Installation

We provide two methods for installing and using FoxMask:

Standalone installation on Linux

This is the recommended method for production.

This method will install FoxMask on your Linux computer. We provide an automated install script, which will take care of installing all the dependencies needed to run FoxMask as well as the software itself. It is made for Ubuntu 16.04. The installation script is located in install-scripts/install-ubuntu16.sh of the FoxMask repository. To execute the script, simply clone the repository and execute the install script as a regular user. Note that you will need to have sudo rights.

$ git clone https://github.com/edevost/foxmask.git
$ cd foxmask
$ sh install-Ubuntu16.sh

Congratulation, you are now ready to start using FoxMask on your Linux Box ! Consult our Usage page to get started.

Note

This installation script have been successfully tested on Ubuntu 16.04, on bare metal computers as well as on GCE (Google Cloud Engine) and Virtual-Box 5.0. Successful installation have also been performed on Debian Stretch and Ubuntu 14.04 container (TravisCI).

Installation through a virtual machine

We do not recommend this installation for production.

We provide a complete virtual environment to run and use FoxMask. The main advantages of this installation is that you can rapidly get FoxMask running on any platform. However, there are important drawbacks to consider:

  • Poor performances compared to standalone installation
  • A bit heavy to manage (Vagrant + Virtual-Box + share USB)

Despite theses drawbacks, we consider that using our FoxMask box can be very useful for first time users wanting to test the software, or for development purposes.

Note

Again, let me emphasize that this method is suitable to rapidly get FoxMask up and running on another platform than Ubuntu. However, anyone serious about implementing an automated image analysis pipeline with FoxMask should consider installing it on bare metal hardware running a Linux OS, or on a virtual infrastructure running libvirt. We provide a fully automated installation script, successfully tested on Ubuntu 16.04. Please see Standalone installation on Linux to install FoxMask on you Linux machine.

To run the FoxMask virtual machine on your Linux, Mac or Windows computer, you will need the following three open source software:

Follow the installation procedure for your platform. Once theses software are installed, you are ready to install FoxMask by issuing the following command:

$ git clone https://github.com/edevost/foxmask.git
$ cd foxmask
$ pip install . --user

This will fetch all needed components to run the virtual machine and update to the latest verstion of FoxMask. You can then start the virtual machine by issuing the following commands:

cd foxmask
vagrant up

This will boot the virtual machine. You can also manage you virtual machine through Virtual-Box software, and start or stop your machine from there. The start process will bring you to the Ubuntu desktop. The default user and password on this virtual environment is vagrant vagrant. Once the machine is ready, you can proceed to our Usage section to launch FoxMask on the provided set of images.

Testing on your own set of images

To test FoxMask on your own set of images, you will have to make your images available to the virtual machine. To do so, we recommend saving your image set on an USB drive, and make the drive available to Virtual-Box. There are many good tutorials on the web explaining the process:

Making this work will demand a bit of work and reading, but nothing out of reach of any computer users with minimal computer knowledge. The main steps to get your FoxMask virtual machine to have access to an USB drive plugged on your host computer are the following:

  • Shutdown your FoxMask virtual machine if it is running
  • Plug your USB drive on your computer (host)
  • Install Virtual Box 5.0 extension pack
  • Activate USB controller on Virtual-Box
  • Add your drive

Once your drive is added, boot your FoxMask virtual machine and check if there is a link to your drive on the desktop. If everything went well, you will have direct access to your USB drive on your virtual machine ! You can then proceed to our Usage section to start using FoxMask on your set of images.