HiGlass App

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

HiGlass App is used to run https://higlass.io but you can also use it as the starting point for building your own application around HiGlass. For example, it is used in Novartis' Peax as the frontend application.

URL: https://higlass.io

Help: http://bit.ly/higlass-slack

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/higlass/higlass
• HiGlass server: https://github.com/higlass/higlass-server
• HiGlass docker: https://github.com/higlass/higlass-docker
• HiGlass manage: https://github.com/higlass/higlass-manage

Install

npm install --save higlass-app

Development

git clone https://github.com/higlass/higlass-app && higlass-app
npm install

Commands

Developmental server: npm start

Production build: npm run build

Autoformat JS code: npm run fix

Configuration

HiGlass App can be configured at build and run time using config.json and public/config.js respectively.

config.json contains the default configuration. For adjustments, 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.

Additionally some settings can be overwritten at run time using public/config.js. For details please see the table below:

| Name | Description | Type | Default | config.js name | Configurable via config.js only | | -------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | -------------------- | ----------------------------------------- | ---------------------------- | --------------------------------- | | homepageDemos | If set to true the start page will feature some demo views. | boolean | false | HGAC_HOMEPAGE_DEMOS | no | | server | Define the default higlass server from which view config are loaded by default. | string | '' (same host, same port) | HGAC_SERVER | no | | basepath | The base path under which higlass-app will run, e.g., if you set it to /cool higlass-app will be available at https://your-server.com/cool. | string | '' (root) | HGAC_BASEPATH | no | | defaultOptions | Default options that are being passed to hglib. | object | none | HGAC_DEFAULT_OPTIONS | no | | defaultViewConfig | Default view config to load. This can either be a uuid or an actual view config. By default, the default view config has the uuid default. | object or string | none (internally defaults to default) | HGAC_DEFAULT_VIEW_CONFIG | no | | runByOrganization | Name of the organization running the HiGlass instance. | string | none | HGAC_RUN_BY_ORGANIZATION | yes | | runByOrganizationURL | Optional URL pointing to the host organization's website. | string | none | HGAC_RUN_BY_ORGANIZATION_URL | yes | | runBySlogan | Slogan to advertise the host organization. | string | Run by | HGAC_RUN_BY_SLOGAN | yes | | runByLogoURL | URL pointing to the host organization's logo. | string | none | HGAC_RUN_BY_LOGO_URL | yes | | runByLogoOnly | If true the footer will only show a logo. Useful when the logo contains the organization name. By default this is false. | boolean | false | HGAC_RUN_BY_LOGO_ONLY | yes | | runByContactURL | URL or mailto link to get in touch with the hosting organization. | string | none | HGAC_RUN_BY_CONTACT_URL | yes |

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.

  • /factories

    Flat folder containing factory functions. See Eric's article for an introduction to factory functions.

• /hocs

  Flat folder containing higher-order components. See the React docs for an introduction.

• /images

  Flat folder containing images.

• /reducers

  Flat folder containing Redux reducers.

• /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 or side effects!)

• /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.)