Conda runtime

Run commands with access to a fully-managed Conda environment.

Conda is a very popular packaging system freely-available for all platforms. When you use Nextstrain CLI’s built-in Conda support, you don’t need to install any other Nextstrain software dependencies yourself as validated versions are already bundled into a package (nextstrain-base) by the Nextstrain team and automatically managed in an isolated location (isolated even from other Conda environments you may manage yourself).

New in version 5.0.0.


On macOS and Linux, run nextstrain setup conda to get started.

This will download compressed packages totaling about 450 MB in size which expand to a final on-disk size of about 2 GB. Transient disk usage during this process peaks at about 3 GB. These numbers are current as of August 2023, as observed on Linux. Numbers will vary over time, with a tendency to slowly increase, and vary slightly by OS.

This runtime is not directly supported on Windows, but you can use WSL2 to “switch” to Linux and run the above setup command.

Environment variables


For development only. You don’t need to set these during normal operation.


Conda channel name (or URL) to use for Nextstrain packages not otherwise available via Bioconda (e.g. nextstrain-base).

Defaults to nextstrain.


Conda meta-package name to use for the Nextstrain base runtime dependencies.

May be a two- or three-part Conda package match spec instead of just a package name. Note that a conda install-style package spec, with a single = or without spaces, is not supported.

Defaults to nextstrain-base.


Version of Micromamba to use for setup and upgrade of the Conda runtime env. Must be a version available from the conda-forge channel, or the special string latest.

Defaults to 1.1.0.