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
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
If you look at the release notes you can see the changes that have been made to Auspice (see your version of Auspice via
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This is useful for debugging, modifying the source code, or using an unpublished feature branch.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
You will, however, have to re-build Auspice whenever the client-related code has changed, via