jbrowse-plugin-ucsc

This plugin adapts the UCSC API

Install

For use in JBrowse Web

No installation required

For use in @jbrowse/react-linear-view

yarn add jbrowse-plugin-ucsc

Usage

In JBrowse Web

Development

git clone https://github.com/cmdcolin/jbrowse-plugin-ucsc-api.git
cd jbrowse-plugin-ucsc-api
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/master/index.html?config=https%3A%2F%2Funpkg.com%2Fjbrowse-plugin-ucsc%2Fdist%2Fconfig.json&session=share-wyY8ZgC9uY&password=CtcMX

Production

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

{
  "plugins": [
    {
      "name": "UCSC",
      "url": "https://unpkg.com/jbrowse-plugin-ucsc/dist/jbrowse-plugin-ucsc.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 UCSC from "jbrowse-plugin-ucsc";

const theme = createJBrowseTheme();

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

Screenshot