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Getting started

Out of date

Please see the updated version of this tutorial.

Welcome!​

We've been working hard on JBrowse 2 and are happy to be able to start sharing it with all of you. We're still in development, so what we use today should be considered "beta" software. The up-side for you, though, is that an suggestions you make are more likely to get quickly integrated into JBrowse 2.

Follow along​

This tutorial was used as the basis for a training session at the Bioinformatics Community Conference 2020. If you'd like, you can follow along with the tutorial using the recording below.

Embedding JBrowse 2 in your website, BCC2020 West Training from Jennifer Vessio on Vimeo.

What you need​

If you use our provided virtual machine (VM) (download here), then you'll have everything you need ready to go. To run the VM, you'll need to download the Oracle VirtualBox software (download here). Also download the extension pack on that page. Once VirtualBox is installed, go to Tools -> Preferences -> Extensions -> Add and select the downloaded extension pack to add it.

Once VirtualBox and the extension pack are installed, open the VM we provided and it will import itself into VirtualBox (the name of the VM will be "JBrowse 2 BOSC"). Then just click Start and it will start an Ubuntu Linux machine with everything you need pre-installed. Note that the user name is 'jbrowse' and the password is 'gmod', which you will need if you ever need to use sudo to run any commands.

A second option is to use an AWS AMI Ubuntu 2020 server set up to work with this course. The AMI ID for the course machine is ami-06d3d077f91ea603e and is located in us-east-1 (Northern Virginia). If you choose to run this machine, be sure to open incoming access on port 80 and 3000 in the security groups. The user name is 'ubuntu' and there is no password, so sudo will just work.

If you're not using the provided virtual machine, you can do most of the tutorial with a simple text editor and some way to serve files (just opening the HTML files we create in a browser won't work, you'll need a server). If you have node installed, you can run a simple server by running npx serve (or you can install it globally with npm install -g serve or yarn global add serve and then run serve).

We'll also be using the JBrowse CLI, although you can technically complete the tutorial without it. You can install it by making sure you have node installed and then running [sudo] npm install -g @jbrowse/cli (or yarn global add @jbrowse/cli). Check that it installed properly by running jbrowse --help.