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Quick start for JBrowse desktop

Installing JBrowse desktop

This guide will walk you through installing jbrowse 2 on the desktop

JBrowse 2 desktop does not require any pre-requisites for your installation, so we can jump right in

Installing on Linux

Visit http://github.com/gmod/jbrowse-components/releases/latest and find the latest Linux AppImage release. Download that file to wherever you would like to keep it and then start it in one of two ways:

In the terminal

Using the AppImage file on linux, all that is needed is to make the file executable which you can do in a terminal

# Make the AppImage file executable, only need to do this once
chmod  a+x jbrowse-desktop-*-linux.AppImage
# Run!
./jbrowse-desktop-*-linux.AppImage

In your file explorer

This may vary slightly depending on your distribution but should basically follow these steps:

  1. Right-click on the AppImage file and select "Properties"
  2. Go to the "Permissions" tab
  3. Check "Allow executing file as program" and close

You can now double-click the AppImage file to launch JBrowse.

Installing on MacOS

Visit http://github.com/gmod/jbrowse-components/releases/latest and find the latest MacOS release artifact in our latest builds.

Download the .dmg file for MacOS, double click, and drag JBrowse 2 into 'applications'.

You can now open JBrowse 2 like any other application on your Mac.

Installing on Windows

Visit http://github.com/gmod/jbrowse-components/releases/latest and download the latest Windows installer executable (will end with win.exe).

Double-click the downloaded installer and it will install and open JBrowse. You can now open JBrowse like any other program.

JBrowse Desktop start screen

After you have installed and started JBrowse Desktop you will see a start screen like this

Screenshot showing the start screen on JBrowse desktop
Figure: Screenshot showing the start screen on JBrowse desktop

The left hand panel, with "Launch new session" can quickly launch a new session using either your own custom genome (which you can load using an indexed FASTA or a twobit file). Also on the left hand panel is the "Quickstart list". Users can click the checkbox next to e.g. hg38 and hit Go.

On the right hand panel is the "Recently opened sessions". This includes sessions that you have specifically saved, and sessions that were autosaved (e.g. ones that you didn't explicitly use "Save as" on). You can re-open your sessions by clicking on the link.

Special features on the start screen

Converting a saved session into a quickstart entry

If you study a rare species, you might find it useful to customize your quickstart panel. We allow you to convert a session in the "Recently opened sessions" into an entry that appears in the quickstart list.

To do so: Click a checkbox next to a session in the "Recently opened sessions" table, and then hit the

icon next to the trash can icon. This is helpful if e.g. you want to make your own custom organism a template for quickstarts in the future.

Selecting multiple entries from the quickstart panel

Users can also hit the checkbox for multiple species in the quickstart list, and then the sessions are combined which is helpful if e.g. you are doing comparative genomics of hg19 and mm10.

Next steps

Check out the user guide for more info on how to use JBrowse Desktop. This covers all the features that are available with screenshots and instructions.