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JBrowse web quick start

In this guide, we'll get an instance of JBrowse running on your computer.

Pre-requisites

  • Ability to run commands on the command line
  • Node.js 10.4+
caution

If you are using apt as your package manager, we recommend not using it to install Node.js. Good alternatives include NodeSource or NVM.

Download

You can download JBrowse 2 by using the JBrowse CLI or by downloading and unpacking it manually. We recommend using the JBrowse CLI since it also includes utilities to help you configure JBrowse 2 once it is set up.

Downloading using the JBrowse CLI

The JBrowse CLI can help perform many tasks to help you manage JBrowse 2, such as:

  • create a new instance of JBrowse 2 automatically
  • update an existing instance of JBrowse 2 with the latest released version
  • configure your JBrowse 2 instance

Installing the CLI tools

To install the JBrowse CLI, run

npm install -g @jbrowse/cli

After running this command you can then test the installation with

jbrowse --version

This will output the current version of the JBrowse CLI.

note

If you can't or don't want to globally install the JBrowse CLI, you can also use the npx command, which is included with Node.js, to run JBrowse CLI without installing it. Simply replace jbrowse with npx @jbrowse/cli in any command, e.g.

npx @jbrowse/cli --version

Using jbrowse create to download JBrowse 2

In the directory where you would like to download JBrowse 2, run this command

jbrowse create jbrowse2

Downloading manually

You can also download JBrowse 2 manually. Go to the releases page of the JBrowse 2 GitHub repository and find the latest release that is tagged @jbrowse/web. Download the ZIP file from that release. Make sure it is the ZIP file that starts with jbrowse-web- and not the "Source code" ZIP file. Once you have downloaded the ZIP file, extract it to the location you would like to have JBrowse 2.

Checking the download

Whether you used the JBrowse CLI or downloaded manually, the directory where you downloaded JBrowse should look something like this:

jbrowse2/
├── a586bb28a5bad4a3aba2.worker.js
├── a586bb28a5bad4a3aba2.worker.js.LICENSE.txt
├── a586bb28a5bad4a3aba2.worker.js.map
├── asset-manifest.json
├── favicon.ico
├── index.html
├── manifest.json
├── precache-manifest.52c8ba3337cf7ae812b37d874b2de030.js
├── robots.txt
├── service-worker.js
├── static/
└── test_data/

Running JBrowse 2

JBrowse 2 requires a web server to run. It won't work if you try to directly open the index.html in your web browser. We can use a simple server to check that JBrowse 2 has been downloaded properly. Run

cd jbrowse2/
npx serve .

This will start a web server in our JBrowse 2 directory. Navigate to the location specified in the tool's output. It will look something like http://localhost:5000. Once at that page, you should see a page that says that the configuration is not found. That is expected, since we haven't configured JBrowse 2 yet. It will look something like this:

JBrowse 2 screen showing no configuration found
Figure: JBrowse 2 screen showing no configuration found

Go ahead an click on the sample config to see a JBrowse 2 running with a demo configuration. It should look like this:

JBrowse 2 screen with a sample configuration
Figure: JBrowse 2 screen with a sample configuration

Congratulations! You're running JBrowse 2.

Next steps

Now that JBrowse 2 is set up, you can configure it with your own genomes and tracks. There are two ways you can configure JBrowse 2: with the JBrowse CLI (guide here) or with JBrowse 2's built-in graphical configuration editing (guide here).