Install Node. Download the source code from our github repo.
- Enter the
frontenddirectory npm install(trynpm install --forceif getting error)npm start
Your local browser is available at localhost:3000/browser.
Enter the backend directory. npm install, and then npm run setup. MongoDB must be installed and running.
Please check all the documentation at https://eg.rtfd.io/.
If you found an issue, please report it along with any relevant details to reproduce it. Thanks.
- The issue tracker.
- The Google groups.
- The Slack channel.
Yes please! Feature requests / pull requests are welcome.
<!-- CSS -->
<link rel="stylesheet" href="https://unpkg.com/epgg@latest/umd/epgg.css" />
<!-- JS -->
<script src="https://target.wustl.edu/dli/eg/epgg.js"></script>
<script>
renderBrowserInElement(contents, container);
</script>Create a HTML page with following contents: (the example shows how to embed a mouse browser with 2 bigWig tracks from ENCODE data portal and 1 from our own server)
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
<meta name="theme-color" content="#000000" />
<title>WashU Epigenome Browser</title>
<link
rel="stylesheet"
href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css"
integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm"
crossorigin="anonymous"
/>
<script src="https://aframe.io/releases/0.8.0/aframe.min.js"></script>
<script
src="https://code.jquery.com/jquery-3.2.1.slim.min.js"
integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN"
crossorigin="anonymous"
></script>
<script
src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js"
integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q"
crossorigin="anonymous"
></script>
<script
src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"
integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl"
crossorigin="anonymous"
></script>
<script crossorigin src="https://unpkg.com/react@16/umd/react.development.js"></script>
<script crossorigin src="https://unpkg.com/react-dom@16/umd/react-dom.development.js"></script>
<script crossorigin src="https://cdn.plot.ly/plotly-cartesian-latest.min.js"></script>
<script crossorigin src="https://unpkg.com/[email protected]/dist/create-plotly-component.min.js"></script>
<!-- the browser script and styles -->
<script src="https://unpkg.com/[email protected]/umd/epgg.js"></script>
<link rel="stylesheet" href="https://unpkg.com/[email protected]/umd/epgg.css" />
</head>
<body>
<noscript> You need to enable JavaScript to run this app. </noscript>
<h1>Embedding test</h1>
<div id="embed" style="width: 1000px"></div>
<h2>some other headings</h2>
<script>
const container = document.getElementById("embed");
const contents = {
genomeName: "mm10",
displayRegion: "chr5:51997494-52853744",
trackLegendWidth: 120,
isShowingNavigator: true,
tracks: [
{
type: "geneannotation",
name: "refGene",
genome: "mm10",
},
{
type: "geneannotation",
name: "gencodeM19Basic",
genome: "mm10",
},
{
type: "ruler",
name: "Ruler",
},
{
type: "bigWig",
name: "ChipSeq of Heart",
url: "https://www.encodeproject.org/files/ENCFF641FBI/@@download/ENCFF641FBI.bigWig",
options: { color: "red" },
metadata: { Sample: "Heart" },
},
{
type: "bigWig",
name: "ChipSeq of Liver",
url: "https://www.encodeproject.org/files/ENCFF555LBI/@@download/ENCFF555LBI.bigWig",
options: { color: "blue" },
metadata: { Sample: "Liver" },
},
{
type: "bedGraph",
name: "test",
url: "https://wangftp.wustl.edu/~rsears/Stuart_Little/RNA_083018/WangT_7176-5_ALDH_STRANDED_Signal.Unique.combo.out.bg.gz",
},
],
metadataTerms: ["Sample"],
regionSets: [],
regionSetViewIndex: -1,
};
renderBrowserInElement(contents, container);
</script>
</body>
</html>The key API is the function renderBrowserInElement, it accepts the contents array as first argument,
and container as second argument which is a DOM element.