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CGAP PORTAL (HMS-BGM)

Build Status Coverage Percentage Documentation Status

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.

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: