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1. Installing a Local Galaxy-ES Development Environment

Galaxy-ES has a large number of dependencies, so installing it by hand is tedious. We recommend either a) installing it using Docker, or b) installing it in an Ubuntu VM using an install shell script.

Option 1: Install With Docker

  1. Install Docker (instructions here)
    1. Since Docker can only run on Linux, the Docker installer for Mac will install VirtualBox and a script called boot2docker, which creates a minimal Linux VM in VirtualBox for running Docker containers.
    2. Make sure to set your DOCKER_HOST environment variable.
  2. Pull and run the galaxy-es docker image by executing:
    1. docker pull faceitproject/galaxy-es
    2. docker run -i -t -p 8080:8080 faceitproject/galaxy-es
  3. Browse to http://<docker_ip>:8080/ to see your running Galaxy instance, where <docker ip> is the IP address Docker is running on. (on a Mac, you can find this by executing boot2docker ip
  4. Proceed to 2. Installing face-it tools into Galaxy

Option 2: Install With Script

How how to set up a Galaxy-ES instance in a VirtualBox VM running Ubuntu 12.04:
  1. Install the latest version of VirtualBox from
  2. Create an Ubuntu 12.04 64-bit VM in VirtualBox
    1. Download Ubuntu 12.04 Server ISO, at: (679 megabytes)
    2. Start VirtualBox and select New. Enter name=GalaxyES-Ubuntu-12.04, type=linux, version=Ubuntu (64 bit). Next.
    3. Select a memory size to use. You can change this later if needed.
    4. Create a virtual hard drive, select vdi, and dynamically allocated.
    5. You will be asked a filesystem maximum. Once you have this set, it is not easy to change - make sure you give yourself plenty of space here.
    6. Start the VM
    7. You will be asked for a virtual optical disk. Select the ISO image you downloaded in step 2.
    8. You will be guided through the Ubuntu installation next. Follow along and select your language, keyboard layout, hostname, a username for your personal account, timezone, etc. Continue along until you arrive at the software select screen.
    9. Select OpenSSH and continue. Select yes to install grub on the MBR and installation should complete. The virtual machine will reboot.
  3. Configure port forwarding for SSH and HTTP in VirtualBox
    1. In VirtualBox, select Settings->Network->Port Forwarding. Add a new rule with host port 3022 and guest port 22. Leave the IP addresses empty. Click ok.
    2. In Port Forwarding, add a new rule for port 8080 (the port galaxy will be running on)
  4. SSH into the running VM to install galaxy
    1. On your host machine,  SSH to the VM (for linux and mac hosts, the command is: ssh -p 3022 youruser@ When you are logged into the virtual machine, run the following commands:
      1. wget
      2. chmod +x
      3. sudo ./  (When prompted, enter your password)
    2. Log into the galaxy account (ssh -p 3022 galaxy@
      1. cd galaxy-python/galaxy
      2. Edit universe_wgsi.ini, and add your email address to the "admin_users" line
      3. Run the command ./
  5. Galaxy is now running in the VM. You can access it in your host machine's browser at
  6. Proceed to 2. Installing face-it tools into Galaxy