Snakemake executor plugin: googlebatch

Warning

No documentation found in repository https://github.com/snakemake/snakemake-executor-plugin-googlebatch. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instructions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-executor-plugin-googlebatch

Usage

In order to use the plugin, run Snakemake (>=8.0) with the corresponding value for the executor flag:

snakemake --executor googlebatch ...

with ... being any additional arguments you want to use.

Settings

The executor plugin has the following settings (which can be passed via command line, the workflow or environment variables, if provided in the respective columns):

Settings

CLI argument	Description	Default	Choices	Required	Type
--googlebatch-project VALUE	The name of the Google Project.	None		✓
--googlebatch-region VALUE	The name of the Google Project region (e.g., us-central1)	None		✓
--googlebatch-container VALUE	A custom container for use with Google Batch COS	None		✗
--googlebatch-docker-password VALUE	A docker registry password for COS if credentials are required	None		✗
--googlebatch-docker-username VALUE	A docker registry username for COS if credentials are required	None		✗
--googlebatch-machine-type VALUE	Google Cloud machine type or VM (mpitune on c2 and c2d family)	'c2-standard-4'		✗
--googlebatch-labels VALUE	Comma separated key value pairs to label job (e.g., model=a3,stage=test)	''		✗
--googlebatch-image-family VALUE	Google Cloud image family (defaults to hpc-centos-7)	'hpc-centos-7'		✗
--googlebatch-image-project VALUE	Selected image project (defaults cloud-hpc-image-public)	'cloud-hpc-image-public'		✗
--googlebatch-work-tasks VALUE	The default number of work tasks (these are NOT MPI ranks)	1		✗
--googlebatch-cpu-milli VALUE	Milliseconds per cpu-second	1000		✗
--googlebatch-boot-disk-gb VALUE	Boot disk size (GB)	None		✗
--googlebatch-network VALUE	The URL of an existing network resource	None		✗
--googlebatch-subnetwork VALUE	The URL of an existing subnetwork resource	None		✗
--googlebatch-service-account VALUE	The email of a customer compute service account	None		✗
--googlebatch-boot-disk-type VALUE	Boot disk type. (e.g., gcloud compute disk-types list)	None		✗
--googlebatch-boot-disk-image VALUE	Boot disk image (e.g., batch-debian, bath-centos)	None		✗
--googlebatch-work-tasks-per-node VALUE	The default number of work tasks per node (NOT MPI ranks)	1		✗
--googlebatch-memory VALUE	Memory in MiB	1000		✗
--googlebatch-mount-path VALUE	Mount path for Google bucket (if defined)	'/mnt/share'		✗
--googlebatch-retry-count VALUE	Retry count (default to 1)	1		✗
--googlebatch-max-run-duration VALUE	Maximum run duration, string (e.g., 3600s)	'3600s'		✗
--googlebatch-snippets VALUE	One or more snippets to add to the Google Batch task setup	None		✗