This document describes how to install the Big Data Genomics workflows. First, you must install Toil into a Python virtualenv. We support Toil versions 3.8.0 to 3.10.1. If you plan to run your workflow on `Amazon Web Services`_, you must install Toil with the AWS extra and configure your AWS account.

Basic Installation

bdgenomics.workflows can be easily installed using pip:

$ pip install bdgenomics.workflows

Building from source

If extending, modifying, or reusing a workflow, you will need to build from source. This allows changes you make to the workflows to be reflected immediately in your runtime environment.

First, clone the source:

$ git clone
$ cd workflows

Then, create and activate a virtualenv:

$ virtualenv venv
$ . venv/bin/activate

Install Toil into this virtualenv:

$ pip install toil==3.10.1

From there, you can list all available Make targets by running make. Now, we can install in development mode (such that changes to the source code will immediately affect the virtualenv):

$ make develop

To build the docs, run make develop with all extras followed by

$ make docs