nextstrain build

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.

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

Positional Arguments

<directory>

Path to pathogen build directory

...

Additional arguments to pass to the executed program

Default: []

Named Arguments

--help, -h

Show a brief help message of common options and exit

--detach

Run the build in the background, detached from your terminal. Re-attach later using –attach.Currently only supported when also using –aws-batch.

Default: False

--attach

Re-attach to a –detach’ed build to view output and download results. Currently only supported when also using –aws-batch.

--cpus

Number of CPUs/cores/threads/jobs to utilize at once. Limits containerized (Docker, AWS Batch) builds to this amount. Informs Snakemake’s resource scheduler when applicable. Informs the AWS Batch instance size selection.

--memory

Amount of memory to make available to the build. Units of b, kb, mb, gb, kib, mib, gib are supported. Limits containerized (Docker, AWS Batch) builds to this amount. Informs Snakemake’s resource scheduler when applicable. Informs the AWS Batch instance size selection.

runner selection options

Select the method for running a Nextstrain computing environment, if the default is not suitable.

--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.

development options

These should generally be unnecessary unless you’re developing Nextstrain.

--image

Container image name to use for the Nextstrain computing environment

Default: “nextstrain/base”

--exec

Program to run inside the build environment

Default: “snakemake”

development options for –docker

--augur

Replace the image’s copy of augur with a local copy

--auspice

Replace the image’s copy of auspice with a local copy

--fauna

Replace the image’s copy of fauna with a local copy

--sacra

Replace the image’s copy of sacra with a local copy

--docker-arg

Additional arguments to pass to docker run

Default: []

development options for –aws-batch

See <https://github.com/nextstrain/cli/tree/master/doc/aws-batch.md> for more information.

--aws-batch-job

Name of the AWS Batch job definition to use

Default: “nextstrain-job”

--aws-batch-queue

Name of the AWS Batch job queue to use

Default: “nextstrain-job-queue”

--aws-batch-s3-bucket

Name of the AWS S3 bucket to use as shared storage

Default: “nextstrain-jobs”

--aws-batch-cpus

Number of vCPUs to request for job

--aws-batch-memory

Amount of memory in MiB to request for job