<commit_before>.. MuG - FastQ Pipelines documentation master file, created by
   sphinx-quickstart on Tue Feb 28 10:22:01 2017.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

MuG - FastQ Pipelines's documentation!
======================================
**Quick Links**: `Source (github) <https://github.com/Multiscale-Genomics/mg-process-fastq>`_ - `Documentation (rtd) <https://mg-process-fastq.readthedocs.io/>`_

Requirements
------------

- bedToBigBed - http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
- HDF5
- Python 2.7.10+
- numpy
- h5py
- pysam

Installation
------------
Directly from GitHub:

.. code-block:: none
   :linenos:
   
   git clone https://github.com/Multiscale-Genomics/mg-process-fastq.git

Using pip:

.. code-block:: none
   :linenos:

   pip install git+https://github.com/Multiscale-Genomics/mg-process-fastq.git

Pipelines
---------
.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   pipelines
   tools
   common
   license



Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
<commit_msg>Test change to the headers<commit_after>.. MuG - FastQ Pipelines documentation master file, created by
   sphinx-quickstart on Tue Feb 28 10:22:01 2017.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

MuG - FastQ Pipelines's documentation!
======================================
**Quick Links**: `Source (github) <https://github.com/Multiscale-Genomics/mg-process-fastq>`_ - `Documentation (rtd) <https://mg-process-fastq.readthedocs.io/>`_

Requirements
------------

- bedToBigBed - http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
- HDF5
- Python 2.7.10+
- numpy
- h5py
- pysam

Installation
------------
Directly from GitHub:

.. code-block:: none
   :linenos:
   
   git clone https://github.com/Multiscale-Genomics/mg-process-fastq.git

Using pip:

.. code-block:: none
   :linenos:

   pip install git+https://github.com/Multiscale-Genomics/mg-process-fastq.git

Pipelines
---------
.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   pipelines

Tools
-----
.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   tools

Common Functions
----------------
.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   common

License
-------
.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   license



Indices and tables
==================

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

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