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Quick Start: Local Compute


  1. Install Virtualbox and Vagrant
  2. Download and unpack bioBakery
  3. 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).


After installing Conda, set up your channels so the biobakery repository is at the top of your list. Next run the command $ conda install $TOOL -c biobakery, replacing $TOOL with the name of the tool. For a short tutorial on how to install and run a demo using a bioBakery Conda package, see the section on bioBakery Conda packages.


After installing Docker, run the command $ docker pull biobakery/$TOOL, replacing $TOOL with the name of the tool. For a short tutorial on how to install and run a demo in a biobakery Docker container, see the section on bioBakery Docker images.

Quick Start: Cloud Compute

Google Cloud

The biobakery tool suite is available pre-installed on a Google Cloud image (Ubuntu 16.04 plus miniconda) from the bucket: biobakery_bucket/biobakery_image_v1.6.tar.gz. For more information see the section on bioBakery in Google Cloud.

Amazon Web Services

The biobakery tool suite is also available pre-installed on an AMI (Ubuntu 16.04 plus miniconda) from Amazon Market Place, search for "biobakery" from the "Community AMIs" list. For more information see the section on bioBakery in Amazon EC2 .

Please note, due to conflicting dependencies the bioBakery tools installed on the cloud images (GCE and AMI) and the Vagrantbox are each installed in their own conda environment. To obtain a list of all of the conda environments on each image run $ conda env list.

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.