bdgenomics.workflows

A package of single-node and distributed workflows for running Big Data Genomics tools using Toil.

For detailed documentation, see our readthedocs site.

Supported workflows

We support Workflows for running:

• Copy number variant calling using DECA.

Quick Start

The latest release of bdgenomics.workflows can be installed using Pip into a virtualenv. You must install Toil first:

$ virtualenv bdg-workflows
$
$ . bdg-workflows/bin/activate
$
$ pip install toil==3.10.1
$
$ pip install bdgenomics.workflows
$
$ bdg-deca

To install from source:

$ virtualenv bdg-workflows
$
$ . bdg-workflows/bin/activate
$
$ pip install toil==3.10.1
$
$ make develop
$
$ bdg-deca

Currently, we only support Python 2. Python 3 support is forthcoming.