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Read BAM header on an AWS lambda with Noodles

This is a small Bioinformatics proof of concept that bundles noodles into an AWS Lambda.

A previous lambda was written using the C-bindgen-based rust-htslib. This iteration gets rid of the unsafe interfacing with the C-based htslib.

Quickstart

This README assumes the following prerequisites:

  1. You are already authenticated against AWS in your shell.
  2. You have a functioning Rust(up) installation.
  3. You have adjusted the KEY, BUCKET, REGION constants in main.rs
  4. You have installed cargo-lambda and prerequisites via cargo install cargo-lambda.
  5. You should prepare small test BAM in some S3 bucket. See event.json

Local Run

Just run the following commands on separate terminal sessions.

Build Local:

cargo build

Start Local Server:

cargo lambda start

Invoke Lambda with event or by pointing it to BAM file:

cargo lambda invoke s3-rust-noodles-bam --data-file events/event.json | jq
cargo lambda invoke s3-rust-noodles-bam --data-ascii '{"bam": "s3://some/key.bam"}' | jq

Invoke Http Lambda with APIGateway mock event:

cargo lambda invoke apigw --data-file events/mock_event.json | jq
cargo lambda invoke apigw --data-file events/mock_event_big.json | jq
cargo lambda invoke apigw --data-file events/mock_event_empty.json | jq

Deployment

Install CDK dependencies:

npm install cdk

Build fresh and deploy:

cargo clean
cdk diff
cdk deploy

Testing

Call Main Lambda Function:

aws lambda invoke --function-name <s3-rust-noodles-bam-...> out.json

NOTE: awscurl requires AWS credentials

Call Endpoint:

awscurl -H "Accept: application/json" --region ap-southeast-2 "https://<my-apigw-ep>.execute-api.ap-southeast-2.amazonaws.com/prod/" | jq

Call Endpoint with POST payload:

awscurl -X POST -d "@event_big.json" -H "Content-Type: application/json" --region ap-southeast-2 "https://<my-apigw-ep>.execute-api.ap-southeast-2.amazonaws.com/prod/" | jq