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This repository was archived by the owner on Aug 9, 2023. It is now read-only.
Copy file name to clipboardExpand all lines: docs/orchestration/cromwell/cromwell-overview.md
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system for scientific workflows developed by the [Broad Institute](https://broadinstitute.org/)
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and supports job execution using [AWS Batch](https://aws.amazon.com/batch/).
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## TL;DR
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## Full Stack Deployment (TL;DR)
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If you need a Cromwell server backed by AWS **now** and will worry about the
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details later, use the CloudFormation template below.
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{{ cfn_stack_row("Cromwell All-in-One", "Cromwell", "cromwell/cromwell-aio.template.yaml", "Create all resources needed to run Cromwell on AWS: an S3 Bucket, AWS Batch Environment, and Cromwell Server Instance") }}
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When the above stack is complete, navigate to the `HostName` that is generated
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in the outputs to access Cromwell via its SwaggerUI.
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in the outputs to access Cromwell via its SwaggerUI, which provides a simple web interface for submitting workflows.
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!!! note
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For a Cromwell server that will run multiple workflows, or workflows with many
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steps (e.g. ones with large scatter steps), it is recommended to setup a
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database to use to store workflow metadata.
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database to store workflow metadata.
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## Custom Compute Resource with Cromwell Additions
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## Cromwell Server
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To ensure the highest level of security, and robustness for long running workflows,
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To ensure the highest level of security and robustness for long running workflows,
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it is recommended that you use an EC2 instance as your Cromwell server for submitting
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workflows to AWS Batch.
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The above file uses the [default credential provider chain](https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/credentials.html) for authorization.
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Replace the following with values appropriate for your accoutn and workload:
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Replace the following with values appropriate for your account and workload:
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*`<your region>` : the AWS region your S3 bucket and AWS Batch environment are
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deployed into - e.g. `us-east-1`
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!!! note
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The CloudFormation template above automatically starts Cromwell on launch.
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Use the instructions below are if you are provisioning your own EC2 instance.
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Use the instructions below if you are provisioning your own EC2 instance.
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Log into your server using SSH. If you setup a port tunnel, you can interact
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with Cromwell's REST API from your local machine:
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## Running a workflow
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To submit a workflow to your Cromwell server, you can use:
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To submit a workflow to your Cromwell server, you can use any of the following:
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* Cromwell's SwaggerUI in a web-browser
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* a REST client like [Insomnia](https://insomnia.rest/) or [Postman](https://www.getpostman.com/)
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*or, the command line with `curl`
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* the command line with `curl`
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After submitting a workflow, you can monitor the progress of tasks via the
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AWS Batch console.
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The next section provides some examples of running Crommwell on AWS.
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The next section provides some examples of running Crommwell on AWS.
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