recipe nextstrain-cli

The Nextstrain command-line interface (CLI)


Developer docs:





The Nextstrain command-line interface (CLI)—a program called nextstrain—aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.

package nextstrain-cli

(downloads) docker_nextstrain-cli



depends boto3:

depends docutils:

depends fasteners:

depends fsspec:


depends importlib_resources:


depends packaging:


depends pyjwt:


depends pyparsing:

depends python:


depends requests:

depends s3fs:


depends typing_extensions:


depends wcmatch:


depends wrapt:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install nextstrain-cli

and update with::

   mamba update nextstrain-cli

To create a new environment, run:

mamba create --name myenvname nextstrain-cli

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `nextstrain-cli/tags`_ for valid values for ``<tag>``)

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