Web app for visualizing pathogen evolution

Install Auspice

Prerequisites

Auspice is a JavaScript program, and requires Node.js to be installed on your system. We've had success running a range of different node versions between 10.8 and 13.

We highly recommend using Conda 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.

To run package scripts, the bash shell and the env command need to be in your PATH. You should already have them on Unix-like systems including Linux and macOS. If you are working from Windows, you can run the installation under Git Bash, MSYS2, or Cygwin. You can also use the Windows Subsystem Linux for a fuller Linux environment.

Create a Conda Environment

conda create --name auspice nodejs=12
conda activate auspice

This parallels the Nextstrain installation docs. You're welcome to use those instead!

Install Auspice from npm

npm install --global auspice

Auspice should now be available as a command-line program -- check by running auspice --help.

If you look at the release notes you can see the changes that have been made to Auspice (see your version of Auspice via auspice --version). To upgrade, you can run

npm update --global auspice

Installing from Source

This is useful for debugging, modifying the source code, or using an unpublished feature branch.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.

# activate the correct conda enviornment
conda activate auspice

# grab the GitHub auspice repo
git clone https://github.com/nextstrain/auspice.git
cd auspice

# install dependencies and make `auspice` available globally
npm install --global .

# build auspice (builds the JS client bundle using webpack)
auspice build

# test it works
auspice --version
auspice --help

# Obtain nextstrain.org datasets to view locally (optional)
npm run get-data

Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any npm commands. You will, however, have to re-build Auspice whenever the client-related code has changed, via auspice build.