Web app for visualizing pathogen evolution
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README.md

Master: Build Status Release: Build Status

Introduction

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. Our goal is to aid epidemiological understanding and improve outbreak response. See nextstrain.org/docs for more details.

Auspice is the code which powers all the nextstrain data viz -- e.g. nextstrain.org/zika. It is a javascript-based web app that gives an interactive visualization of genomic data (which is normally, but not necessarily, produced by augur).

Local Installs

Step 1: clone the git repository

cd nextstrain # or whichever folder you'd like to contain nextstrain repos in
git clone https://github.com/nextstrain/auspice.git
cd auspice

Step 2: Install Node.js

If you are comfortable using conda, installing nodejs is as simple as conda install -c conda-forge nodejs=9.11.1. If you'd prefer not to use conda, I recommend using nvm in order to manage nodejs & npm versions -- here's a great guide to help you do this.

Step 3: Install required dependencies

npm install

Step 4: Create / obtain data files (if you'd like to view local datasets)

Auspice can either source data from your computer or from a server. If you'd like to view data files locally, the JSON(s) need to be present in the data directory (see the docs for the format of these). If you have local data files (e.g. produced via augur) then copy them into this directory. If you'd like to download the latest JSONs which we are using for nextstrain.org then run npm run get-data which will download JSONs into data

Step 5: Build auspice & server the server

  • Simplest: npm run build && npm run server:local. This builds the relevant bundles & starts the server accessing the datasets in ./data.

  • To access datasets online (e.g. to mimic the live nextstrain site), instead run npm run build && npm run server.

  • In order to run the development server, which allows you to edit the source code on-the-fly, run npm run dev or npm run dev:local (the latter sources data from ./data)

Step 6: Open a browser

Auspice can now be used via localhost:4000. If you have JSONS in data named flu_europe_tree.json & flu_europe_meta.json, then these can be viewed at localhost:4000/flu/europe.

License and copyright

Copyright 2014-2018 Trevor Bedford and Richard Neher.

Source code to Nextstrain is made available under the terms of the GNU Affero General Public License (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.