README.rst

CGAP PORTAL (HMS-BGM)

Welcome to CGAP!

CGAP is the Computational Genome Analysis Platform.

We are a team of scientists, clinicians, and developers who aim to streamline the clinical genetics workflow.

• For useful information about CGAP's features, see the CGAP informational site.

• CGAP is orchestrated technology capable of being easily deployed in hospital setting. Our flagship site is CGAP-MGB.

  For information on how to set your hospital up to use this technology, contact us.

• CGAP is an open source system under continuous development. For documentation, see the CGAP Portal page at ReadTheDocs.

• For information about governance and other policies, see the CGAP Governance repository.

Repository Structure

These are some important files and directories you might want to be aware of:

• .dockerignore specifies paths ignored by the Dockerfile
• .github/workflows/ contains Github Action Workflows
• bin/ contains a few legacy scripts, though most are in scripts/
• deploy/docker contains containerization related scripts/configuration
• docker-compose.yml builds the new local deployment (see docker-local.rst)
• Dockerfile contains the Docker build instructions for the cgap-portal (see docker-production.rst)
• docs/ contains documentation
• Makefile contains macros for common build operations (see make info)
• package.json and package-lock.json specify the front-end dependencies
• pyproject.toml and poetry.lock specify the back-end dependencies
• scripts/ contains misc scripts
• setup_eb.py performs final installation setup
• src/encoded/ where the code is

Navigating core functionality (src/encoded/)

Top level files are modules that make up the core functionality of the back-end. Some modules differ greatly from or do not even exist in fourfront. Directories are outlined below.

• annotations/ contains mapping table and ingestion related metadata
• commands/ contains Python commands that can be run on the system from the command line
• docs/ contains ReadTheDocs documentation
• ingestion/ contains ingestion related code, such as mapping table intake and VCF processing
• schemas/ contains the metadata schemas
• search/ contains the search/filter_set APIs
• static/ contains front-end code
• tests/ contains back-end unit tests and insert data
• types/ contains metadata type definitions
• upgrade/ contains collection schema version upgraders

Related Repositories

Note that cgap-portal is bound on supporting functionality in numerous libaries, but importantly:

• dcicsnovault [pypi library] [source repo]
• dcicutils [pypi library] [source repo]