Toil workflows for bigdatagenomics tools. Apache 2 licensed.
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bdgenomics
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README.rst

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.