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.. ehive_user_manual documentation master file, created by
   sphinx-quickstart on Thu Dec 15 12:59:35 2016.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

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.. Have a look at https://raw.githubusercontent.com/rtfd/readthedocs.org/master/docs/index.rst for inspiration

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Welcome to the eHive user manual
================================
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eHive is great, and the user manual is great.

The code is open source, and `available on GitHub`_.

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.. _available on GitHub: https://github.com/Ensembl/ensembl-hive
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The main documentation for eHive is organized into a couple sections:

* :ref:`user-docs`
* :ref:`dev-docs`

.. _user-docs:

User documentation
==================
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.. toctree::
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   :caption: Quickstart

   quickstart/install
   quickstart/quickstart
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.. toctree::
   :caption: Walkthrough

   walkthrough/long_mult_walkthrough
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.. toctree::
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   :caption: Running pipelines
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   running_pipelines/running
   running_pipelines/monitoring
   running_pipelines/management
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   running_pipelines/tweaking
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   running_pipelines/error-recovery
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   running_pipelines/troubleshooting
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.. toctree::
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   :caption: Creating pipelines

   creating_pipelines/events
   creating_pipelines/dataflows
   creating_pipelines/dataflow_targets
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   creating_pipelines/accumulators
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   creating_pipelines/parameters
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   creating_pipelines/semaphores
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   creating_pipelines/pipeconfigs
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   creating_pipelines/included_runnables
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.. toctree::
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   :caption: Creating runnables

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   creating_runnables/runnables_overview
   creating_runnables/IO_and_errors
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.. toctree::
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   :caption: Advanced usage

   advanced_usage/mpi
   advanced_usage/slack
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   advanced_usage/continuous_pipelines
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.. toctree::
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   :caption: Appendix
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   :maxdepth: 1

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   appendix/presentations
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   appendix/analyses_pattern
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   appendix/scripts
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   appendix/hive_schema
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   appendix/api
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.. _dev-docs:

Developer documentation
=======================

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.. toctree::
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   :caption: Developer documentation
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   dev/release_checklist
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   dev/build_the_docs
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Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`