higlass-app

HiGlass App

The web application for viewing, exploring, and annotating 1D and 2D genomic data.

URL: http://higlass.io

Note: This is the source code for the web application only! You might want to check out the following repositories as well:

• HiGlass viewer: https://github.com/hms-dbmi/higlass
• HiGlass server: https://github.com/hms-dbmi/higlass-server
• HiGlass docker: https://github.com/hms-dbmi/higlass-docker

Development

Installation

$ git clone --recursive https://github.com/hms-dbmi/higlass-app && higlass-app
$ npm install

Note: If you forgot to add --recursive do the following to pull the submodules

$ git submodule update --init --recursive --remote

In order to update the wiki run:

$ git submodule update --recursive --remote

Commands

Developmental server: npm start

Production build: npm run build

Run tests: npm test

Update wiki: npm run update-wiki

Configuration

HiGlass App can be configured at build time using config.json. config.json contains the default configuration. To adjust it copy it to config.dev.json, config.prod.json, or config.local.json. dev is used in developmental mode, prod is picked up in production, and local can be used for local testing. The config is overwritten in the following order: default, dev, prod, local.

Folder Structure

HiGlass App is based on react-create-app and implements the following folder structure:

• /build [Do not edit.]

  Contains the build files.

• /config

  Contains the build configs for webpack and converting Markdown into JSX. Except the JSX, the files are derived from react-create-app.

• /node_modules [Do not edit.]

  Contains thrid party libraries.

• /public

  Contains the public index files of HiGlassApp.

• /scripts

  Contains node scripts for webpack and converting Markdown into JSX. Except the JSX, the files are derived from react-create-app.

• /src

  Entry point for the application source.

  • /actions

    Flat folder containing Redux actions. All actions should be exported in the index.js.

  • /components

    Flat folder containing presentational components. See Dan's article for a comparison between presentational and container components.

  • /configs

    Flat folder containing config files. Configs should host all constant variables.

  • /containers

    Flat folder containing container components. See Dan's article for a comparison between presentational and container components.

  • /images

    Flat folder containing images.

  • /reducers

    Flat folder containing Redux reducers.

  • /services

    Flat folder containing services. (A service is considered to be an object or function with a app-wide state, not managed by the Redux store. E.g., the Redux store itself is a service to provide convinient helper functions for undo etc.)

  • /styles

    Flat folder containing generic style components. Note: this is kind of arbitrary but I like to separate reusable CSS classes from index.scss such that I can quickly drop them into other apps.

  • /utils

    Flat folder containing utility functions. (Utility function must be pure and should not have any state.)

  • /views

    Flat folder containing all view components. (View components are just like presentational components with the only difference that they are associated to a specific URL. This separation is again arbitrary but I like having all views separated as I consider them uncomposable. Only Main should import views.)