This is a template github repository for others to copy and use as a starter to develop and share their own extensions and profiles from the GA4GH Genomic Knowledge Standards (GKS).
The instructions below are for copying this repo to make it your own. Once you have done that you should replace this top-level heading in this README.md file with information about your specific schema and project.
You will want to replace all the YOUR_GITHUB_ID and YOUR_PROJECT tags below with your github project id and github project or repo name.
You will also want to go through the schema folder and change all the references to my-project in folder names, file names and file content to YOUR_PROJECT.
This starter GA4GH GKS repo is set up to refere va-spec and all the submodules nested within it. If you wish to only use a subset of the GKS projects starting at cat-vrs and lower you may want to change the submodule configuration. But it is not necessary.
<--- Remove this line and all the above from the README.md before saving your copy and sharing.
The schema is available in the schema/ directory, in both yaml and json versions. It conforms to JSON Schema Draft 2020-12. For a list of libraries that support JSON schema, see JSONSchema>Tools.
Fork the repo at https://github.com/YOUR_GITHUB_ID/YOUR_PROJECT.
git clone --recurse-submodules git@github.com:YOUR_GITHUB_ID/YOUR_PROJECT.git
cd YOUR_PROJECT
make devready
source venv/3.12/bin/activate
pre-commit install
If you already cloned the repo, but forgot to include --recurse-submodules you can run:
git submodule update --init --recursive
YOUR_PROJECT uses YOUR_PROJECT-source.yaml as the source document for JSON Schema.
To create the corresponding def and json files after making changes to the source document, from the root directory:
cd schema
make all
Note: We have a custom pre-commit hook to run these commands after you stage a source document
The YOUR_PROJECT specification documentation is written in reStructuredText and located in docs/source. Commits to this repo are built automatically at https://YOUR_RTD_URL.
To build documentation locally, you must install entr:
brew install entr
Then from the root directory:
cd docs
make clean watch &
Then, open docs/build/html/index.html. The above make command should build docs when source changes. (Some types of changes require recleaning and building.)
The VRS repo contains two kinds of tests. Basic smoke tests in tests/ ensure that the schema is parsable and works with certain tools. These tests provide a basic sanity check during development.
Validation tests (in validation/) provide language-neutral tests for those implementing tools with YOUR_PROJECT.
To run the smoke tests:
make test