters.message" class="message"></span>
4594 26 Sep 17 nicklas 169             Select the cluster to use for running the software.
4594 26 Sep 17 nicklas 170           </td>
4594 26 Sep 17 nicklas 171         </tr>
4594 26 Sep 17 nicklas 172         <tr id="job-priority" style="display: none;">
4594 26 Sep 17 nicklas 173           <td class="subprompt">Job priority</td>
4594 26 Sep 17 nicklas 174           <td class="input">
4594 26 Sep 17 nicklas 175             <select name="priority" id="priority"></select>
4594 26 Sep 17 nicklas 176           </td>
4594 26 Sep 17 nicklas 177           <td class="status" id="priority.status"></td>
4594 26 Sep 17 nicklas 178           <td class="help">
4594 26 Sep 17 nicklas 179             <span id="priority.message" class="message"></span>
4594 26 Sep 17 nicklas 180             Select the priority of the job.
4594 26 Sep 17 nicklas 181           </td>
4594 26 Sep 17 nicklas 182         </tr>
6980 17 Jan 23 nicklas 183         <tr id="job-partition" style="display: none;">
6980 17 Jan 23 nicklas 184           <td class="subprompt">Job partition</td>
6980 17 Jan 23 nicklas 185           <td class="input">
6980 17 Jan 23 nicklas 186             <select name="partition" id="partition"></select>
6980 17 Jan 23 nicklas 187           </td>
6980 17 Jan 23 nicklas 188           <td class="status" id="partition.status"></td>
6980 17 Jan 23 nicklas 189           <td class="help">
6980 17 Jan 23 nicklas 190             <span id="partition.message" class="message"></span>
6980 17 Jan 23 nicklas 191             Select the partition/queue that the job should be submitted to.
6980 17 Jan 23 nicklas 192           </td>
6980 17 Jan 23 nicklas 193         </tr>
7372 06 Oct 23 nicklas 194       </tbody>
7372 06 Oct 23 nicklas 195       <tbody class="info-section">
7372 06 Oct 23 nicklas 196         <tr class="align-top">
7372 06 Oct 23 nicklas 197           <td class="subprompt">Job options</td>
7372 06 Oct 23 nicklas 198           <td class="info input">
7372 06 Oct 23 nicklas 199             <div id="submitOptions" class="item-description code"></div>
7372 06 Oct 23 nicklas 200             <textarea id="submitOptionsOverride" name="submitOptionsOverride" rows="4" style="display: none;"></textarea>
7372 06 Oct 23 nicklas 201           </td>
7372 06 Oct 23 nicklas 202           <td class="status" id="submitOptions.status">
7372 06 Oct 23 nicklas 203             <input type="checkbox" id="override" name="override" title="Override the default options" disabled>
7372 06 Oct 23 nicklas 204           </td>
7372 06 Oct 23 nicklas 205           <td class="help">
7372 06 Oct 23 nicklas 206             Parameters are configured in the &lt;align-hisat&gt;/&lt;submit&gt; 
7372 06 Oct 23 nicklas 207             section in reggie-config.xml. Select the checkbox to manually 
7372 06 Oct 23 nicklas 208             override the default options.
7372 06 Oct 23 nicklas 209           </td>
7372 06 Oct 23 nicklas 210         </tr>
7372 06 Oct 23 nicklas 211       </tbody>
7372 06 Oct 23 nicklas 212       <tbody>
4594 26 Sep 17 nicklas 213         <tr>
4594 26 Sep 17 nicklas 214           <td class="subprompt">Auto-confirm</td>
4594 26 Sep 17 nicklas 215           <td class="input"><input type="checkbox" name="autoConfirm" checked></td>
4594 26 Sep 17 nicklas 216           <td class="status" id="autoConfirm.status"></td>
4594 26 Sep 17 nicklas 217           <td class="help">
4594 26 Sep 17 nicklas 218             <span id="autoConfirm.message" class="message"></span>
4661 29 Jan 18 nicklas 219             If the alignment is successful and aligned pairs &gt;1M it is automatically confirmed
4663 29 Jan 18 nicklas 220             and StringTie is started. If aligned pairs is &lt;5M the RNA is flagged.
4594 26 Sep 17 nicklas 221           </td>
4594 26 Sep 17 nicklas 222         </tr>
4594 26 Sep 17 nicklas 223         <tr>
4594 26 Sep 17 nicklas 224           <td class="subprompt">Debug</td>
7372 06 Oct 23 nicklas 225           <td class="input"><input type="checkbox" name="debug" id="debug"></td>
4594 26 Sep 17 nicklas 226           <td class="status" id="debug.status"></td>
4594 26 Sep 17 nicklas 227           <td class="help">
4594 26 Sep 17 nicklas 228             <span id="debug.message" class="message"></span>
4594 26 Sep 17 nicklas 229             When running in debug mode temporary files are not removed from the
4594 26 Sep 17 nicklas 230             cluster node.
4594 26 Sep 17 nicklas 231           </td>
4594 26 Sep 17 nicklas 232         </tr>
4594 26 Sep 17 nicklas 233       </tbody>
4594 26 Sep 17 nicklas 234       </table>
4594 26 Sep 17 nicklas 235     </div>
4594 26 Sep 17 nicklas 236   </div>
4594 26 Sep 17 nicklas 237     
4594 26 Sep 17 nicklas 238     <div id="wizard-status"></div>
4594 26 Sep 17 nicklas 239   
4594 26 Sep 17 nicklas 240     <table class="navigation" id="navigation">
4594 26 Sep 17 nicklas 241     <tr>
4594 26 Sep 17 nicklas 242       <td><base:button id="gocancel" title="Cancel" /></td>
4594 26 Sep 17 nicklas 243       <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
4594 26 Sep 17 nicklas 244       <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
4594 26 Sep 17 nicklas 245       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
4594 26 Sep 17 nicklas 246       <td id="gonext-message" class="message"></td>
4594 26 Sep 17 nicklas 247     </tr>
4594 26 Sep 17 nicklas 248     </table>
4594 26 Sep 17 nicklas 249   
4594 26 Sep 17 nicklas 250   </form>
4594 26 Sep 17 nicklas 251   </div>
4594 26 Sep 17 nicklas 252   
4594 26 Sep 17 nicklas 253 </base:body>
4594 26 Sep 17 nicklas 254 </base:page>
4594 26 Sep 17 nicklas 255 <%
4594 26 Sep 17 nicklas 256 }
4594 26 Sep 17 nicklas 257 finally
4594 26 Sep 17 nicklas 258 {
4594 26 Sep 17 nicklas 259   if (dc != null) dc.close();
4594 26 Sep 17 nicklas 260 }
4594 26 Sep 17 nicklas 261 %>

Generated on Tue Nov 21 03:29:59 2023 (UTC) by svndigest 0.11.2pre (dev build 1672)