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Cohort Analysis App with public gene/tissue/cell line data.

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coral_product Phovea

Coral is a web-based visual analysis tool for creating and characterizing cohorts.
This repository described how to setup a Coral instance. Please have a look into the Coral repository for more information on Coral.


Coral is based on the Target Discovery Platform and Phovea framework, runs the backend with Phovea Server, and uses multiple other plugins. To ease the set up process, this repository describes all required components for the front and back end of Coral, as used by the public Coral instances:

Coral Branch app status
main https://coral.caleydoapp.org CircleCI
develop https://coral-daily.caleydoapp.org CircleCI

A running Coral instance consists of:

🔧 Setup a Coral workspace

Follow the steps below the set up a workspace with the above components.

  1. Make sure that you meet all the prerequisites described in the Wiki
  2. The phovea generator will check out repositories and setup a workspace for you. Check the package.json for the generator version compatible with this build.
  3. To prepare the workpace, run:
yo phovea:setup-workspace coral_product -b main
  1. Follow the instructions of the generator and Coral will be ready to use.
  2. The database credentials and location are not included in the repositories. Provde them via the config.jon file at the root of the workspace:
 {
 "tdp_publicdb" : {
   "dburl": "postgresql://read_user:[email protected]/database_name"
  },
  "coral": {
    "dburl": "postgresql://read_write_user:[email protected]/database_name"
  }
}

That's it! 🎉
For any questions or problems, wirte us an email to [email protected] or create an issue on GitHub.

🔼 Update the Coral workspace

Updating an exisiting workspace is a straight forward process:

  1. Fetch the latest commits from the repositories in your workspace. There is a forEach script to ease the process. Run: ./forEach git pull
  2. Incorporate possible changes into the workspace: yo phovea:update
  3. If necessary, update npm dependencies : npm install
  4. Restart Docker and webpack builds.

This repository is part of Phovea, a platform for developing web-based visualization applications.

For tutorials, API docs, and more information about the build and deployment process, see the documentation page.