basepair/connected-cloud-cdk

Connected Cloud for Basepair

Connected Cloud for Basepair

This project contains the AWS CDK code to set up Connected Cloud for Basepair.

What is connected cloud?

• Connected Cloud is a solution that allows you to run NSG workflows on Basepair platform with your own AWS account.
• Customer will interact with Basepair platform to upload samples and start workflows.
• Basepair platform will then connect with customer's AWS account to fetch samples, run workflows and upload results.
• Customer will be able to view results on Basepair platform.

Sequence Diagram

sequenceDiagram
actor User
box rgb(165,188,250) Basepair AWS Cloud
participant App
end
box rgb(252,192,131) Customer AWS Cloud
participant Storage
participant Compute
end
User->>App: Upload Samples
App->>Storage: Store Samples
User->>App: Start a Workflow
App->>Compute: Start EC2 Instance
Compute->>Storage: Fetch Samples
Compute->>Compute: Execute Workflow
Compute->>Storage: Upload Results
App->>Storage: Fetch Results
App->>User: Display Results

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Pre-requisites

1. Download and install AWS CLI
2. Download and install CDK CLI
3. Configure AWS CLI with your AWS account credentials
4. Bootstrap your AWS account with CDK CLI
   1. cdk bootstrap aws://<ACCOUNT-NUMBER>/<REGION>
   2. Make sure you have permissions to create IAM roles and policies in your AWS account
5. Create python virtual environment and activate it
   1. python3 -m venv venv
   2. source venv/bin/activate
6. Install dependencies
   1. pip install -r requirements.txt

Deployment

1. If you want to use Connected cloud with Health Omics, please click on the Launch Stack button above and follow the instructions

2. If you want to use Connected cloud without Health Omics, please click on the Launch Basepair Stack button above and follow the instructions

Development

1. Request BasepairAccountId and BasepairRoleName from Basepair Team
2. Run the below command and wait for the deployment to complete

   cdk deploy \
       --parameters BasepairAccountId=<Basepair Account Id> \
       --parameters BasepairRoleName=<Basepair Role Name> \
       --require-approval never \ 
       --outputs-file cdk.out.json
   

3. After the above command is successfully completed, Please share the cdk.out.json file with Basepair Team
4. For any support, please reach out to Basepair Team