Auspice fork from github of https://github.com/urbanslug/auspice
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Install Auspice</h1></header><article><div><span><h2><a class="anchor" aria-hidden="true" id="prerequisites"></a><a href="#prerequisites" 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>Prerequisites</h2>
<p>Auspice is a JavaScript program, and requires <a href="https://nodejs.org/">Node.js</a> to be installed on your system.
For best results, please use Node.js version 10.</p>
<p>We highly recommend using <a href="https://conda.io/docs/">Conda</a> to manage environments, i.e. use Conda to create an environment with Node.js installed where you can use Auspice.
It's possible to use other methods, but this documentation presupposes that you have Conda installed.</p>
<h2><a class="anchor" aria-hidden="true" id="create-a-conda-environment"></a><a href="#create-a-conda-environment" 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>Create a Conda Environment</h2>
<pre><code class="hljs css language-bash">conda create --name auspice nodejs=10
<span class="hljs-built_in">source</span> activate auspice
</code></pre>
<blockquote>
<p>This parallels <a href="https://nextstrain.org/docs/getting-started/local-installation#install-augur--auspice-with-conda-recommended">the Nextstrain installation docs</a>.
You're welcome to use those instead!</p>
</blockquote>
<h2><a class="anchor" aria-hidden="true" id="install-auspice-from-npm"></a><a href="#install-auspice-from-npm" 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>Install Auspice from npm</h2>
<pre><code class="hljs css language-bash">npm install --global auspice
</code></pre>
<p>Auspice should now be available as a command-line program -- check by running <code>auspice --help</code>.</p>
<p>If you look at the <a href="/auspice/releases/changelog">release notes</a> you can see the changes that have been made to Auspice (see your version of Auspice via <code>auspice --version</code>).
To upgrade, you can run</p>
<pre><code class="hljs css language-bash">npm update --global auspice
</code></pre>
<h2><a class="anchor" aria-hidden="true" id="installing-from-source"></a><a href="#installing-from-source" 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>Installing from Source</h2>
<p>This is useful for debugging, modifying the source code, or using an unpublished feature branch.
We're going to assume that you have used Conda to install Node.js as above.</p>
<pre><code class="hljs css language-bash"><span class="hljs-comment"># activate the correct conda enviornment</span>
conda activate auspice
<span class="hljs-comment"># grab the GitHub auspice repo</span>
git checkout https://github.com/nextstrain/auspice.git
<span class="hljs-built_in">cd</span> auspice
<span class="hljs-comment"># install dependencies</span>
npm install
<span class="hljs-comment"># make `auspice` available globally</span>
npm install --global .
<span class="hljs-comment"># build auspice</span>
auspice build
<span class="hljs-comment"># test it works</span>
auspice --version
auspice --<span class="hljs-built_in">help</span>
</code></pre>
<p>Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any <code>npm</code> commands.
You will, however, have to re-build Auspice whenever the client-related code has changed, via <code>auspice build</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></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 &amp; Trevor Bedford</section></footer></div></body></html>