auspice
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Web app for visualizing pathogen evolution
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Extending Auspice</h1></header><article><div><span><p>It's possible to "extend" auspice and change the aesthetics and/or functionality.
This allows custom builds of auspice each with their own appearence.
<a href="https://nextstrain.org">nextstrain.org</a> is one such custom build.</p>
<h2><a class="anchor" aria-hidden="true" id="developing-and-building-auspice-with-extensions"></a><a href="#developing-and-building-auspice-with-extensions" 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>Developing and building auspice with extensions.</h2>
<p>Auspice has two forms of extensions:</p>
<h3><a class="anchor" aria-hidden="true" id="client-extensions"></a><a href="#client-extensions" 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>Client extensions</h3>
<p>Customising the appearence and functionality of the client is achieved through code injection at build time.
The available customisations are accessed through a <code><clientConfig></code> JSON with the following properties:</p>
<ul>
<li>"splashComponent" -- see <a href="/auspice/customisations/client/componentInterfaces">custom components</a></li>
<li>"navbarComponent" -- see <a href="/auspice/customisations/client/componentInterfaces">custom components</a></li>
<li>"browserTitle" -- the page title (i.e. the name in the tab of the browser window)</li>
<li>"sidebarTheme" -- see <a href="/auspice/customisations/client/sidebarTheme">visual themes</a></li>
<li>"entryPage" -- not yet documented</li>
<li>"hardcodedDataPaths" -- not yet documented, see <a href="/auspice/customisations/server/charonAPI">these docs</a>.</li>
</ul>
<h3><a class="anchor" aria-hidden="true" id="server-extensions"></a><a href="#server-extensions" 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>Server extensions</h3>
<p>The client makes a number of requests which can be dynamically handled.
Alternativly, the files can defined at build time such that no server is needed.
See <a href="/auspice/customisations/server/charonAPI">these docs</a> for how to define the <code><serverHandlers></code> javascript file.</p>
<h3><a class="anchor" aria-hidden="true" id="developing-building-custom-auspice-versions"></a><a href="#developing-building-custom-auspice-versions" 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>Developing & Building custom auspice versions</h3>
<p>While it's possible to run these commands from the auspice source directory (using <code>node auspice.js ...</code>), it's preferable to run them from the repo containing the client / server customisations.
This requires <code>auspice</code> to be installed globally (see above).</p>
<pre><code class="hljs css language-bash"><span class="hljs-comment">## DEVELOPMENT</span>
auspice develop --verbose --extend <clientConfig> --handlers <serverHandlers>
<span class="hljs-comment">## BUILD</span>
auspice build --verbose --extend <clientConfig>
<span class="hljs-comment">## VIEW (using auspice server with custom handlers)</span>
auspice view --verbose --handlers <serverHandlers> --customBuild
</code></pre>
<h2><a class="anchor" aria-hidden="true" id="examples-of-customisations"></a><a href="#examples-of-customisations" 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>Examples of customisations:</h2>
<ul>
<li>Auspice.us -- <em>to do</em></li>
<li>Nextstrain -- <a href="https://github.com/nextstrain/nextstrain.org/tree/whitelabel">documentation</a></li>
<li>ZEBOV (serverless) -- <a href="https://github.com/blab/ZEBOV">documentation</a></li>
<li>Simulated viral outbreak for a ARTIC workshop in Ghana -- <a href="https://artic-network.github.io/artic-workshop">here</a></li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 1/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/inputs"><span class="arrow-prev">← </span><span>Input file formats</span></a><a class="docs-next button" href="/auspice/customisations/client/componentInterfaces"><span>Injecting custom components</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#developing-and-building-auspice-with-extensions">Developing and building auspice with extensions.</a><ul class="toc-headings"><li><a href="#client-extensions">Client extensions</a></li><li><a href="#server-extensions">Server extensions</a></li><li><a href="#developing-building-custom-auspice-versions">Developing & Building custom auspice versions</a></li></ul></li><li><a href="#examples-of-customisations">Examples of customisations:</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>