corneliusroemer / conda

Nextstrain environment for the Conda package manager

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.