This distribution creates a Docker image with all of the system requirements for running the Proteinpaint application.

NOTE: The reference data files will still need to be downloaded.

TODO:

• automate or simplify reference data download
• ideal???: make a GDC-like API for PP reference data, so that there will not be a need to download really large reference data files. Only when there are performance and reliability concerns will local copies of reference data be desirable.

Requirements:

• npm
• Docker Engine or Desktop

echo "@stjude:registry=https://npm.pkg.github.com/" > .npmrc

# for non-global installation in a folder
npm install @stjude/proteinpaint-container

# --- OR ---
# for global installation from any folder
npm install -g @stjude/proteinpaint-container

NOTE: The installation will trigger a Docker image build, which may take approximately 10 minutes.

To pull updates:

npm update @stjude/proteinpaint-container

Example usage, where the current working directory has:

• a serverconfig.json, which has a "url": "http://localhost:[PORT]" entry (default PORT=3456, can be set to any valid, non-conflicting numeric port value)
• an optional dataset folder, containing js files of any serverconfig.genomes.datasets[] entry that is not already included in proteinpaint/server/dataset
• an optional public folder, containing any html page that embed proteinpaint views

# for a full portal with html pages
npx proteinpaint-container

# open the browser to your serverconfig.url entry
# example routes to check, assuming serverconfig.url=http://localhost:3456
# http://localhost:3456/healthcheck
# http://localhost:3456/genomes
# http://localhost:3456: should open the Proteinpaint landing page

To run only the Proteinpaint server data api, without a static file server:

npm proteinpaint-container server

To run a fully customized server, follow the docker run commands in run.sh.

The Dockerfile may optionally use the various proteinpaint-* as packed from source code.

# will pack workspaces and replace each package.json's dependency versions
# with the tarball location as copied into the Docker build
./pack.sh

# will run docker build
./build.sh