nextstrain check-setup

Checks for supported build environments (aka Nextstrain runtimes).

Four runtimes are tested by default:

  • Our Docker image is the preferred build environment. Docker itself must be installed and configured on your computer first, but once it is, the build environment is robust and reproducible.

  • Our Conda environment will be tested for existence and appearance of completeness. This runtime is more isolated and reproducible than your ambient environment, but is less isolated and robust than the Docker runtime.

  • Your ambient environment will be tested for snakemake, augur, and auspice. Their presence implies a working build environment, but does not guarantee it.

  • Remote jobs on AWS Batch. Your AWS account, if credentials are available in your environment or via aws-cli configuration, will be tested for the presence of appropriate resources. Their presence implies a working AWS Batch environment, but does not guarantee it.

Provide one or more runtime names as arguments to test just those instead.

Exits with an error code if the default runtime (docker) is not supported or, when the default runtime is omitted from checks, if none of the checked runtimes are supported.

usage: nextstrain check-setup [-h] [--set-default] [<runtime> ...]

Positional Arguments

<runtime>

The Nextstrain build environments (aka Nextstrain runtimes) to check. (default: docker, conda, ambient, aws-batch)

Default: [<module ‘nextstrain.cli.runner.docker’ from ‘/home/docs/checkouts/readthedocs.org/user_builds/nextstrain-cli/envs/stable/lib/python3.10/site-packages/nextstrain/cli/runner/docker.py’>, <module ‘nextstrain.cli.runner.conda’ from ‘/home/docs/checkouts/readthedocs.org/user_builds/nextstrain-cli/envs/stable/lib/python3.10/site-packages/nextstrain/cli/runner/conda.py’>, <module ‘nextstrain.cli.runner.ambient’ from ‘/home/docs/checkouts/readthedocs.org/user_builds/nextstrain-cli/envs/stable/lib/python3.10/site-packages/nextstrain/cli/runner/ambient.py’>, <module ‘nextstrain.cli.runner.aws_batch’ from ‘/home/docs/checkouts/readthedocs.org/user_builds/nextstrain-cli/envs/stable/lib/python3.10/site-packages/nextstrain/cli/runner/aws_batch/__init__.py’>]

Named Arguments

--set-default

Set the default environment to the first which passes check-setup. Checks run in the order given, if any, otherwise in the default order: docker, conda, ambient, aws-batch.

Default: False