nopaste

usage: nextstrain build [options] <directory> [...]
       nextstrain build --help

Runs a pathogen build in the Nextstrain build environment.

The build directory should contain a Snakefile, which will be run with
snakemake.

The default build environment is inside an ephemeral Docker container which has
all the necessary Nextstrain components available.  You may instead run the
build in the native ambient environment by passing the --native flag, but all
dependencies must already be installed and configured.  For larger builds, you
may want to use the --aws-batch flag to launch jobs on AWS Batch instead of
running locally (if the required AWS resources are configured in your AWS
account).

You can test if Docker, native, or AWS Batch build environments are properly
supported on your computer by running:

    nextstrain check-setup

The `nextstrain build` command is designed to cleanly separate the Nextstrain
build interface from provisioning a build environment, so that running builds
is as easy as possible.  It also lets us more seamlessly make environment
changes in the future as desired or necessary.

positional arguments:
  <directory>           Path to pathogen build directory
  ...                   Additional arguments to pass to the executed program

optional arguments:
  --help, -h            Show a brief help message of common options and exit
  --help-all            Show a full help message of all options and exit
  --docker              Run commands inside a container image using Docker.
                        (default)
  --native              Run commands on the native host, outside of any
                        container image.
  --aws-batch           Run commands remotely on AWS Batch inside the
                        Nextstrain container image.

Run again with --help-all instead to see more options.