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Quick Start

  1. Install Virtualbox
  2. Install Vagrant
  3. Download and unpack bioBakery
  4. Run bioBakery by double clicking (or executing from the command line) the file for your operating system
  • Linux and MacOS: start_biobakery.command
  • Windows: start_biobakery.bat

Please note the first time you run bioBakery it will download and extract the box (~10 GB in size). This can take a bit of time depending on your internet connection. When you run bioBakery in the future, it will start up much faster (~30 seconds).

You can also run bioBakery in Google Cloud or Amazon EC2 or you can install individual bioBakery tools. Individual tools, along with the full tool suite, can be installed with Linuxbrew (Homebrew for MacOS) without root permissions. This is the recommended install method for users on a cluster who do not have elevated permissions as the software will be installed in your $HOME folder. If you have root permissions or a container engine is available, the tools can be run from Docker images.

Please see the sections and links that follow for detailed information about bioBakery.


bioBakery is an easy to use, virtual environment that provides a platform for the research community to use the Huttenhower tools without having to install the tool suite directly on their personal machines. This documentation provides in depth instructions on all topics related to bioBakery (installation, basic setup and advanced configuration).

We provide support for bioBakery users. Please join the bioBakery users google group and feel free to post questions directly to the group or by emailing

Please select one of the three options for documentation.

  • Basic usage provides information about installation, basic setup, how to run a demo, and sharing documents and folders
  • Advanced configuration documents useful tools for advanced users on how to run bioBakery with modified components of the virtual environment
  • Internal documentation is for the Huttenhower Lab users and other members of the bioinformatics community to document the mechanism of bioBakery (e.g. how to add new tools and package and release new virtual images etc.)

We strongly recommend new users read the Basic Usage documentation to get started.

Please feel free to log any errors in the bioBakery Issue Tracker system.