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<%@ page |
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pageEncoding="UTF-8" |
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session="false" |
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import="net.sf.basedb.core.User" |
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import="net.sf.basedb.core.DbControl" |
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import="net.sf.basedb.core.SessionControl" |
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import="net.sf.basedb.core.Application" |
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import="net.sf.basedb.clients.web.Base" |
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import="net.sf.basedb.clients.web.util.HTML" |
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import="net.sf.basedb.clients.web.extensions.ExtensionsControl" |
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%> |
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<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %> |
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<% |
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final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true); |
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final String ID = sc.getId(); |
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final float scale = Base.getScale(sc); |
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final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie"); |
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DbControl dc = null; |
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try |
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{ |
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dc = sc.newDbControl(); |
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final User user = User.getById(dc, sc.getLoggedInUserId()); |
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%> |
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<base:page type="default" > |
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<base:head |
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scripts="~../reggie-2.js,~create_flowcells.js" |
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styles="path.css,~../css/reggie-2.css,~../css/plate.css"> |
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<style> |
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.nondefault |
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{ |
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background: #FFF066; |
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} |
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.nondefault:after |
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{ |
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content: '›'; |
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} |
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.nondefault:before |
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{ |
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content: '‹'; |
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} |
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|
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|
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#numSelected |
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{ |
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font-style: italic; |
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margin-top: 0.25em; |
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margin-left: 1em; |
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} |
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|
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.plate .header |
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{ |
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height: 2em; |
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} |
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|
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.plate .header th.col-0, .plate .header th.col-1 |
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{ |
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border-bottom: 1px solid #A0A0A0; |
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} |
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|
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.well |
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{ |
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height: 2em; |
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max-height: 2em; |
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min-height: 2em; |
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width: 10em; |
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max-width: 10em; |
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min-width: 10em; |
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font-size: 100%; |
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text-align: center; |
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vertical-align: middle; |
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} |
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|
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.plate tbody .lane |
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{ |
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border-right: 1px solid #A0A0A0; |
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width: 3em; |
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} |
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|
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.well.col-1 |
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{ |
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border-left-style: solid; |
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} |
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|
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.hide-fc-1 .col-1 |
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{ |
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display: none; |
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} |
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|
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#select-pool-all |
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{ |
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max-height: 20em; |
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overflow: auto; |
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} |
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|
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#select-pool .menuitem |
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{ |
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padding-left: 16px; |
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} |
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|
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#select-pool div.current |
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{ |
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font-weight: bold; |
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background-image: url('../images/selected.gif'); |
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background-position: 2px 50%; |
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background-repeat: no-repeat; |
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} |
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|
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#select-pool div.default:after |
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{ |
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content: ' (default)'; |
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} |
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|
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#select-pool .menuitem:hover |
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{ |
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padding-left: 14px; |
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background-position: 0px 50%; |
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} |
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|
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</style> |
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</base:head> |
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<base:body> |
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|
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<p:path><p:pathelement |
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title="Reggie" href="<%="../index.jsp?ID="+ID%>" |
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/><p:pathelement title="Create flow cells" |
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/></p:path> |
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|
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<div class="content"> |
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|
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<form name="reggie" id="wizard" class="wizard"> |
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<div id="select-pool" class="menu vertical bg-filled-100" style="width: 15em; z-index: 2; display: none;"> |
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<div id="select-pool-all"></div> |
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</div> |
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|
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<div class="step" id="step-1"> |
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<div class="step-no">1</div> |
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<div class="step-title">Select pools</div> |
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<div class="step-content"> |
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<table class="step-form"> |
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<tr> |
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<td class="prompt">Flow cell type</td> |
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<td class="input"> |
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<select name="preset" id="preset"> |
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<option value="NextSeq" selected>NextSeq |
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<option value="">Custom |
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</select> |
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</td> |
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<td class="status" id="preset.status"></td> |
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<td class="help"> |
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<span id="preset.message" class="message"></span> |
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The selected preset affects number of lanes per flow cell. |
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</td> |
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</tr> |
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<tr> |
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<td class="prompt">Lanes/flow cell</td> |
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<td class="input" id="lanes"> |
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<label><input type="radio" name="num_lanes" id="num_lanes_2" value="2">2</label> |
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<label><input type="radio" name="num_lanes" id="num_lanes_4" value="4" checked>4</label> |
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<label><input type="radio" name="num_lanes" id="num_lanes_8" value="8">8</label> |
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</td> |
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<td class="status" id="lanes.status"></td> |
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<td class="help"> |
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<span id="lanes.message" class="message"></span> |
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Select the number of lanes on each flow cell. |
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</td> |
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</tr> |
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<tr> |
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<td class="prompt">Number of flow cells</td> |
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<td class="input"> |
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<label><input type="radio" name="num_flowcells" id="num_flowcells_1" value="1" checked>1</label> |
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<label><input type="radio" name="num_flowcells" id="num_flowcells_2" value="2">2</label> |
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</td> |
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<td class="status" id="numFlowCells.status"></td> |
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<td class="help"> |
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<span id="numFlowCells.message" class="message"></span> |
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Select if you want to create 1 or 2 flow cells. |
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</td> |
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</tr> |
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<tr class="align-top"> |
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<td class="prompt">Pools</td> |
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<td class="input"> |
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<select name="pools" id="pools" size="6" multiple></select> |
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<div id="numSelected"></div> |
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<base:buttongroup style="margin-top: 0.5em;"> |
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<base:button title="Select manually…" id="btnSelectPools" /> |
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</base:buttongroup> |
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</td> |
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<td class="status" id="pools.status"></td> |
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<td class="help"> |
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<span id="pools.message" class="message"></span> |
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Select the pools that should be used in the flow cells. The list contain pools that has |
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not yet been used on any flow cell. |
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</td> |
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</tr> |
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</table> |
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</div> |
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</div> |
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|
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<div class="step" id="step-2"> |
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<div class="step-no">2</div> |
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<div class="step-title">Flow cell information</div> |
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<div class="step-content"> |
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|
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<table class="step-form"> |
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<tr> |
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<td class="prompt">Sequencing cycles</td> |
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<td class="input"> |
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<table> |
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<tr> |
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<td colspan="3">Read 1</td> |
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<td colspan="3">Index</td> |
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<td colspan="3">Read 2</td> |
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</tr> |
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<tr> |
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<td> |
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<input type="text" class="required" name="read1" id="read1" |
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style="width: 4em;" maxlength="4"> |
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</td> |
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<td class="status" id="read1.status"></td> |
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<td style="width: 2em;"></td> |
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<td> |
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<input type="text" class="required" name="indexRead" id="indexRead" |
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style="width: 4em;" maxlength="4"> |
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</td> |
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<td class="status" id="indexRead.status"></td> |
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<td style="width: 2em;"></td> |
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<td> |
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<input type="text" class="required" name="read2" id="read2" |
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style="width: 4em;" maxlength="4"> |
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</td> |
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<td class="status" id="read2.status"></td> |
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<td style="width: 2em;"></td> |
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</tr> |
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<tr> |
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<td colspan="3" class="help"><span id="read1.message" class="message"></span></td> |
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<td colspan="3" class="help"><span id="indexRead.message" class="message"></span></td> |
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<td colspan="3" class="help"><span id="read2.message" class="message"></span></td> |
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</tr> |
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</table> |
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|
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</td> |
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<td class="status"></td> |
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<td class="help"> |
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Planned number of sequencing cycles. The actual numbers used may be changed in the |
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registration wizard. |
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</td> |
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</tr> |
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<tr> |
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<td class="prompt">Volume to use from pool</td> |
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<td class="input"> |
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<select name="volumeToUseFromPool" id="volumeToUseFromPool" class="required" style="width: 4em;"> |
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<option value="10">10 |
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<option value="20">20 |
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</select> |
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µl |
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</td> |
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<td class="status" id="volumeToUseFromPool.status"></td> |
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<td class="help"> |
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<span id="volumeToUseFromPool.message" class="message"></span> |
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Select the amount to use from each pool. This depends on the molarity |
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1nM = 20µl, 2nM = 10µl. |
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</td> |
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</tr> |
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<tr class="align-top"> |
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<td class="prompt">Flow cell layout</td> |
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<td class="input"> |
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268 |
<table class="plate" id="plate" style="margin-bottom: 1em;"> |
2028 |
30 Sep 13 |
nicklas |
269 |
<thead> |
2020 |
13 Sep 13 |
nicklas |
270 |
<tr class="header"> |
2028 |
30 Sep 13 |
nicklas |
271 |
<th class="lane">Lane</th> |
2020 |
13 Sep 13 |
nicklas |
272 |
<% |
2020 |
13 Sep 13 |
nicklas |
273 |
for (int fcNo = 0; fcNo < 2; fcNo++) |
2020 |
13 Sep 13 |
nicklas |
274 |
{ |
2020 |
13 Sep 13 |
nicklas |
275 |
%> |
2020 |
13 Sep 13 |
nicklas |
276 |
<th class="col-<%=fcNo%>" id="fc.<%=fcNo%>">FlowCell<%=fcNo%></th> |
2020 |
13 Sep 13 |
nicklas |
277 |
<% |
2020 |
13 Sep 13 |
nicklas |
278 |
} |
2020 |
13 Sep 13 |
nicklas |
279 |
%> |
2020 |
13 Sep 13 |
nicklas |
280 |
</tr> |
2028 |
30 Sep 13 |
nicklas |
281 |
</thead> |
2020 |
13 Sep 13 |
nicklas |
282 |
<tbody> |
2020 |
13 Sep 13 |
nicklas |
283 |
<% |
2020 |
13 Sep 13 |
nicklas |
284 |
for (int laneNo = 0; laneNo < 8; laneNo++) |
2020 |
13 Sep 13 |
nicklas |
285 |
{ |
2020 |
13 Sep 13 |
nicklas |
286 |
%> |
2020 |
13 Sep 13 |
nicklas |
287 |
<tr class="row-<%=laneNo%>" id="lane.<%=laneNo%>"> |
2028 |
30 Sep 13 |
nicklas |
288 |
<th class="lane"><%=laneNo+1%></th> |
2020 |
13 Sep 13 |
nicklas |
289 |
<% |
2020 |
13 Sep 13 |
nicklas |
290 |
for (int fcNo = 0; fcNo < 2; fcNo++) |
2020 |
13 Sep 13 |
nicklas |
291 |
{ |
2020 |
13 Sep 13 |
nicklas |
292 |
%> |
2020 |
13 Sep 13 |
nicklas |
293 |
<td class="well col-<%=fcNo%>" id="lane.<%=laneNo%>.<%=fcNo%>" |
2652 |
11 Sep 14 |
nicklas |
294 |
data-fc-no="<%=fcNo%>" data-lane-no="<%=laneNo%>"></td> |
2020 |
13 Sep 13 |
nicklas |
295 |
<% |
2020 |
13 Sep 13 |
nicklas |
296 |
} |
2020 |
13 Sep 13 |
nicklas |
297 |
%> |
2020 |
13 Sep 13 |
nicklas |
298 |
</tr> |
2020 |
13 Sep 13 |
nicklas |
299 |
<% |
2020 |
13 Sep 13 |
nicklas |
300 |
} |
2020 |
13 Sep 13 |
nicklas |
301 |
%> |
2020 |
13 Sep 13 |
nicklas |
302 |
</tbody> |
2020 |
13 Sep 13 |
nicklas |
303 |
</table> |
2020 |
13 Sep 13 |
nicklas |
304 |
|
2020 |
13 Sep 13 |
nicklas |
305 |
</td> |
2020 |
13 Sep 13 |
nicklas |
306 |
<td class="status" id="flowCells.status"></td> |
2652 |
11 Sep 14 |
nicklas |
307 |
<td class="help"> |
2652 |
11 Sep 14 |
nicklas |
308 |
<span id="flowCells.message" class="message"></span> |
2028 |
30 Sep 13 |
nicklas |
309 |
Assign a pool to each flow cell lane. Click on each lane to select a different pool. |
2020 |
13 Sep 13 |
nicklas |
310 |
</td> |
2020 |
13 Sep 13 |
nicklas |
311 |
</tr> |
2045 |
07 Oct 13 |
nicklas |
312 |
<tr valign="top"> |
2045 |
07 Oct 13 |
nicklas |
313 |
<td class="prompt">Comments</td> |
2652 |
11 Sep 14 |
nicklas |
314 |
<td class="input"></td> |
2045 |
07 Oct 13 |
nicklas |
315 |
<td class="status" id="comments.status"></td> |
2652 |
11 Sep 14 |
nicklas |
316 |
<td class="help"> |
2652 |
11 Sep 14 |
nicklas |
317 |
<span id="comments.message" class="message"></span> |
2652 |
11 Sep 14 |
nicklas |
318 |
Comments about the flow cells. |
2652 |
11 Sep 14 |
nicklas |
319 |
</td> |
2045 |
07 Oct 13 |
nicklas |
320 |
</tr> |
2045 |
07 Oct 13 |
nicklas |
321 |
<tbody id="flowcell-comments"> |
2045 |
07 Oct 13 |
nicklas |
322 |
<% |
2045 |
07 Oct 13 |
nicklas |
323 |
for (int fcNo = 0; fcNo < 2; fcNo++) |
2045 |
07 Oct 13 |
nicklas |
324 |
{ |
2045 |
07 Oct 13 |
nicklas |
325 |
%> |
2652 |
11 Sep 14 |
nicklas |
326 |
<tr class="align-top" id="comments.<%=fcNo%>"> |
2045 |
07 Oct 13 |
nicklas |
327 |
<td class="subprompt" id="comments.<%=fcNo%>.name">FlowCell<%=fcNo%></td> |
2652 |
11 Sep 14 |
nicklas |
328 |
<td class="input"> |
2652 |
11 Sep 14 |
nicklas |
329 |
<textarea rows="3" name="comments.<%=fcNo%>"></textarea> |
2652 |
11 Sep 14 |
nicklas |
330 |
</td> |
2045 |
07 Oct 13 |
nicklas |
331 |
<td class="status"></td> |
2045 |
07 Oct 13 |
nicklas |
332 |
<td class="help"></td> |
2045 |
07 Oct 13 |
nicklas |
333 |
</tr> |
2045 |
07 Oct 13 |
nicklas |
334 |
<% |
2045 |
07 Oct 13 |
nicklas |
335 |
} |
2045 |
07 Oct 13 |
nicklas |
336 |
%> |
2045 |
07 Oct 13 |
nicklas |
337 |
</tbody> |
2020 |
13 Sep 13 |
nicklas |
338 |
</table> |
2652 |
11 Sep 14 |
nicklas |
339 |
</div> |
2020 |
13 Sep 13 |
nicklas |
340 |
</div> |
2020 |
13 Sep 13 |
nicklas |
341 |
|
2652 |
11 Sep 14 |
nicklas |
342 |
<div id="wizard-status"></div> |
2020 |
13 Sep 13 |
nicklas |
343 |
|
2652 |
11 Sep 14 |
nicklas |
344 |
<table class="navigation" id="navigation"> |
2652 |
11 Sep 14 |
nicklas |
345 |
<tr> |
2652 |
11 Sep 14 |
nicklas |
346 |
<td><base:button id="gocancel" title="Cancel" /></td> |
2652 |
11 Sep 14 |
nicklas |
347 |
<td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td> |
2652 |
11 Sep 14 |
nicklas |
348 |
<td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>" /></td> |
2652 |
11 Sep 14 |
nicklas |
349 |
<td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td> |
2652 |
11 Sep 14 |
nicklas |
350 |
<td id="gonext-message" class="message"></td> |
2652 |
11 Sep 14 |
nicklas |
351 |
</tr> |
2020 |
13 Sep 13 |
nicklas |
352 |
</table> |
2020 |
13 Sep 13 |
nicklas |
353 |
|
2020 |
13 Sep 13 |
nicklas |
354 |
</form> |
2020 |
13 Sep 13 |
nicklas |
355 |
</div> |
2020 |
13 Sep 13 |
nicklas |
356 |
|
2020 |
13 Sep 13 |
nicklas |
357 |
</base:body> |
2020 |
13 Sep 13 |
nicklas |
358 |
</base:page> |
2020 |
13 Sep 13 |
nicklas |
359 |
<% |
2020 |
13 Sep 13 |
nicklas |
360 |
} |
2020 |
13 Sep 13 |
nicklas |
361 |
finally |
2020 |
13 Sep 13 |
nicklas |
362 |
{ |
2020 |
13 Sep 13 |
nicklas |
363 |
if (dc != null) dc.close(); |
2020 |
13 Sep 13 |
nicklas |
364 |
} |
2020 |
13 Sep 13 |
nicklas |
365 |
%> |