Getting started

Required packages

Enrich2 runs on Python 2.7 and has the following dependencies:

The configuration GUI requires Tkinter. Building a local copy of the documentation requires Sphinx.


We recommend using a scientific Python distribution such as Anaconda or Enthought Canopy to install and manage dependencies.


PyTables may not be installed when using the default settings for your distribution. If you encounter errors, check that the tables module is present.

Installation and example dataset

  1. Make sure the required packages are installed.

    1. To set up a new Anaconda environment for Enrich2, use the following environment file (click to download). Detailed instructions for setting up conda environments can be found in the conda documentation.

      name: enrich2
        - python=2.7
        - numpy
        - scipy
        - pandas=0.19
        - pytables
        - statsmodels
        - matplotlib
  2. Download Enrich2 from the GitHub repository and unzip it.

  3. Using the terminal, navigate to the Enrich2 directory and run the setup script by typing python install

To download the example dataset, visit the Enrich2-Example GitHub repository. Running this preconfigured analysis will create several Automatically generated plots. The Example notebooks demonstrate how to explore the Output HDF5 files.

Enrich2 executables

The Enrich2 installer places two executable scripts into the user’s path. Both executables run the same analysis, but through different interfaces.

  • enrich_gui launches the Enrich2 graphical user interface. This is the recommended way to create a configuration file for Enrich2. See Using the GUI for a step-by-step guide.
  • enrich_cmd launches the program from the command line. This is recommended for users performing analyses on a remote server who have already created configuration files. For a detailed list of command line options, type enrich_cmd --help