ProteinPaint

a genomics visualization tool for exploring a cohort's genotype and phenotype data

Source Code

git clone git@github.com:stjude/proteinpaint.git

Installation

If working on the server code: Install the system depedencies as listed in the installation instructions.

cd proteinpaint
npm run sethooks
nvm use 20
npm install
# follow the instructions at https://docs.google.com/document/d/1tkEHG_vYtT-OifPV-tlPeWQUMsEd3aWAKf5ExOT8G34/edit

Develop

These scripts require npm v7.7.6+ and are tested with Node v16+. Bundles were also tested to run in Node v12.21+ in a SJ host machine.

# develop BOTH server and client code using 2 terminal windows/tabs
npm run dev # rebundles frontend code
npm start # in separate terminal runs the ProteinPaint server, requires a serverconfig.json at the project root

# --- OR --- 
# to display both server/client bundling logs, 
# plus server process logs in one terminal window/tab
npm run dev1

# --- OR ---
# see build/dev/README.md to use a Docker container for development

When running your dev server, you can see marked up README's in the browser.

Test

npm testws # tests all workspaces

You can also set your serverconfig.debugmode: true, and open http://localhost:3000/testrun.html to see available client-side unit and integration tests.

Build

Package Release

The build and release steps can be triggered via Github Actions using the Create Release workflow.

Docker Build

See container/README.md.

Version

Use Github Actions to coordinate the release of related package updates. The package versioning, build, and deployment uses the standard npm tooling under the hood (version, pack, and publish, respectively).

You may dry-run a version change by running the following:

cd ~/proteinpaint
# see the comments in the script for arguments
./build/jump.sh patch

# to undo changes if the `-w` option was used 
git restore .

Document

To auto-generate documentation to public/docs,

npm run doc

TODOs:

• Organize the leftbar links by API topics, by using typescript namespaces or coding a custom plugin
• Display test code that are specific to a documented type or interface