index.rst 2 KB
Newer Older
Brandon Walts's avatar
Brandon Walts committed
1 2 3 4 5
.. 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.

6 7
.. Have a look at https://raw.githubusercontent.com/rtfd/readthedocs.org/master/docs/index.rst for inspiration

8 9
Welcome to the eHive user manual
================================
Brandon Walts's avatar
Brandon Walts committed
10

11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
eHive is great, and the user manual is great.

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

.. _available on GitHub: http://github.com/Ensembl/ensembl-hive

The main documentation for eHive is organized into a couple sections:

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

.. _user-docs:

User documentation
==================
Brandon Walts's avatar
Brandon Walts committed
26 27

.. toctree::
28 29 30 31
   :caption: Quickstart

   quickstart/install
   quickstart/quickstart
Brandon Walts's avatar
Brandon Walts committed
32

33 34 35 36
.. toctree::
   :caption: Walkthrough

   walkthrough/long_mult_walkthrough
37 38

.. toctree::
39
   :caption: Running pipelines
40

41 42 43
   running_pipelines/running
   running_pipelines/monitoring
   running_pipelines/management
Brandon Walts's avatar
Brandon Walts committed
44
   running_pipelines/tweaking
Brandon Walts's avatar
Brandon Walts committed
45
   running_pipelines/error-recovery
46
   running_pipelines/troubleshooting
47 48 49


.. toctree::
50 51 52 53 54
   :caption: Creating pipelines

   creating_pipelines/events
   creating_pipelines/dataflows
   creating_pipelines/dataflow_targets
55
   creating_pipelines/accumulators
Matthieu Muffato's avatar
Matthieu Muffato committed
56
   creating_pipelines/parameters
57
   creating_pipelines/semaphores
58
   creating_pipelines/pipeconfigs
59
   creating_pipelines/included_runnables
60

Brandon Walts's avatar
Brandon Walts committed
61

62
.. toctree::
63 64
   :caption: Creating runnables

65 66
   creating_runnables/runnables_overview
   creating_runnables/IO_and_errors
Brandon Walts's avatar
Brandon Walts committed
67 68


69
.. toctree::
70 71 72 73
   :caption: Advanced usage

   advanced_usage/mpi
   advanced_usage/slack
74
   advanced_usage/continuous_pipelines
75 76


77
.. toctree::
78
   :caption: Appendix
79 80
   :maxdepth: 1

81
   appendix/presentations
82
   appendix/scripts
83
   appendix/hive_schema
84 85 86 87 88 89 90


.. _dev-docs:

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

91 92 93
.. toctree::

   dev/api
94
   dev/release_checklist
95 96


Brandon Walts's avatar
Brandon Walts committed
97 98 99 100 101 102 103
Indices and tables
==================

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