Nextstrain environment for Conda

Conda is a package and environment manager for Windows, macOS, and Linux that can help ease software installation and usage.

The nextstrain.yml file in this repo is hosted at http://data.nextstrain.org/nextstrain.yml and serves as an environment definition for Conda.

Setup the Nextstrain environment by running:

curl http://data.nextstrain.org/nextstrain.yml -o nextstrain.yml
conda env create -f nextstrain.yml
conda activate nextstrain
npm install --global auspice

For a faster installation process, use Mamba as a drop-in replacement for Conda's installer.

# Install Mamba
conda install -c conda-forge mamba

# Create environment with Mamba.
curl http://data.nextstrain.org/nextstrain.yml -o nextstrain.yml
mamba env create -f nextstrain.yml
conda activate nextstrain
npm install --global auspice

For more details, refer to our local installation documentation.

Continuous integration and deployment

A GitHub Actions workflow is defined in this repository to test creation of the Conda environment on Linux (Ubuntu) and macOS every time commits are pushed or a PR is opened.

If all tests are successful and the push is made to the master branch, the ./publish script is run to deploy the file to data.nextstrain.org.

AWS credentials are stored in this repository's secrets and are associated with the nextstrain-conda-publisher IAM user in the Bedford Lab AWS account, which is locked down to publishing only that file.

Why does this repo exist?

Historically there were lots of ad-hoc Conda environment files for Nextstrain (and various subprojects, like Augur). Some of these still linger because they were never removed. They probably should be.

There was also an "official" environment file at https://data.nextstrain.org/nextstrain.yml used in some common installation instructions. This file was not in source control and did not have an authoritative source other than the nextstrain-data S3 bucket itself.

In an attempt to address both the proliferation and lack of authoritative source control for the environment file, I (@tsibley) created this repo in 2019. It let us start to standardize the Conda environment for Nextstrain.

These days, we no longer refer to https://data.nextstrain.org/nextstrain.yml in our installation docs, because we moved to having official Conda packages instead of an environment definition. However, it's still referenced widely enough (for example) that I wouldn't want to just remove it unceremoniously.