bdgenomics.workflows

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

.. _Big Data Genomics: https://github.com/bigdatagenomics .. _Toil: https://github.com/BD2KGenomics/toil

For detailed documentation, see our readthedocs site_.

.. _readthedocs site: https://bdg-workflows.readthedocs.io

Supported workflows

We support Workflows for running:

• Copy number variant calling using DECA_.

.. _DECA: https://github.com/bigdatagenomics/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.