Snakemake executor plugin: azure-batch

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Warning

No documentation found in repository https://github.com/snakemake/snakemake-executor-plugin-azure-batch. 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 instractions presented in this catalog.

Installation

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

pip install snakemake-executor-plugin-azure-batch

Usage

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

snakemake --executor azure-batch ...

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

The executor plugin has the following settings:

Settings

CLI argument

Description

Default

Choices

Required

Type

--azure-batch-account-url VALUE

Azure batch account url.

None

✓

--azure-batch-account-key VALUE

Azure batch account key.

None

✓

--azure-batch-pool-subnet-id VALUE

Azure batch pool subnet id.

None

✗

--azure-batch-autoscale VALUE

Enable autoscaling of the azure batch pool nodes, this option will set the initial dedicated node count to zero, and requires five minutes to resize the cluster, so is only recommended for longer running workflows.

False

✗

--azure-batch-managed-identity-resource-id VALUE

Azure managed identity resource id.

None

✗

--azure-batch-managed-identity-client-id VALUE

Azure managed identity client id.

None

✗

--azure-batch-node-start-task-sasurl VALUE

Azure batch node start task bash script sas url.

None

✗

--azure-batch-pool-image-publisher VALUE

Azure batch pool image publisher.

'microsoft-azure-batch'

✗

--azure-batch-pool-image-offer VALUE

Azure batch pool image offer.

'ubuntu-server-container'

✗

--azure-batch-pool-image-sku VALUE

Azure batch pool image sku.

'20-04-lts'

✗

--azure-batch-pool-vm-node-agent-sku-id VALUE

Azure batch pool vm node agent sku id.

'batch.node.ubuntu 20.04'

✗

--azure-batch-pool-vm-size VALUE

Azure batch pool vm size.

'Standard_D2_v3'

✗

--azure-batch-pool-node-count VALUE

Azure batch pool node count.

1

✗

--azure-batch-tasks-per-node VALUE

Azure batch tasks per node.

1

✗

--azure-batch-node-fill-type VALUE

Azure batch node fill type.

'spread'

✗

--azure-batch-node-communication-mode VALUE

Azure batch node communication mode.

None

✗

--azure-batch-container-registry-url VALUE

Azure container registry url.

None

✗

--azure-batch-container-registry-user VALUE

Azure container registry user.

None

✗

--azure-batch-container-registry-pass VALUE

Azure container registry password.

None

✗