AWS Cloud Computing at Fred Hutch

Updated: May 26, 2023

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There are multiple methods by which you might leverage AWS cloud computing here at the Hutch. For less experienced cloud computing users, a workflow manager such as Cromwell or Nextflow may be of interest. These tools abstract away the actual running of the jobs in the cloud or on Gizmo, and for very new users, Cromwell may be a simple place to start as it abstracts away the most about where the jobs actually run. For more advanced users or for those who are more adept at programming or know they need to run primarily jobs in AWS (not in multiple locations), Nextflow may be ideal for you. For those with needs that do not focus on the running of workflows, such as genomic analyses, AWS Batch itself may be the ideal service.

Cromwell at Fred Hutch

Cromwell is a workflow manager software that is in use at the Hutch that works more like a work management tool than just a way to run individual workflows as it can run multiple workflows at a time and on multiple compute infrastructures (e.g., primarily both Gizmo and AWS at the Hutch, but also GCP and Azure). It can interpret WDL and CWL based workflow languages, which are open source specifications for workflow definitions used widely. A configuration for Hutch users that will allow for a Cromwell server to run on Gizmo, but submit workflow jobs to either Gizmo or AWS as defined by the user at the time of workflow submission is available. More about this resource can be found in the documentation for Cromwell at Fred Hutch.

Nextflow at Fred Hutch

Another option for using cloud resources, especially when performing a series of tasks (a workflow) repeated, while not necessarily having to understand or coordinate the individual components of the AWS infrastructure is to use the workflow manager Nextflow. Nextflow can be configured to use AWS as the backend execution resource, and thus it is very helpful to understand the basics of AWS Batch in order to get your data to a place where it can be analyzed easily via Nextflow.

Ultimately, Nextflow will reduce the amount of backend retooling required when transitioning from on-premise computing to cloud computing. This is an emerging service that is not currently fully supported. However, resource documentation is available here and will be updated with forthcoming releases.

AWS Batch

AWS Batch: a service which wraps around AWS EC2 resources such that researchers can more easily do computing processes with EC2 instances on data stored in S3.
For more information on using AWS Batch, please see this entry in the Resource Library.

AWS Batch is an AWS service that uses Docker containers to build a batch computing system. Batch is made up of a queueing system where jobs are defined and queued, and a computational resource made up of Docker containers to process those jobs. Resources are provisioned when there are jobs to be processed and destroyed when the work is complete. This results in a very efficient and cost-effective solution for some work.

Batch is useful if you have a fairly standard processing workflow or at least a step which is fairly consistent. The classic example for Batch is image processing: converting a raw image to some other format. Batch is capable of much more complicated analyses and pipelines.

As Batch is very much a cloud service, some familiar resources aren’t available when using this. Our ubiquitous file systems (home directories, fast-file, scratch) are not available- data used in Batch is typically stored in S3 or some other web-available source. There have been some recent changes which expand options for data storage which may make some workloads more accessible to Batch.

[CloudShell at Fred Hutch] (COMING FEB 2023)

CloudShell is a browser-based shell that’s native to AWS. With CloudShell, you can quickly run scripts with the AWS Command Line Interface (CLI), experiment with service APIs using the AWS CLI, and use other tools to increase your productivity. The CloudShell icon appears in AWS Regions where CloudShell is available. CloudShell inherits the credentials of the user who is signed in to the AWS Management Console. This makes authentication simpler and reduces operational burden by eliminating the need to configure and manage credentials locally. CloudShell comes with 1 GB of persistent storage for your home directory. Persistent storage enables you to store your frequently used scripts and configuration files between CloudShell sessions. For more details on persistent storage, see the AWS CloudShell User Guide.

CloudShell will enable low-level access to AWS services when you need to create services that are not handled by the ones listed above (e.g. if you wanted to spin up a RedShift data warehouse). There is no charge for CloudShell, but there may be charges for any services you enable.

How do I access my other AWS account resources?

You can read more about AWS Storage in our wiki page.

I have more questions

Please check out the FAQ for more information.

Updated: May 26, 2023

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