@gmod/jbrowse/docs/site/jbrowse_desktop.md

JBrowse - client-side genome browser

---
id: jbrowse_desktop
title: JBrowse Desktop
---

This page provides a reference guide for "Desktop JBrowse" or "JBrowse
Desktop", which is a [electron application](https://electron.atom.io)
that was unveiled for the release of JBrowse 1.12.0.

The operation of JBrowse Desktop is comparable to other desktop genome
browsers like IGV or IGB, and it can be run without setting up a
webserver (most of the time normal jbrowse runs on apache and is viewed
in a web browser). In contrast, JBrowse Desktop is a simple exe file
that can easily be run locally on Windows, Mac OS, or Linux.

## Installation

At the most basic level, setting up JBrowse Desktop consists of:

  - Downloading a zip file script from jbrowse.org e.g. from
    <http://jbrowse.org/jbrowse-1-12-1/> and OSX and a Windows version
    exists JBrowse-1.12.1-desktop-osx.zip and
    JBrowse-1.12.1-desktop-win.zip
  - After downloading unzip the file to somewhere. There is no official
    uninstaller but you can move it to the Program files or Applications
    directory as needed.

Note: on Mac, you can alternatively use Homebrew and run \`brew cask
install jbrowse\` which will download and place jbrowse in your
Application directory

## Overview of JBrowse Desktop

When you run JBrowse Desktop you will see a sort of "welcome screen"
that gives you several options

  - View Volvox sample data
  - Open sequence file, this allows you to open FASTA, Indexed FASTA, or
    .2bit
  - Open data directory, this allows you to open a data directory that
    has been prepared with normal jbrowse tools

Note: it is highly recommended to use Indexed FASTA (selecting both a
fasta and a fai file generated by \`samtools faidx file.fasta\`) or
2bit. Even small genomes with normal FASTA will be much slower\!

## Screenshot

![800px|center|thumb|JBrowse desktop.](assets/config/Jbrowse_desktop_screenshot.png)

This is the welcome page when you open up the jbrowse app. You can open
up sequence files such as fasta, 2bit, or indexed fasta here. Or, you
can open up a pre-existing jbrowse data directory. You can also see a
list of past "sessions" which can be revisited later. The red warning is
sort of awkward but it does not have any meaning here, it just means
that you aren't currently in jbrowse main screen

## Limitations

  - The "Save session" function will not save some configuration
    customizations, so if you have advanced customizations it would be
    recommended to make a data directory by hand the trackList.json and
    tracks.conf format files
  - If you open a data directory on the web, then "Save session" won't
    work

## Features

  - Can open files from shared network folders and external hard drives
    on both windows and mac
  - Can open files from remote URLs
  - Can open data directories from remote URL
  - Saves "sessions" to the OS "application data" folders
  - Has a "home screen" that lists previous sessions

## Technical details

The folder where sessions are saved is generally

  - OSX - "~/Library/Application Support/jbrowse"
  - Windows - "C:\\Users\\username\\AppData\\Roaming\\jbrowse"

## Tested platforms

  - OSX Mavericks
  - macOS sierra
  - Windows 7
  - Windows 10

Note: JBrowse Desktop doesn't work on windows XP and Vista (in fact all
electron apps require Windows 7+)

# External Links

  - [JBrowse: a dynamic web platform for genome visualization and
    analysis](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1)
    paper