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Toil Documentation
==================
Toil is an open-source pure-Python workflow engine that lets people write better pipelines.
Check out our `website`_ for a comprehensive list of Toil's features and read our `paper`_ to learn what Toil can do
in the real world. Please subscribe to our low-volume `announce`_ mailing list and feel free to also join us on `GitHub`_ and `Gitter`_.
If using Toil for your research, please cite
Vivian, J., Rao, A. A., Nothaft, F. A., Ketchum, C., Armstrong, J., Novak, A., … Paten, B. (2017).
Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology, 35(4), 314–316.
http://doi.org/10.1038/nbt.3772
.. _website: http://toil.ucsc-cgl.org/
.. _announce: https://groups.google.com/forum/#!forum/toil-announce
.. _GridEngine: http://gridscheduler.sourceforge.net/
.. _Apache Mesos: http://mesos.apache.org/
.. _spot market: https://aws.amazon.com/ec2/spot/
.. _Amazon Web Services: https://aws.amazon.com/
.. _Google Compute Engine: https://cloud.google.com/compute/
.. _OpenStack: https://www.openstack.org/
.. _GitHub: https://github.com/BD2KGenomics/toil
.. _Gitter: https://gitter.im/bd2k-genomics-toil/Lobby
.. _paper: http://biorxiv.org/content/early/2016/07/07/062497
.. todolist::
.. toctree::
:caption: Getting Started
gettingStarted/quickStart
.. toctree::
:caption: Common Workflow Language (CWL)
cwl/introduction
cwl/running
cwl/conformance
.. toctree::
:caption: Workflow Description Language (WDL)
wdl/introduction
wdl/running
wdl/developing
wdl/conformance
wdl/tutorial
.. toctree::
:caption: Advanced Toil Usage
running/introduction
running/cliOptions
running/utils
running/debugging
running/cloud/cloud
running/hpcEnvironments
running/server/wes
.. toctree::
:caption: Toil Python API
python/developing
python/toilAPI
python/toilAPIJobstore
python/toilAPIJobFunctions
python/toilAPIMethods
python/toilAPIRunner
python/toilAPIFilestore
python/toilAPIBatchsystem
python/toilAPIService
python/toilAPIExceptions
.. toctree::
:caption: Contributing to Toil
contributing/contributing
contributing/checklists
.. toctree::
:caption: Appendices
appendices/architecture
appendices/aws_min_permissions
appendices/deploy
appendices/environment_vars
* :ref:`genindex`
* :ref:`search`
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