nextstrain build

Runs a pathogen build in a Nextstrain runtime.

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

You need at least one runtime available to run a build. You can test if the Docker, Conda, ambient, or AWS Batch runtimes 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 runtime environment, so that running builds is as easy as possible. It also lets us more seamlessly make runtime 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. By default, no constraints are placed on how many CPUs are used by a build; builds may use all that are available if they’re able to.

--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.

--download

Only download new or modified files matching <pattern> from the remote build. Shell-style advanced globbing is supported, but be sure to escape wildcards or quote the whole pattern so your shell doesn’t expand them. May be passed more than once. Currently only supported when also using –aws-batch. Default is to download every new or modified file.

Besides basic glob features like single-part wildcards (*), character classes ([…]), and brace expansion ({…, …}), several advanced globbing features are also supported: multi-part wildcards (**), extended globbing (@(…), +(…), etc.), and negation (!…).

Default: True

--no-download

Do not download any files from the remote build when it completes. Currently only supported when also using –aws-batch.

Default: True

--no-logs

Do not show the log messages of the remote build. Currently only supported when also using –aws-batch. Default is to show all log messages, even when attaching to a completed build.

Default: True

runtime selection options

Select the Nextstrain runtime to use, if the default is not suitable.

--docker

Run commands inside a container image using Docker. (default)

--conda

Run commands with access to a fully-managed Conda environment.

--singularity

Run commands inside a container image using Singularity.

--ambient

Run commands in the ambient environment, outside of any container image.

--aws-batch

Run commands remotely on AWS Batch inside the Nextstrain container image.

runtime options

Options shared by all runtimes.

--env

Set the environment variable <name> to the value in the current environment (i.e. pass it thru) or to the given <value>. May be specified more than once. Overrides any variables of the same name set via –envdir. When this option or –envdir is given, the default behaviour of automatically passing thru several “well-known” variables is disabled. The “well-known” variables are AUGUR_RECURSION_LIMIT, AUGUR_MINIFY_JSON, AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_SESSION_TOKEN, ID3C_URL, ID3C_USERNAME, ID3C_PASSWORD, RETHINK_HOST, and RETHINK_AUTH_KEY. Pass those variables explicitly via –env or –envdir if you need them in combination with other variables.

Default: []

--envdir

Set environment variables from the envdir at <path>. May be specified more than once. An envdir is a directory containing files describing environment variables. Each filename is used as the variable name. The first line of the contents of each file is used as the variable value. When this option or –env is given, the default behaviour of automatically passing thru several “well-known” variables is disabled. See the description of –env for more details.

Default: []

development options

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

--image

Container image name to use for the Nextstrain runtime (default: “nextstrain/base” for Docker and AWS Batch, docker://nextstrain/base for Singularity)

Default: “nextstrain/base”

--exec

Program to run inside the runtime

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://docs.nextstrain.org/projects/cli/page/aws-batch> 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