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Version: 23.1.0

Azure Batch

The Tower support for Azure Batch is currently in beta. Any feedback and suggestions are welcome.

Depending on your region and subscription type, a newly-created account may not be entitled to any VMs without first making a service request to Azure. See Azure Batch service quotas and limits for more information.

This guide assumes you have an existing Azure account.

There are two ways to create an Azure Batch compute environment in Tower:

  • Batch Forge: This option automatically creates the Azure Batch resources needed for your Tower compute environment. This eliminates the need to set up your Azure Batch infrastructure manually.

  • Manual: This option allows Tower to use existing Azure Batch resources.

Batch Forge​

Batch Forge creates the Azure Batch resources needed for your compute environment, recommended if you do not yet have an Azure Batch environment fully set up. Note that this will create resources that may have associated costs in your Azure account.

Resource group​

To create Azure Batch and Azure Storage accounts, first create a resource group in the region of your choice.

If you are logged in to your Azure account, select Create new resource group on this page.

  1. Enter a name for the resource group (e.g. towerrg).

  2. Select the preferred region for this resource group.

  3. Select Review and Create to proceed to the review screen.

  4. Select Create to create the resources.

Storage account​

The next step is to create the necessary Azure Storage.

If you are logged in to your Azure account, select Create a storage account on this page.

  1. Enter a name for the storage account (e.g., towerrgstorage).

  2. Select the preferred region for this storage account.

  3. Select Review and Create to proceed to the review screen.

  4. Select Create to create the Azure Storage account.

  5. Navigate to your new storage account and select Container.

  6. Create a new Blob container by selecting + Container.

    A new container dialogue will open. Enter a suitable name (e.g. towerrgstorage-container).

  7. Once the new Blob container is created, navigate to the Access Keys section of the storage account (towerrgstorage in this example).

  8. Store the access keys for the newly created Azure Storage account.

    Blob container storage credentials are associated with the Batch pool configuration when it is created. Once your compute environment has been created with Batch Forge, these credentials should not be changed in Tower.

Batch account​

The next step is to create the necessary Batch account.

If you are logged in to your Azure account, select Create a batch account on this page.

  1. Enter a name for the Batch account (e.g. towerrgbatch).

  2. Select the preferred region for this Batch account.

  3. Select Review and Create to proceed to the review screen.

  4. Select Create to create the Azure Batch account.

Compute environment​

Batch Forge automates the configuration of an Azure Batch compute environment and the queues required for the deployment of Nextflow pipelines.

Once the Azure resources are set up, add a new compute environment in Tower:

  1. In a workspace, select Compute Environments and then New Environment.

  2. Enter a descriptive name for this environment, e.g. "Azure Batch (east-us)"

  3. Select Azure Batch as the target platform.

  4. From the Credentials drop-down, select existing Azure credentials, or select + to add new credentials. If you have existing credentials, skip to step 7.

  5. Enter a name, e.g. "Azure Credentials".

  6. Add the Batch account and Blob Storage credentials that we created previously.

    You can create multiple credentials in your Tower environment.

  7. Select a Region, for example "eastus (East US)".

  8. In the Pipeline work directory field, enter the Azure blob container created previously, e.g., az://towerrgstorage-container/work.

    The blob container must be in the same Region from step 7.

  9. Set the Config mode to Batch Forge.

  10. Enter the default VM type, depending on your quota limits. The default is Standard_D4_v3.

  11. Enter the VMs count. This is the number of VMs you wish to deploy.

  12. Enable Autoscale if you'd like to scale up and down automatically based on the number of pipeline tasks. The number of VMs will vary from 0 to VMs count.

  13. Enable Dispose resources if you'd like Tower to automatically delete the Batch pool once the workflow is complete.

  14. Select or create a Container registry credential to authenticate to an Azure registry (used by the Wave containers service).

  15. Apply Resource labels to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled.

  16. Expand Staging options to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment.

  17. You can use the Environment variables option to specify custom environment variables for the Head job and/or Compute jobs.

  18. Configure any advanced options (see below), as needed.

  19. Select Create to finalize the compute environment setup. It will take a few seconds for all the resources to be created before the compute environment is ready to launch pipelines.

Jump to the documentation for launching pipelines.

Advanced options​

  • Use Jobs cleanup policy to control how jobs are deleted upon workflow completion.

  • Use Token duration to control the duration of the SAS token generated by Nextflow.

Manual​

This section is for users with a pre-configured Azure environment. You will need an Azure Batch account and Storage account already set up.

To create a new compute environment for AWS Batch (without Forge):

  1. In a workspace, select Compute Environments, then New Environment.

  2. Enter a descriptive name for this environment, e.g. "Azure Batch (east-us)".

  3. Select Azure Batch as the target platform.

  4. Select your existing Azure credentials or add new credentials by selecting the + button. If you are using existing credentials, skip to step 7.

  5. Enter a name, e.g. "Azure Credentials".

  6. Add the Batch account and Blob Storage credentials that we created previously.

    You can create multiple credentials in your Tower environment.

  7. Select a Region, for example "eastus (East US)".

  8. In the Pipeline work directory field, add the Azure blob container created previously, e.g. az://towerrgstorage-container/work.

    The Blob container must be in the same Region specified in step 7 above.

  9. Set the Config mode to Manual.

  10. Enter the Compute Pool name. This is the name of the Azure Batch pool provided to you by your Azure administrator.

  11. Use the Environment variables option to specify custom environment variables for the Head job and/or Compute jobs.

  12. Configure any advanced options described below, as needed.

  13. Select Create to finalize the compute environment setup. It will take a few seconds for all the resources to be created, and then you will be ready to launch pipelines.

Jump to the documentation for launching pipelines.

Advanced options​

  • Use Jobs cleanup policy to control how jobs are deleted upon workflow completion.

  • Use Token duration to control the duration of the SAS token generated by Nextflow.