jbrowse-plugin-gdc

jbrowse-plugin-gdc

JBrowse 2 plugin for the NCI Genomic Data Commons (GDC)

Install

For use in JBrowse Web

No installation required

For use in @jbrowse/react-linear-view

yarn add jbrowse-plugin-gdc

Usage

In JBrowse Web

Development

git clone https://github.com/GMOD/jbrowse-plugin-gdc.git
cd jbrowse-plugin-gdc
yarn
yarn start

Then open JBrowse Web to (assuming it is running on port 3000):

http://localhost:3000/?config=http://localhost:9000/config.json

Demo

https://s3.amazonaws.com/jbrowse.org/code/jb2/main/index.html?config=https%3A%2F%2Funpkg.com%2Fjbrowse-plugin-gdc%2Fdist%2Fconfig.json

Production

Add to the "plugins" of your JBrowse Web config:

{
  "plugins": [
    {
      "name": "GDC",
      "url": "https://unpkg.com/jbrowse-plugin-gdc/dist/jbrowse-plugin-gdc.umd.production.min.js"
    }
  ]
}

In @jbrowse/react-linear-view

import React from 'react'
import 'fontsource-roboto'
import {
  createViewState,
  createJBrowseTheme,
  JBrowseLinearGenomeView,
  ThemeProvider,
} from '@jbrowse/react-linear-view'
import GDC from 'jbrowse-plugin-gdc'

const theme = createJBrowseTheme()

function View() {
  const state = createViewState({
    assembly: {
      /* assembly */
    },
    tracks: [
      /* tracks */
    ],
    plugins: [GDC],
  })
  return (
    <ThemeProvider theme={theme}>
      <JBrowseLinearGenomeView viewState={state} />
    </ThemeProvider>
  )
}

Screenshot

Changelog

v2.0.0

• Adds new 'Add GDC Data' widget to the File menu which enables use of GDC files and resources
• Adds adaptability for all GDC-originating data/files that have location information through the Add GDC Data widget
• Adds drag and drop interface for local files that have originated from the GDC
• Adds ability to bulk-import files from the GDC using JSON export
• Adds ability to copy and paste 'Explore' sessions/URLs from the GDC and import them into JBrowse (i.e. https://portal.gdc.cancer.gov/exploration)
• Adds ability to copy and paste file URLs from the GDC and import the file into JBrowse (i.e. https://portal.gdc.cancer.gov/files/<some file UUID>)
• Adds ability to quick-add GDC explore tracks to maintain multiple sessions of Exploring GDC mutations and genes using the built-in track filtering interface