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index.php
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<?php
$REQUIRED_BINARIES = array('tabix', 'samtools', 'bigBedInfo', 'bigBedSearch', 'bigBedSummary' ,'bigBedToBed',
'bigWigSummary', 'bigWigInfo', 'twoBitToFa');
include('lib/setup.php');
$MISSING_BINARIES = find_and_link_binaries($REQUIRED_BINARIES);
$genomes = file_get_contents(file_exists('genomes.json') ? 'genomes.json' : 'genomes.dist.json');
$genomes = json_decode($genomes, TRUE);
redirect_to_default_db($genomes);
?><!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
<meta name="apple-mobile-web-app-status-bar-style" content="black">
<meta name="keywords" content="ChromoZoom, genome, genome browser, human genome, yeast genome, html5" />
<meta name="description" content="ChromoZoom is the most interactive, easy-to-use online genome browser for both curated and custom data." />
<title>ChromoZoom, the interactive genome browser</title>
<script src="build/chromozoom.js"></script>
<link rel="stylesheet" type="text/css" href="css/syngrey/jquery-ui-1.8.6.custom.css" />
<link rel="stylesheet" type="text/css" href="css/style.css" />
<!--[if lte IE 11]><link rel="stylesheet" type="text/css" href="css/iehax.css" /><![endif]-->
</head>
<body>
<div id="wrapper">
<!-- Navbar area (top light grey bar) -->
<div id="navbar" class="shadow">
<div id="controls">
<div class="control-seg">
<a class="smaller" id="tracks">
<span>show<span class="even-less"> tracks</span><span class="less">…</span></span>
</a>
<div id="track-picker" class="ui-widget ui-widget-content ui-corner-bottom shadow picker"></div>
</div>
<div class="control-seg">
<a class="smaller" id="custom-tracks">
<span>custom<span class="even-less"> tracks</span><span class="less">…</span></span>
</a>
<div id="custom-picker" class="ui-widget ui-widget-content ui-corner-bottom shadow picker">
<div class="form-line"><div class="spinner"></div><strong>add file</strong><label></label></div>
<div class="help-line">
<a target="_blank" href="http://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a>,
<a target="_blank" href="http://genome.ucsc.edu/goldenPath/help/bedgraph.html">bedGraph</a>,
and
<a target="_blank" href="http://genome.ucsc.edu/goldenPath/help/wiggle.html">WIG</a>
files can be loaded from your hard disk.
</div>
<div class="form-line"><div class="spinner"></div><strong class="fullwidth">paste URLs or data</strong>
<label>
<textarea class="paste" name="customPaste" rows="1" cols="30"></textarea>
<input type="button" name="customPasteAdd" value="add"/>
</label>
</div>
<div class="help-line">
<a target="_blank" href="http://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a>,
<a target="_blank" href="http://genome.ucsc.edu/goldenPath/help/bedgraph.html">bedGraph</a>,
<a target="_blank" href="http://genome.ucsc.edu/goldenPath/help/wiggle.html">WIG</a>,
<a target="_blank" href="http://samtools.github.io/hts-specs/">BAM</a>,
<a target="_blank" href="http://genome.ucsc.edu/goldenPath/help/bigBed.html">bigBed</a>,
<a target="_blank" href="http://genome.ucsc.edu/goldenPath/help/bigWig.html">bigWig</a>,
and <a target="_blank" href="http://genome.ucsc.edu/goldenPath/help/vcf.html">VCFTabix</a><br/>
are currently supported, using the UCSC specifications.<br/>
For more details, please see the <a target="_blank" href="docs/#custom-tracks">User Guide.</a>
</div>
</div>
</div>
<div class="control-seg">
<div id="loc-picker" class="ui-widget ui-widget-content ui-corner-bottom shadow"></div>
<input type="text" id="loc" name="loc" placeholder="location, gene, or keyword"/>
<a class="smaller" id="jump">go</a>
</div>
<div class="control-seg">
<label id="zoom-label" for="zoom">zoom</label>
<a id="zoom-out">–</a>
</div>
<div class="control-seg">
<div id="zoom-cont" class="ui-widget ui-widget-content ui-corner-all"><div id="zoom"></div></div>
</div>
<div class="control-seg">
<a id="zoom-in">+</a>
</div>
<div class="control-seg last">
<div id="line-mode">
<input type="radio" id="line-mode-multi" name="linemode" value="multi" />
<label id="for-line-mode-multi" for="line-mode-multi">
<img src="css/multi-line.png" alt="multi" /><span class="wide"> multi</span>
</label>
<input type="radio" id="line-mode-single" name="linemode" checked="checked" value="single" />
<label id="for-line-mode-single" for="line-mode-single">
<img src="css/single-line.png" alt="single" /><span class="wide"> single</span>
</label>
</div>
<a href="#" id="linking">
<img src="css/link.svg" alt="link" class="zondicon"/><span class="wide"> links</span>
</a>
<div id="link-picker" class="ui-widget ui-widget-content ui-corner-bottom shadow picker">
<div class="form-line">
<strong>link to this view: </strong>
<label><input name="linkhere" readonly class="url" /><br/><a class="copy-btn">copy to clipboard</a></label>
</div>
<div class="form-line">
<strong>open region in: </strong><label><a name="ucsc" href="#" target="_blank">the UCSC Genome Browser</a></label>
</div>
</div>
<a id="warnings"><img src="css/alert-circled.svg" alt="alert" class="zondicon"/></a>
</div>
</div>
</div>
<!-- Browser area (textured dark grey area containing brower lines and tracks) -->
<div id="browser">
<div id="overlay" class="ui-widget-overlay"></div>
<div id="overlay-message"></div>
</div>
<!-- Footer area (black area at bottom of viewport with links and genome picker) -->
<div id="footerbar" class="shadow">
<div id="logo">
<p class="slogan">The genome browser that lets you <em>fly</em></p>
</div>
<div id="footerlinks">
<p>
<a href="#quickstart">Getting started</a> ·
<a href="docs/" target="_blank">User guide</a> ·
<a href="#about">About</a> ·
<a href="http://chromozoom.uservoice.com" id="feedback-link">Feedback</a> ·
<a href="http://github.com/rothlab/chromozoom" target="_blank">Source code</a>
</p>
</div>
<div id="genome">
<a id="change-genome">∧</a>
<h1 class="title"></h1>
<h2 class="description"></h2>
<div id="genome-picker" class="ui-widget ui-widget-content ui-corner-top shadow picker picker-dark"></div>
</div>
<a href="#old-msie" style="display: none"></a>
<a href="#binaries-warning" style="display: none"></a>
</div>
<!-- UI for all of the dialogs used by chromozoom -->
<div id="dialogs">
<div class="ui-dialog ui-widget ui-widget-content ui-corner-all big-shadow" tabindex="-1" role="dialog" aria-labelledby="ui-dialog-title-intro-dialog" id="intro-dialog-cont">
<div id="intro-dialog" class="ui-dialog-content ui-widget-content">
<h2 id="quickstart">Welcome! Here's how to get around the genome:</h2>
<div class="panel-three">
<div id="intro-panel-1" class="intro-panel"></div>
<div class="desc"><strong class="num">1.</strong> To <strong>move</strong>,
drag and throw the track area</div>
</div>
<div class="panel-three">
<div id="intro-panel-2" class="intro-panel"></div>
<div class="desc"><strong class="num">2.</strong> <strong>Zoom</strong> with two fingers or mousewheel</div>
</div>
<div class="panel-three last">
<div id="intro-panel-3" class="intro-panel"></div>
<div class="desc"><strong class="num">3.</strong> <strong>Resize</strong> the track label to unpack elements</div>
</div>
<p>
<strong class="num">4.</strong> <strong>Add more tracks</strong> using the
<a class="ui-button smaller ui-widget ui-state-default ui-corner-all ui-button-text-only ui-state-fake">show tracks...</a>
button in the top left corner.
</p>
</div>
<div class="ui-dialog-buttonpane ui-widget-content ui-helper-clearfix">
<button type="button" class="ui-state-default ui-corner-all loading glowing">Alright, I got this!</button>
<a class="tell-me-more" href="docs/" target="_blank">What else can I do?</a>
</div>
</div>
<div class="ui-dialog ui-widget ui-widget-content ui-corner-all big-shadow" tabindex="-1" role="dialog" aria-labelledby="ui-dialog-title-intro-dialog" id="about-dialog-cont">
<div id="about-dialog" class="ui-dialog-content ui-widget-content">
<h2 id="about">About ChromoZoom v2</h2>
<p>
ChromoZoom was written by Theodore Pak, Miha Skalic, and Adrian Pasculescu with the support of Dr. Frederick "Fritz" Roth and Dr. Andrew Kasarskis from 2012-<?= date('Y'); ?>. To cite ChromoZoom, please use <a href="http://bioinformatics.oxfordjournals.org/content/early/2012/12/06/bioinformatics.bts695.short">our article in <em>Bioinformatics</em></a>.
</p>
<p>
Takafumi Yamaguchi, Joseph Mellor, members of the <a href="http://llama.mshri.on.ca">Roth Laboratory</a>, and students in the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534145/">Practical Analysis of Your Personal Genome class</a> at <a href="http://icahn.mssm.edu/research/genomics">Mount Sinai</a> provided valuable design input and sample data.
</p>
<p>
ChromoZoom v2 would not have been possible without the following open-source programs and libraries:
<ul>
<li><a href="http://genome.ucsc.edu">UCSC Genome Browser</a> and
<a href="http://www.htslib.org/">samtools/htslib</a></li>
<li><a href="http://www.ruby-lang.org">Ruby</a> and <a href="http://rake.rubyforge.org/">Rake</a>;
<a href="https://nodejs.org/">NodeJS</a>, <a href="http://browserify.org/">browserify</a>, and
<a href="https://github.com/substack/watchify">watchify</a></li>
<li><a href="http://documentcloud.github.com/underscore/">underscore.js</a>,
<a href="http://jquery.com">jQuery</a>, <a href="http://jqueryui.com">jQuery UI</a>, and the
<a href="https://greensock.com/">Greensock Animation Platform</a></li>
<li>The <a href="http://httpd.apache.org/">Apache HTTP Server</a>,
<a href="http://php.net">PHP</a>,
and <a href="http://curl.haxx.se">cURL</a></li>
<li>The <a href="http://code.drewwilson.com/entry/tiptip-jquery-plugin">TipTip</a>,
<a href="http://github.com/kpozin/jquery-nodom">NoDOM</a>,
<a href="https://github.com/jeresig/jquery.hotkeys">Hotkeys</a>,
and <a href="http://github.com/furf/jquery-ui-touch-punch">touch-punch</a> extensions for jQuery</li>
<li>JavaScript by <a href="http://github.com/shinout">Shin Suzuki</a></li>
</ul>
</p>
</div>
<div class="ui-dialog-buttonpane ui-widget-content ui-helper-clearfix">
<button type="button" class="ui-state-default ui-corner-all loading">Close</button>
</div>
</div>
<div class="ui-dialog ui-widget ui-widget-content ui-corner-all big-shadow" id="custom-dialog-cont">
<div id="custom-dialog" class="ui-dialog-content ui-widget-content">
<h2 class="custom-name"></h2>
<h3><span class="custom-format"></span> format; <span class="custom-desc"></span> </h3>
<div class="form-line">
<label>color:</label>
<div class="inputs"><input type="text" name="color" value="0,0,0" class="color mono" /></div>
</div>
<div class="custom-opts-form bam">
<div class="form-line">
<label>view as pairs:</label>
<div class="inputs"><input type="checkbox" class="chk" name="viewAsPairs" value="1" /></div>
</div>
<div class="form-line">
<label>convert chrN ↔ N:</label>
<div class="inputs">
<select name="convertChrScheme">
<option value="auto">automatic</option>
<option value="ensembl_ucsc">Ensembl BAM ↔ UCSC genome</option>
<option value="ucsc_ensembl">UCSC BAM ↔ Ensembl genome</option>
<option value="never">disable</option>
</select>
</div>
</div>
</div>
<div class="custom-opts-form vcftabix">
<div class="form-line">
<label>convert chrN ↔ N:</label>
<div class="inputs">
<select name="convertChrScheme">
<option value="auto">automatic</option>
<option value="ensembl_ucsc">Ensembl BAM ↔ UCSC genome</option>
<option value="ucsc_ensembl">UCSC BAM ↔ Ensembl genome</option>
<option value="never">disable</option>
</select>
</div>
</div>
</div>
<div class="custom-opts-form bed bigbed">
<div class="form-line">
<label>alt color:</label>
<div class="inputs">
<input type="checkbox" class="chk enabler" name="colorByStrandOn" value="1" />
<input type="text" name="colorByStrand" value="0,0,0" class="color mono" />
<div class="input-note">This color is used for features on the – (minus) strand</div>
</div>
</div>
<div class="form-line">
<label>shade by score:</label>
<div class="inputs"><input type="checkbox" class="chk" name="useScore" value="1" /></div>
</div>
<div class="form-line">
<label>color by column 9:</label>
<div class="inputs"><input type="checkbox" class="chk" name="itemRgb" value="1" /></div>
</div>
<div class="form-line">
<label>item url format:</label>
<div class="inputs">
<input type="text" name="url" value="" class="full-length" />
<div class="input-note">Instances of $$ will be replaced with the feature name</div>
</div>
</div>
</div>
<div class="custom-opts-form wiggle_0 bigwig bedgraph">
<div class="form-line">
<label>alt color:</label>
<div class="inputs">
<input type="checkbox" class="chk enabler" name="altColorOn" value="1" />
<input type="text" name="altColor" value="128,128,128" class="color mono" />
<div class="input-note">This color is used for values below 0</div>
</div>
</div>
<div class="form-line">
<label>Y axis range:</label>
<div class="inputs">
<input type="checkbox" class="chk enabler" name="autoScale" value="1" />
<input type="text" name="viewLimitsMin" class="sm" value="0" />
<div class="range-slider view-limits"></div>
<input type="text" name="viewLimitsMax" class="sm" value="100" />
</div>
</div>
<div class="form-line">
<label>Y axis line:</label>
<div class="inputs">
<input type="checkbox" class="chk enabler" name="yLineOnOff" value="1" />
<input type="text" name="yLineMark" class="sm" />
</div>
</div>
<div class="form-line">
<label>graph type:</label>
<div class="inputs">
<select name="graphType"><option>bar</option><option>points</option></select>
</div>
</div>
<div class="form-line">
<label>windowing func:</label>
<div class="inputs">
<select name="windowingFunction">
<option>maximum</option><option>mean</option><option>minimum</option>
</select>
</div>
</div>
<div class="form-line">
<label>restrict height:</label>
<div class="inputs">
<input type="checkbox" class="chk enabler" name="maxHeightPixelsOn" value="1" />
<input type="text" name="maxHeightPixelsMin" class="sm" value="11" />
<div class="range-slider max-height-pixels"></div>
<input type="text" name="maxHeightPixelsMax" class="sm" value="200" />
</div>
</div>
</div>
</div>
<div class="ui-dialog-buttonpane ui-widget-content ui-helper-clearfix">
<button type="button" class="ui-state-red delete ui-corner-all left ui-priority-secondary dont-close show" name="delete">Remove this track</button>
<div class="delete-confirm hidden left">
<label>Are you sure?
<button type="button" class="ui-state-red delete ui-corner-all ui-priority-secondary" name="really_delete">Yes, remove it</button>
</label>
</div>
<button type="button" class="ui-state-default ui-corner-all right" name="save">Save</button>
<button type="button" class="ui-state-default ui-corner-all right ui-priority-secondary">Cancel</button>
</div>
</div>
<div class="ui-dialog ui-widget ui-widget-content ui-corner-all big-shadow" id="genomes-dialog-cont">
<div id="genomes-dialog" class="ui-dialog-content ui-widget-content">
<h2>Load another genome or sequence</h2>
<div class="tabs">
<ul>
<li><a href="#search-dbs-tab">From a database</a></li>
<li><a href="#open-file-url-tab">Open file or URL</a></li>
<li><a href="#chrom-sizes-tab">Specify contig sizes</a></li>
</ul>
<div id="search-dbs-tab">
<div class="col">
<div class="search-bar">
<input type="search" name="filterGenomes" value="" class="search full-width"
placeholder="Search by keyword or accession" />
<span class="search-icon" />
</div>
<ul class="genome-list choices loading">
</ul>
</div>
<div class="col second-col">
<label class="source-list-title">Databases</label>
<ul class="source-list choices">
<li class="choice">
<label class="clickable ucsc">
<input type="checkbox" checked name="source" value="ucsc"/>
<span class="source-tag">UCSC</span>
</label>
</li>
<li class="choice">
<label class="clickable genbank">
<input type="checkbox" checked name="source" value="genbank"/>
<span class="source-tag">GenBank</span><span class="secondary">(use the search box)</span>
</label>
</li>
<li class="choice add-choice">
<label>
<button class="ui-state-default ui-corner-all loading">Add IGB Quickload site</button>
</label>
</li>
</ul>
<div class="limit">
Fetch
<select name="limit">
<option>1000</option>
<option selected="selected">5000</option>
<option>10000</option>
<option>20000</option>
</select>
largest contigs
</div>
</div>
</div>
<div id="open-file-url-tab">
<div class="help-line">
<a target="_blank" href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html">GenBank</a> and
<a target="_blank" href="http://en.wikipedia.org/wiki/FASTA_format">FASTA</a>
files are supported; EMBL is coming soon.
</div>
<div class="form-line">
<div class="spinner"></div><strong>add file</strong><label></label>
<div class="help-line indented">
Files are read locally, not sent to the server.
</div>
</div>
<div class="form-line"><div class="spinner"></div>
<strong class="fullwidth">paste URL or data</strong>
<textarea class="paste" name="customGenomePaste" rows="3" cols="30"></textarea>
</div>
</div>
<div id="chrom-sizes-tab">
<p>One contig name per line, followed by spaces or tab, then the size in bp.</p>
<textarea class="placeholder" name="chromsizes" rows="7" cols="80">chr1 1000000
chr2 350000
chr3 2000000</textarea>
<label>genome name (optional):</label>
<input type="text" name="name" value="custom" class="full-length" />
</div>
</div>
</div>
<div class="ui-dialog-buttonpane ui-widget-content ui-helper-clearfix">
<div class="loading-msg type-more"><img src="css/loading-sm.gif" alt="loading"/><span> Keep typing to search GenBank…</span></div>
<div class="loading-msg contigs-loading"><img src="css/loading-sm.gif" alt="loading"/><span> Fetching contigs…</span></div>
<div class="loading-msg genbank-loading"><img src="css/loading-sm.gif" alt="loading"/><span> Searching GenBank…</span></div>
<div class="ui-state-error ui-corner-all">
<span class="ui-icon ui-icon-alert" style="float: left; margin-right: .3em;"></span>
<span class="contig-load-error">
<strong>Error:</strong> Could not load this genome, sorry!
</span>
<span class="skipped-warning">
<strong>Warning:</strong>
<span class="skipped-num"></span> additional contigs not fetched
</span>
</div>
<button type="button" class="ui-state-default ui-corner-all right" name="save">Load</button>
<button type="button" class="ui-state-default ui-corner-all right ui-priority-secondary">Cancel</button>
</div>
</div>
<!--[if lte IE 11]>
<div class="ui-dialog ui-widget ui-widget-content ui-corner-all big-shadow" tabindex="-1" role="dialog" aria-labelledby="ui-dialog-title-intro-dialog" id="old-msie-dialog-cont">
<div id="old-msie-dialog" class="ui-dialog-content ui-widget-content">
<div id="old-msie-icon"></div>
<h2 id="old-msie">Old browser alert!</h2>
<p>
We've detected you're using an older version of Internet Explorer.
ChromoZoom runs well only on Internet Explorer <strong>11</strong>.
</p>
<p>
On Windows 7 or later, you can run Windows Update to upgrade Internet Explorer.
</p>
<p>
If you are using an older version of Windows, we suggest that you try
<a href="http://getfirefox.com">Mozilla Firefox</a> or <a href="http://www.google.com/chrome">Google Chrome</a>,
both of which are free and supported by ChromoZoom.
</p>
</div>
<div class="ui-dialog-buttonpane ui-widget-content ui-helper-clearfix">
<button type="button" class="ui-state-default ui-corner-all loading">Proceed anyway</button>
</div>
</div>
<![endif]-->
<?php if (count($MISSING_BINARIES) > 0): ?>
<div class="ui-dialog ui-widget ui-widget-content ui-corner-all big-shadow" tabindex="-1" role="dialog" id="binaries-warning-dialog-cont">
<div id="binaries-warning-dialog" class="ui-dialog-content ui-widget-content">
<h2 id="binaries-warning">Installing extra binaries</h2>
<p>
In order for certain features of custom tracks to work, you will need to install the following
binaries on PATH for the account that your webserver runs under:
</p>
<ul>
<?php foreach ($MISSING_BINARIES as $bin): ?>
<li><?php echo $bin; ?></li>
<?php endforeach; ?>
</ul>
<p>Visit the <a href="http://www.htslib.org/download/">HTSLib</a>,
<a href="https://github.com/powerpak/bigBedSearch">bigBedSearch</a>,
and <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">Jim Kent big* tools</a> sites
for download links and installation instructions.
</p>
</div>
<div class="ui-dialog-buttonpane ui-widget-content ui-helper-clearfix">
<button type="button" class="ui-state-default ui-corner-all loading">Proceed anyway</button>
</div>
</div>
<?php endif; ?>
<div class="ui-dialog ui-widget ui-widget-content ui-corner-all big-shadow" tabindex="-1" role="dialog" aria-labelledby="ui-dialog-title-intro-dialog" id="warnings-dialog-cont">
<div id="warnings-dialog" class="ui-dialog-content ui-widget-content">
<div class="intro"><img src="css/alert-circled.svg" alt="alert" class="zondicon"/>
Errors were encountered while loading data</div>
<div class="messages-fade"></div>
<div class="messages"><ol></ol></div>
</div>
<div class="ui-dialog-buttonpane ui-widget-content ui-helper-clearfix">
<button type="button" class="ui-state-default ui-corner-all right ui-priority-secondary">Close</button>
</div>
</div>
</div>
</div>
<script type="text/javascript">
$(function() {
var genomes = <?php echo json_encode($genomes); ?>;
var options = CustomGenomes.blank().options({width: window.innerWidth});
$("#browser").genobrowser($.extend(options, {genomes: genomes}));
});
</script>
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