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This repository was archived by the owner on Aug 9, 2023. It is now read-only.
**batch.onDemendMaxVCPUs** - The limit on vcpus when using on-demand instances.
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**batch.instanceTypes** - The [EC2 instance types](https://aws.amazon.com/ec2/instance-types/) to use in AWS Batch.
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**stepFunctions.launchDemoPipeline** - If set to true, the application will deploy a demo pipeline using step fuinctions.
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**stepFunctions.jobDefinitions** - List of parametrs for the demo application bioinformatics tools.
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**batch.instanceTypes** - The
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[EC2 instance types](https://aws.amazon.com/ec2/instance-types/) to use in
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AWS Batch.
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**workflows** - A list of workflows that you would like to launch. There are
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demo workflows under the `lib/workflows` directory. To add a workflow, update
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the code in the `lib/aws-genomics-cdk-stack.ts` file. Look for the workflows
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section.
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```
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{
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"accountID": "111111111111",
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"region": "us-west-2",
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"projectName": "genomics",
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"tags": [{
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"name": "Environment",
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"value": "production"
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},
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{
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"name": "Project",
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"value": "genomics-pipeline"
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}
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]
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"S3": {
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"existingBucket": true,
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"bucketName": ""
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"bucketName": "YOUR-BUCKET-NAME"
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},
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"VPC": {
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"createVPC": true,
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"existingVPCName": "",
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"VPCName": "genomics-vpc",
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"maxAZs": 2,
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"cidr": "10.0.0.0/16",
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"cidrMask": 24
@@ -79,44 +112,27 @@ for the new VPC.
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"c5.24xlarge"
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]
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},
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"stepFunctions": {
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"launchDemoPipeline": true,
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"jobDefinitions": {
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"fastqc": {
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"repository": "genomics/fastqc",
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"memoryLimit": 8000,
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"vcpus": 4,
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"spot": true,
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"retryAttempts":1,
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"timeout": 600
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},
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"minimap2": {
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"repository": "genomics/minimap2",
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"memoryLimit": 16000,
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"vcpus": 8,
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"spot": true,
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"retryAttempts":1,
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"timeout": 3600
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}
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}
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}
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"workflows": [{
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"name": "variantCalling",
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"spot": true
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}]
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}
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```
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## Deploy
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To deploy the CDK application, use the command line and make sure you are in the root folder of the CDK application.
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(`src/aws-genomics-cdk`).
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To deploy the CDK application, use the command line and make sure you are in
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the root folder of the CDK application (`src/aws-genomics-cdk`).
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First install the neccessary node.js modules
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```
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npm install
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```
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Then deploy the application.
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```
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# The "--require-approval never" parameter will skip the question to approve specific resouce creation,
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# such as IAM roles. You can remove this parameter if you want to be prompted to approve creating these
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# resources.
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# The "--require-approval never" parameter will skip the question to approve
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# specific resouce creation, such as IAM roles. You can remove this parameter
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# if you want to be prompted to approve creating these resources.
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cdk deploy --all --require-approval never
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```
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@@ -129,7 +145,7 @@ cdk deploy --all --require-approval never
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|`lib/vpc/vpc-stack.ts`| An optional stack that will launch a VPC |
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|`lib/batch/batch-stack.ts`| An AWS Batch stack with 2 comnpute environments (spot and on demand) and 2 queues (default and high priority) |
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|`lib/batch/batch-iam-stack.ts`| An IAM stack with roles and policies required for running AWS Batch |
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|`lid/step-fuinctions/genomics-state-machine-stack.ts`| A step function demo of running a pipeline |
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|`llib/workflows`| A folder containing pipeline stacks|
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## Constructs
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|`lib/batch/batch-compute-environmnet-construct.ts`| A construct for creating an [AWS Batch compute environment](https://docs.aws.amazon.com/batch/latest/userguide/compute_environments.html)|
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|`lib/batch/job-queue-construct.ts`| A construct for creating an [AWS Batch job queue](https://docs.aws.amazon.com/batch/latest/userguide/job_queues.html)|
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|`lib/batch/launch-template-construct.ts`| A construct for creating an [EC2 launch template](https://docs.aws.amazon.com/autoscaling/ec2/userguide/LaunchTemplates.html)|
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|`lib/step-functions/genomics-task-construct.ts`| A construct for creating a step function task that submits a batch job |
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|`lib/step-functions/job-definition-construct.ts`| A construct for creating an [AWS Batch job definition](https://docs.aws.amazon.com/batch/latest/userguide/job_definitions.html) to be used as a task in step functions |
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|`lib/workflows/genomics-task-construct.ts`| A construct for creating a step function task that submits a batch job |
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|`lib/workflows/job-definition-construct.ts`| A construct for creating an [AWS Batch job definition](https://docs.aws.amazon.com/batch/latest/userguide/job_definitions.html) to be used as a task in step functions |
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