auspice
Version:
Web app for visualizing pathogen evolution
90 lines (83 loc) • 14.9 kB
HTML
<html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Overview · Auspice</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="<h1><a class="anchor" aria-hidden="true" id="auspice-an-open-source-interactive-tool-for-visualising-phylogenomic-data"></a><a href="#auspice-an-open-source-interactive-tool-for-visualising-phylogenomic-data" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Auspice: an open-source interactive tool for visualising phylogenomic data</h1>
"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Overview · Auspice"/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="<h1><a class="anchor" aria-hidden="true" id="auspice-an-open-source-interactive-tool-for-visualising-phylogenomic-data"></a><a href="#auspice-an-open-source-interactive-tool-for-visualising-phylogenomic-data" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Auspice: an open-source interactive tool for visualising phylogenomic data</h1>
"/><meta property="og:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><meta name="twitter:card" content="summary"/><meta name="twitter:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><link rel="shortcut icon" href="/auspice/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/solarized-dark.min.css"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><link rel="stylesheet" href="/auspice/css/main.css"/><script src="/auspice/js/codetabs.js"></script></head><body class="sideNavVisible separateOnPageNav"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/auspice/"><img class="logo" src="/auspice/img/logo-light.svg" alt="Auspice"/><h2 class="headerTitleWithLogo">Auspice</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive siteNavItemActive"><a href="/auspice/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="container docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><i></i></div><h2><i>›</i><span>Introduction</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">Introduction</h3><ul class=""><li class="navListItem navListItemActive"><a class="navItem" href="/auspice/overview">Overview</a></li><li class="navListItem"><a class="navItem" href="/auspice/installation">Installing auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/inputs">Input file formats</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Customisations</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/customisations/introduction">Extending Auspice</a></li><div class="navGroup subNavGroup"><h4 class="navGroupSubcategoryTitle">Customising the Client</h4><ul><li class="navListItem"><a class="navItem" href="/auspice/customisations/client/componentInterfaces">Injecting custom components</a></li><li class="navListItem"><a class="navItem" href="/auspice/customisations/client/sidebarTheme">Sidebar theming</a></li></ul></div><div class="navGroup subNavGroup"><h4 class="navGroupSubcategoryTitle">Customising the Server</h4><ul><li class="navListItem"><a class="navItem" href="/auspice/customisations/server/charonAPI">Auspice Server API</a></li><li class="navListItem"><a class="navItem" href="/auspice/customisations/server/serverless">Deploying auspice without a server</a></li></ul></div><li class="navListItem"><a class="navItem" href="/auspice/customisations/authentication">Authentication</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Tutorial</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/tutorial/overview">Auspice functionality</a></li></ul></div></div></section></div><script>
var coll = document.getElementsByClassName('collapsible');
var checkActiveCategory = true;
for (var i = 0; i < coll.length; i++) {
var links = coll[i].nextElementSibling.getElementsByTagName('*');
if (checkActiveCategory){
for (var j = 0; j < links.length; j++) {
if (links[j].classList.contains('navListItemActive')){
coll[i].nextElementSibling.classList.toggle('hide');
coll[i].childNodes[1].classList.toggle('rotate');
checkActiveCategory = false;
break;
}
}
}
coll[i].addEventListener('click', function() {
var arrow = this.childNodes[1];
arrow.classList.toggle('rotate');
var content = this.nextElementSibling;
content.classList.toggle('hide');
});
}
document.addEventListener('DOMContentLoaded', function() {
createToggler('#navToggler', '#docsNav', 'docsSliderActive');
createToggler('#tocToggler', 'body', 'tocActive');
const headings = document.querySelector('.toc-headings');
headings && headings.addEventListener('click', function(event) {
if (event.target.tagName === 'A') {
document.body.classList.remove('tocActive');
}
}, false);
function createToggler(togglerSelector, targetSelector, className) {
var toggler = document.querySelector(togglerSelector);
var target = document.querySelector(targetSelector);
if (!toggler) {
return;
}
toggler.onclick = function(event) {
event.preventDefault();
target.classList.toggle(className);
};
}
});
</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"></header><article><div><span><h1><a class="anchor" aria-hidden="true" id="auspice-an-open-source-interactive-tool-for-visualising-phylogenomic-data"></a><a href="#auspice-an-open-source-interactive-tool-for-visualising-phylogenomic-data" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Auspice: an open-source interactive tool for visualising phylogenomic data</h1>
<blockquote>
<p>Please not that these docs describe the newest version of auspice (versions 1.35+).
The new APIs are in flux and we expect they will change before version 2.0 is released.
If you use these versions of auspice we would love to hear about your experiences! (Contact links at the bottom of the page).</p>
</blockquote>
<p>Auspice is an interactive visualisation platform for phylogenomic and other other datasets related to evolution.
It was originally designed for nextstrain.org, which aims to aims to provide a continually-updated view of publicly available pathogen genome data.
Auspice can be used locally to view datasets, or deployed to server- or serverless-websites.
It allows easy customisation of aesthetics and functionality, and powers the visualisations on <a href="https://nextstrain.org">nextstrain.org</a>.</p>
<ul>
<li><a href="/auspice/tutorial/overview">overview of functionality</a></li>
<li><a href="/auspice/installation">installation instructions</a></li>
<li><a href="/auspice/customisations/introduction">customising your auspice build</a></li>
<li><a href="/auspice/releasing">releasing</a></li>
<li><a href="/auspice/inputs">data formats</a>.</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="running-auspice-locally"></a><a href="#running-auspice-locally" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Running Auspice Locally</h2>
<p>Auspice by itself is a visualisation tool for local datasets.
It runs a local server to deliver the files the the visualisation to <a href="http://localhost:4000">localhost:4000</a>.
After <a href="/auspice/installation">installing</a>, you can access datasets in the current directory by running</p>
<pre><code class="hljs css language-bash">auspice view
</code></pre>
<p>Please see <code>auspice view -h</code> for all available options.</p>
<p>The provided server (<code>node auspice.js view</code> or <code>auspice view</code>) could be used as a production server, perhaps with custom handlers provided (see <a href="/auspice/customisations/server/charonAPI">these docs</a>).</p>
<h2><a class="anchor" aria-hidden="true" id="building-auspice-locally"></a><a href="#building-auspice-locally" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Building Auspice Locally</h2>
<blockquote>
<p>Building auspice shouldn't be necessary if you have installed it as a npm dependency.
Building auspice is necessary if you have installed it from source, or if you would like to extend it with your customisations.</p>
</blockquote>
<p>From the auspice source direcory:
<code>node auspice.js build --verbose</code></p>
<p>If auspice is installed globally:
<code>auspice build --verbose</code></p>
<h2><a class="anchor" aria-hidden="true" id="license-and-copyright"></a><a href="#license-and-copyright" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>License and copyright</h2>
<p>Copyright © 2014-2018 Trevor Bedford and Richard Neher.</p>
<p>Source code to Nextstrain is made available under the terms of the <a href="LICENSE.txt">GNU Affero General Public License</a> (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 1/1/2019</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/installation"><span>Installing auspice</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#running-auspice-locally">Running Auspice Locally</a></li><li><a href="#building-auspice-locally">Building Auspice Locally</a></li><li><a href="#license-and-copyright">License and copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><img src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></div><div><h5>Docs</h5><a href="/auspice/">Splash Page</a><a href="/auspice/overview">Overview</a></div><div><h5>Links</h5><a href="https://github.com/nextstrain/auspice">GitHub</a><a href="https://www.npmjs.com/package/auspice">NPM</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher & Trevor Bedford</section></footer></div></body></html>