Installing auspice

Auspice is written in Javascript and will require nodejs and npm (the node package manager) to install. If you are comfortable using conda these may be easily installed in your environment (see here). If you are on Linux or MacOS, you could also use nvm to insall these (see here).

Global NPM install

Auspice is avaliable as a npm package and can be installed simply via:

npm install --global auspice

Auspice is now available as a command-line program -- check by running auspice -h. Documentation for how to run auspice locally is available here.

Installing as a project's dependency

If you are building a customised version of auspice, you may want to include it as a dependency of that project. This allows you to pin the version, use continuous integration tooling and simplifies any code imports you may wish to use.

npm install --save auspice

Note that auspice is not available as a command line tool this way, but can be accessed from within the repo via npx auspice. See customising auspice for more information.

Installing from source

git clone git@github.com:nextstrain/auspice.git
cd auspice
npm install # install dependencies
npm install -g . # make "auspice" available globally

Note that (at least on MacOS) this symlinks the source directory into the global node_modules folder so that changes to source code are automatically reflected in the globally available auspice command. We have had good success using a conda environment for development.

Developing

Install auspice from source (see above). Running auspice in development mode will automatically update as you change the source code:

auspice develop --verbose

(See auspice develop -h for further options)

Building auspice

Install auspice from source (see above).

auspice build --verbose

(See auspice build -h for further options)

Running auspice

See running locally documentation.