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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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This manual describes how to run, develop, and troubleshoot eHive pipelines. It describes eHive's "swarm of autonomous agents" paradigm, shows how different components work together, and provides code examples. There are also links to API documentation for eHive classes.
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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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   quickstart/tips
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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/initializing
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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

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   creating_pipelines/pipeconfigs
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   creating_pipelines/dataflows
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   creating_pipelines/semaphores
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   creating_pipelines/accumulators
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   creating_pipelines/parameters
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   creating_pipelines/meadows_and_resources
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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
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   creating_runnables/runnable_api
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   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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   advanced_usage/json
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.. toctree::
   :caption: External plugins

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   contrib/alternative_meadows
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   contrib/docker-swarm
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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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   appendix/changelog
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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/development_guidelines
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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`

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..  LocalWords:  api