Auspice fork from github of https://github.com/urbanslug/auspice
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<!DOCTYPE html><html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>How to Run Auspice · Auspice</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="Auspice is run as a command line program -- `auspice` -- with various subcommands."/><meta name="docsearch:language" content="en"/><meta property="og:title" content="How to Run Auspice · Auspice"/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="Auspice is run as a command line program -- `auspice` -- with various subcommands."/><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><script src="/auspice/js/scrollSpy.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"><a href="/auspice/introduction/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><div class="hamburger-menu"><div class="line1"></div><div class="line2"></div><div class="line3"></div></div></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"><a class="navItem" href="/auspice/introduction/overview">Overview</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/install">Install Auspice</a></li><li class="navListItem navListItemActive"><a class="navItem" href="/auspice/introduction/how-to-run">How to Run Auspice</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced Functionality</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/second-trees">Displaying mutliple trees</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/misc">Miscellaneous</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Customising Auspice</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/customise-client/introduction">Customising Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/api">Client Customisation API</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/requests">Requests Made from the Client</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Using a Custom Server</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/server/introduction">Auspice servers</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/api">Server API</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/authentication">Authentication</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Narratives</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/narratives/introduction">Communicating Results Using Narratives</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/how-to-write">Writing a Narrative</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Release Notes</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/releases/changelog">Changelog</a></li><li class="navListItem"><a class="navItem" href="/auspice/releases/v2">Auspice Version 2.0</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Contributing</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/contributing/overview">Contributing</a></li></ul></div></div></section></div><script>
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">How to Run Auspice</h1></header><article><div><span><p>Auspice is run as a command line program -- <code>auspice</code> -- with various subcommands.
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You can run each command with <code>--help</code> attached to see help from the command line.</p>
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<ul>
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<li><code>auspice view --help</code> (this is the main command for interacting with Auspice)</li>
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<li><code>auspice build --help</code></li>
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<li><code>auspice develop --help</code></li>
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<li><code>auspice convert --help</code></li>
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</ul>
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<h2><a class="anchor" aria-hidden="true" id="how-to-get-an-example-dataset-up-and-running"></a><a href="#how-to-get-an-example-dataset-up-and-running" 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>How to Get an Example Dataset Up and Running</h2>
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<p>In order to get up and running you'll need to have some datasets to visualise.
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For the purposes of getting Auspice up and running you can download the current Zika dataset via:</p>
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<pre><code class="hljs css language-bash">mkdir datasets
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curl http://data.nextstrain.org/zika_meta.json --compressed -o datasets/zika_meta.json
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curl http://data.nextstrain.org/zika_tree.json --compressed -o datasets/zika_tree.json
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</code></pre>
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<p>And then run <code>auspice</code> via:</p>
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<pre><code class="hljs css language-bash">auspice view --datasetDir datasets
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</code></pre>
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<p>This will allow you to run Auspice locally (i.e. from your computer) and view the dataset which is behind <a href="https://nextstrain.org/zika">nextstrain.org/zika</a>.
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<a href="#obtaining-a-set-of-input-files">See below</a> for how to download all of the data available on <a href="https://nextstrain.org">nextstrain.org</a>.</p>
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<p>To analyse your own data, please see the tutorials on the <a href="https://nextstrain.org/docs/">nextstrain docs</a>.</p>
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<h2><a class="anchor" aria-hidden="true" id="auspice-view"></a><a href="#auspice-view" 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><code>auspice view</code></h2>
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<p>This is the main command we'll run Auspice with, as it makes Auspice available in a web browser for you.
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There are two common arguments used:</p>
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<table>
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<thead>
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<tr><th>argument name</th><th>data supplied</th><th>description</th></tr>
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</thead>
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<tbody>
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<tr><td>datasetDir</td><td>PATH</td><td>Directory where datasets (JSONs) are sourced. This is ignored if you define custom handlers.</td></tr>
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<tr><td>narrativeDir</td><td>PATH</td><td>Directory where narratives (Markdown files) are sourced. This is ignored if you define custom handlers.</td></tr>
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</tbody>
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</table>
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<p>For more complicated setups, where you define your own server handlers, see <a href="/auspice/server/api#suppling-custom-handlers-to-the-auspice-server">suppling custom handlers to the Auspice server</a>.</p>
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<h2><a class="anchor" aria-hidden="true" id="auspice-build"></a><a href="#auspice-build" 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><code>auspice build</code></h2>
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<p>Build the client source code bundle.
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This is needed in three cases:</p>
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<ol>
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<li>You have installed Auspice from source, or updated the source code.</li>
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<li>You are editing the source code and need to rebuild the client</li>
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<li>You wish to build a customised version of the Auspice client.
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See <a href="/auspice/customise-client/introduction">Customising Auspice</a> for more info.</li>
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</ol>
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<h2><a class="anchor" aria-hidden="true" id="auspice-develop"></a><a href="#auspice-develop" 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><code>auspice develop</code></h2>
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<p>Launch Auspice in development mode. This runs a local server and uses
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hot-reloading to allow automatic updating as you edit the code.</p>
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<p>This is only useful if you are editing the client source code!</p>
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<h2><a class="anchor" aria-hidden="true" id="auspice-convert"></a><a href="#auspice-convert" 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><code>auspice convert</code></h2>
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<p>This is a utility command to convert between dataset formats.
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Currently, it only converts "Auspice v1" JSONs into "Auspice v2" JSONs, using the same code that is <a href="/auspice/server/api#convertfromv1">programatically importable</a>.</p>
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<p>Right now, <code>auspice view</code> will automatically convert "v1" JSONs into "v2" JSONs, so there's no need to do this yourself.</p>
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<h2><a class="anchor" aria-hidden="true" id="input-file-formats"></a><a href="#input-file-formats" 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>Input File Formats</h2>
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<blockquote>
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<p>Auspice is agnostic about the data it visualises -- they don't have to be viral genomes, or real-time, or generated in Augur.
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(They do, however have to be in a specific file format.)</p>
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</blockquote>
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<p>Auspice takes two different file types: datasets (the tree, map, etc.), which are defined as one or more JSON files and narratives, which are specified as a Markdown file.</p>
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<h3><a class="anchor" aria-hidden="true" id="dataset-jsons"></a><a href="#dataset-jsons" 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>Dataset JSONs</h3>
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<p>For datasets, Auspice (v2.x) can currently load either</p>
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<ul>
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<li>"Auspice v1" JSONs (metadata + tree JSONs) -- see the JSON schemas <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-meta.json">here</a> and <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v1-tree.json">here</a>.
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<em>The zika dataset we download above is in this format</em></li>
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<li>"Auspice v2" JSONs. See the JSON schema <a href="https://github.com/nextstrain/augur/blob/v6/augur/data/schema-export-v2.json">here</a>.</li>
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</ul>
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<p>See the <a href="/auspice/server/api">Server API</a> for more details about the file formats an Auspice server (e.g. <code>auspice view</code>) sends to the client.</p>
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<p>Currently we mainly use <a href="https://github.com/nextstrain/augur">Augur</a> to create these datasets.
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See <a href="https://nextstrain.org/docs/bioinformatics/introduction-to-augur">the Nextstrain documentation</a> for more details.</p>
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<blockquote>
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<p>We are working on ways to make datasets in Newick / Nexus formats available. You can see an early prototype of this at <a href="https://auspice-us.herokuapp.com/">auspice-us.herokuapp.com</a> where you can drop on Newick (and CSV) files.
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Using BEAST trees is possible, but you have to use Augur to convert them first.</p>
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</blockquote>
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<h3><a class="anchor" aria-hidden="true" id="narratives"></a><a href="#narratives" 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>Narratives</h3>
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<p>For narratives, please see <a href="/auspice/narratives/how-to-write">Writing a Narrative</a> for a description of the file format.</p>
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<h2><a class="anchor" aria-hidden="true" id="obtaining-a-set-of-input-files"></a><a href="#obtaining-a-set-of-input-files" 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>Obtaining a Set of Input Files</h2>
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<p>If you'd like to download the datasets and narratives on <a href="https://nextstrain.org">nextstrain.org</a> then there are two scripts which allow you to do this:</p>
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<ul>
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<li>You can download the dataset JSONs by running <a href="https://github.com/nextstrain/auspice/blob/master/scripts/get-data.sh">this script</a> which will create a <code>./data</code> directory for you.</li>
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<li>You can download the narrative Markdown files by running <a href="https://github.com/nextstrain/auspice/blob/master/scripts/get-narratives.sh">this script</a> which will create a <code>./narratives</code> directory for you.</li>
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</ul>
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<p>You can then run <code>auspice view --datasetDir data --narrativeDir narratives</code> to visualise all of the <a href="https://nextstrain.org">nextstrain.org</a> datasets locally.</p>
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</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/install"><span class="arrow-prev">← </span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying mutliple trees</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</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 & Trevor Bedford</section></footer></div></body></html>
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