{"id":21662831,"url":"https://github.com/higlass/higlass-app","last_synced_at":"2025-04-11T23:42:23.446Z","repository":{"id":53905751,"uuid":"98570710","full_name":"higlass/higlass-app","owner":"higlass","description":"A fully featured application around HiGlass for viewing, exploring, and annotating 1D and 2D genomic data","archived":false,"fork":false,"pushed_at":"2023-09-21T02:44:09.000Z","size":4209,"stargazers_count":7,"open_issues_count":11,"forks_count":4,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-03-25T19:38:27.221Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/higlass.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-07-27T18:58:48.000Z","updated_at":"2024-03-26T06:46:46.000Z","dependencies_parsed_at":"2023-10-20T21:15:15.139Z","dependency_job_id":null,"html_url":"https://github.com/higlass/higlass-app","commit_stats":null,"previous_names":[],"tags_count":51,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-app","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-app/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-app/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-app/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/higlass","download_url":"https://codeload.github.com/higlass/higlass-app/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248497902,"owners_count":21113982,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-25T10:18:17.519Z","updated_at":"2025-04-11T23:42:23.413Z","avatar_url":"https://github.com/higlass.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# HiGlass App\n\n[![HiGlass](https://img.shields.io/badge/higlass-👍-red.svg?colorB=3676b4)](http://higlass.io)\n[![npm version](https://img.shields.io/npm/v/higlass-app.svg)](https://www.npmjs.com/package/higlass-app)\n[![Build Status](https://travis-ci.org/higlass/higlass-app.svg?branch=master)](https://travis-ci.org/higlass/higlass-app)\n[![code style prettier](https://img.shields.io/badge/code_style-prettier-ff69b4.svg)](https://github.com/prettier/prettier)\n\n![User interface](teaser.png)\n\n\u003e The web application for viewing, exploring, and annotating 1D and 2D genomic data.\n\nHiGlass 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](https://github.com/Novartis/peax) as the frontend application.\n\n**URL**: https://higlass.io\n\n**Help**: http://bit.ly/higlass-slack\n\n**Note**: This is the source code for the web application only! You might want to check out the following repositories as well:\n\n- HiGlass viewer: https://github.com/higlass/higlass\n- HiGlass server: https://github.com/higlass/higlass-server\n- HiGlass docker: https://github.com/higlass/higlass-docker\n- HiGlass manage: https://github.com/higlass/higlass-manage\n\n## Install\n\n```bash\nnpm install --save higlass-app\n```\n\n## Development\n\n```bash\ngit clone https://github.com/higlass/higlass-app \u0026\u0026 higlass-app\nnpm install\n```\n\n### Commands\n\n**Developmental server**: `npm start`\n\n**Production build**: `npm run build`\n\n**Autoformat JS code**: `npm run fix`\n\n### Configuration\n\nHiGlass App can be configured at build and run time using [`config.json`](config.json) and [`public/config.js`](public/config.js) respectively.\n\n[`config.json`](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.\n\nAdditionally some settings can be overwritten at run time using [`public/config.js`](public/config.js). For details please see the table below:\n\n| Name                 | Description                                                                                                                                     | Type                 | Default                                   | config.js name               | Configurable via `config.js` only |\n| -------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | -------------------- | ----------------------------------------- | ---------------------------- | --------------------------------- |\n| homepageDemos        | If set to `true` the start page will feature some demo views.                                                                                   | `boolean`            | `false`                                   | HGAC_HOMEPAGE_DEMOS          | no                                |\n| server               | Define the default higlass server from which view config are loaded by default.                                                                 | `string`             | `''` (same host, same port)               | HGAC_SERVER                  | no                                |\n| 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                                |\n| defaultOptions       | Default options that are being passed to `hglib`.                                                                                               | `object`             | _none_                                    | HGAC_DEFAULT_OPTIONS         | no                                |\n| 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                                |\n| runByOrganization    | Name of the organization running the HiGlass instance.                                                                                          | `string`             | _none_                                    | HGAC_RUN_BY_ORGANIZATION     | yes                               |\n| runByOrganizationURL | Optional URL pointing to the host organization's website.                                                                                       | `string`             | _none_                                    | HGAC_RUN_BY_ORGANIZATION_URL | yes                               |\n| runBySlogan          | Slogan to advertise the host organization.                                                                                                      | `string`             | `Run by`                                  | HGAC_RUN_BY_SLOGAN           | yes                               |\n| runByLogoURL         | URL pointing to the host organization's logo.                                                                                                   | `string`             | _none_                                    | HGAC_RUN_BY_LOGO_URL         | yes                               |\n| 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                               |\n| runByContactURL      | URL or mailto link to get in touch with the hosting organization.                                                                               | `string`             | _none_                                    | HGAC_RUN_BY_CONTACT_URL      | yes                               |\n\n### Folder Structure\n\nHiGlass App is based on [react-create-app](https://github.com/facebookincubator/create-react-app) and implements the following folder structure:\n\n- **[`/build`](build)** [_Do not edit._]\n\n  Contains the build files.\n\n- **[`/config`](config)**\n\n  Contains the build configs for webpack and converting Markdown into JSX. Except the JSX, the files are derived from [react-create-app](https://github.com/facebookincubator/create-react-app).\n\n- **[`/node_modules`](node_modules)** [_Do not edit._]\n\n  Contains thrid party libraries.\n\n- **[`/public`](public)**\n\n  Contains the public _index_ files of HiGlassApp.\n\n- **[`/scripts`](scripts)**\n\n  Contains node scripts for webpack and converting Markdown into JSX. Except the JSX, the files are derived from [react-create-app](https://github.com/facebookincubator/create-react-app).\n\n- **[`/src`](src)**\n\n  Entry point for the application source.\n\n  - **[`/actions`](actions)**\n\n    Flat folder containing Redux actions. All actions should be exported in the [`index.js`](src/actions/index.js).\n\n  - **[`/components`](components)**\n\n    Flat folder containing _presentational_ components. See [Dan's article](https://medium.com/@dan_abramov/smart-and-dumb-components-7ca2f9a7c7d0) for a comparison between presentational and container components.\n\n  - **[`/configs`](configs)**\n\n    Flat folder containing config files. Configs should host all constant variables.\n\n  - **[`/containers`](containers)**\n\n    Flat folder containing _container_ components. See [Dan's article](https://medium.com/@dan_abramov/smart-and-dumb-components-7ca2f9a7c7d0) for a comparison between presentational and container components.\n\n  - **[`/factories`](factories)**\n\n    Flat folder containing factory functions. See [Eric's article](https://medium.com/javascript-scene/javascript-factory-functions-with-es6-4d224591a8b1) for an introduction to factory functions.\n\n* **[`/hocs`](hocs)**\n\n  Flat folder containing _higher-order_ components. See the [React docs](https://reactjs.org/docs/higher-order-components.html) for an introduction.\n\n* **[`/images`](images)**\n\n  Flat folder containing images.\n\n* **[`/reducers`](reducers)**\n\n  Flat folder containing [Redux](https://github.com/reduxjs/redux) reducers.\n\n* **[`/styles`](styles)**\n\n  Flat folder containing generic style components. Note: this is kind of arbitrary but I like to separate reusable CSS classes from [`index.scss`](src/index.scss) such that I can quickly drop them into other apps.\n\n* **[`/utils`](utils)**\n\n  Flat folder containing utility functions. (Utility function **must** be pure and should not have any state or side effects!)\n\n* **[`/views`](views)**\n\n  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`](src/components/Main.js) should import views.)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-app","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhiglass%2Fhiglass-app","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-app/lists"}