Installation¶
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 https://github.com/bigdatagenomics/workflows
$ 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