https://github.com/bigdatagenomics/workflows

Toil workflows for bigdatagenomics tools. Apache 2 licensed.
https://github.com/bigdatagenomics/workflows

Last synced: about 2 months ago
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Toil workflows for bigdatagenomics tools. Apache 2 licensed.

• Host: GitHub
• URL: https://github.com/bigdatagenomics/workflows
• Owner: bigdatagenomics
• License: apache-2.0
• Created: 2017-04-28T07:13:52.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2021-04-22T17:22:14.000Z (over 3 years ago)
• Last Synced: 2024-09-18T09:06:08.427Z (4 months ago)
• Language: Python
• Homepage: http://www.bdgenomics.org
• Size: 155 KB
• Stars: 5
• Watchers: 4
• Forks: 5
• Open Issues: 9
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        
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.