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.
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 Workflowsbin/
contains a few legacy scripts, though most are inscripts/
deploy/docker
contains containerization related scripts/configurationdocker-compose.yml
builds the new local deployment (seedocker-local.rst
)Dockerfile
contains the Docker build instructions for the cgap-portal (seedocker-production.rst
)docs/ contains
documentationMakefile
contains macros for common build operations (seemake info
)package.json
andpackage-lock.json
specify the front-end dependenciespyproject.toml
andpoetry.lock
specify the back-end dependenciesscripts/
contains misc scriptssetup_eb.py
performs final installation setupsrc/encoded/
where the code is
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 metadatacommands/
contains Python commands that can be run on the system from the command linedocs/
contains ReadTheDocs documentationingestion/
contains ingestion related code, such as mapping table intake and VCF processingschemas/
contains the metadata schemassearch/
contains the search/filter_set APIsstatic/
contains front-end codetests/
contains back-end unit tests and insert datatypes/
contains metadata type definitionsupgrade/
contains collection schema version upgraders
Note that cgap-portal
is bound on supporting functionality in numerous libaries, but importantly:
- dcicsnovault [pypi library] [source repo]
- dcicutils [pypi library] [source repo]