nextstrain check-setup

Checks your local setup to see if you have a supported build environment.

Three environments are supported, each of which will be tested:

• 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.

• Your native 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.

usage: nextstrain check-setup [-h] [--set-default]

Named Arguments

--set-default

Set the default environment to the first which passes check-setup. Checks run in the order: docker, native, aws-batch.

Default: False