opencb/opencga — reverse-engineered prompt

Build me an open source genomics data platform for research teams working with very large BAM and VCF files. I want it to store and index genomic data at huge scale, keep a catalog of studies, files, samples, annotations, users, and permissions, and let people run analysis jobs over the stored data.

It should expose a clean REST API and a command line client so labs can upload files, search variants, manage metadata, and check job status without touching the database directly. Use Java with Maven, target Java 8 compatibility, and make MongoDB the main storage option since that is the supported database.

Include sensible local development config for ports, workspace folders, authentication settings, and storage settings. Please set up the modules cleanly for catalog, storage, analysis, client, server, and tests, and include build instructions using mvn clean install with tests skipped if needed. Look up current docs online if you need to.