Swarm: A Federated Cloud Framework for Large-scale Variant Analysis

This is a Spring Boot server that queries genomic variants from Google BigQuery and Amazon Athena.

Pre-requisites

• Obtain a GCP Service Account key file in JSON format
• Obtain an AWS Access Key/Secret. Place in top level directory file aws.properties with names accessKey and secretKey. Also include outputLocationRoot, which is the s3 bucket url including optional directory.

Build

Run the following once to install the Simba Athena JDBC driver into the local maven cache.

$ bash lib/install-lib.sh

Run the following to build.

$ mvn package

Run

Maven builds a jar and puts it in target/ directory. It defaults to port 8080, which must be unbound prior to running.

$ java -jar target/swarm-1.0-SNAPSHOT.jar

Information about service endpoints are in API.md.

More details about installing and running are in Using.md.

Details about connecting to data sources are in Data.md.

Details about future extensions are in Extending.md.

Details about Federated Swarm extensions are in README.md.

• Logo Credit: Camille Berry