Skip to content

Latest commit

 

History

History
72 lines (52 loc) · 3.17 KB

README.md

File metadata and controls

72 lines (52 loc) · 3.17 KB
Raw

Developer Deployment / Local Deployment

To deploy Foldy locally for development or testing purposes, you can follow these steps:

Prerequisites

Make sure you have the following tools installed on your machine:

  • Docker (for running the local deployment)
  • Conda (for creating the environment and installing dependencies)

Backend and Databases

  1. Start by setting up the backend and databases using Docker Compose. Open a terminal window and navigate to the project directory.

  2. Run the following command to bring up the backend and databases:

    docker compose \
  --file deployment/development/docker-compose.yml \
  --project-directory . \
  up

    This command will start the frontend & backend servers and the required databases. Note that it takes a few minutes for the images to build, and then a few more minutes for the frontend to start up (the logs will say "Starting the development server...", then it takes ~60 seconds to build the frontend, then it will say "No issues found.").

  3. Install the databases by running the following command:

    docker compose \
  --file deployment/development/docker-compose.yml \
  --project-directory . \
  exec backend flask db upgrade

  4. Access the Foldy website at http://localhost:3000 in your browser.

That's it! You have successfully deployed Foldy locally for development or testing purposes. Explore the website and make any necessary changes to the codebase.

Upgrading Database in development

If any changes are made to the database models, execute the following commands to create a revision and migrate database

docker compose \
     --file deployment/development/docker-compose.yml \
     --project-directory . \
     exec backend flask db stamp $CURRENT_REVISION_NUMBER
docker compose \
     --file deployment/development/docker-compose.yml \
     --project-directory . \
     exec backend flask db migrate
docker compose \
     --file deployment/development/docker-compose.yml \
     --project-directory . \
     exec backend flask db upgrade

Development Tasks

Protein structure prediction tasks in the development environment are not actually performed. Instead a few test cases have been precomputed that auto-complete once queued. Example outputs are stored in a read-only on-disk object store, at /backend/backend/integration_tests/testdata/. You can queue the following proteins and docks to have their structures auto-populated in the UI:

  • Fold 1
    • Name:
    • Sequence: MNKREILKRLLSYLFEDKKGFAIAAVFLLIAAAADVSGPWLIRIFLDDYVSKDHYPAMMLWALAIGYITVTILSGFLHYAYGIRFSRIAVSIVQTIRKKVYASIINQPLSSFDYVPAGKLVSRVTNDTESLKELYVQVVASFLQSLALITAMLTAMYLLSPTLTLVVAILLPSVVLVMYYYQRRSSDPYRESRDLLTDINGVMSESIQGMSLIQLMGQEQRFSERFASLNERHLGAEVRIVKINGIFLRPLIDLLSGIALVSLVAIFGWQGHEVIGVGVLYAFISYLGRVTEPLIELMQRLSLLQQAIMAGERLFELMDAKQHQYGEDDAPIARGDINVSDVNFSYDGTTPVLNNISVSVKEGGFLALVGHTGSGKSTLASLLMGFYPPSSGEIQLGGRPIASLSQNALRNGIALVQQDPHVLPSSFRDNVTLGRNVSDEAVWDALFLVDMADYVRELPNALNTLLGTGDVSLSAGQKQLLALARVLVDKPRILILDEATANIDSGTEERVQQALSALRNTMTIVVIAHRLSTIADADNIMVLHRGHVEEQGAHQALLAQQGRYWQMYQLQKTRAHLKELEEQARD
    • Dock:
      • Name: nadhd2
      • Tool: diffdock
      • SMILES: