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.
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