Checks for supported runtimes.
Five runtimes are tested by default:
Our Docker image is the preferred runtime. Docker itself must be installed and configured on your computer first, but once it is, the runtime is robust and reproducible.
Our Conda runtime will be tested for existence and appearance of completeness. This runtime is more isolated and reproducible than your ambient runtime, but is less isolated and robust than the Docker runtime.
Our Singularity runtime uses the same container image as our Docker runtime. Singularity must be installed and configured on your computer first, although it is often already present on HPC systems. This runtime is more isolated and reproducible than the Conda runtime, but potentially less so than the Docker runtime.
Your ambient setup will be tested for snakemake, augur, and auspice. Their presence implies a working runtime, 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 runtime, 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> ...]
The Nextstrain runtimes to check. (default: docker, conda, singularity, ambient, aws-batch)
Default: [<module ‘nextstrain.cli.runner.docker’ from ‘/home/docs/checkouts/readthedocs.org/user_builds/nextstrain-cli/envs/latest/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/latest/lib/python3.10/site-packages/nextstrain/cli/runner/conda.py’>, <module ‘nextstrain.cli.runner.singularity’ from ‘/home/docs/checkouts/readthedocs.org/user_builds/nextstrain-cli/envs/latest/lib/python3.10/site-packages/nextstrain/cli/runner/singularity.py’>, <module ‘nextstrain.cli.runner.ambient’ from ‘/home/docs/checkouts/readthedocs.org/user_builds/nextstrain-cli/envs/latest/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/latest/lib/python3.10/site-packages/nextstrain/cli/runner/aws_batch/__init__.py’>]
Set the default runtime to the first which passes check-setup. Checks run in the order given, if any, otherwise in the default order: docker, conda, singularity, ambient, aws-batch.