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Installation guide for ezBAMQC for from source installs
=====================================================

When installing ezBAMQC there are several options, but the main point is: since ezBAMQC uses C++ STD 11 you'll need a version of GCC that can support that, this useally means 4.8 or 4.9. beyond that, you'll need Python, R and Corrplot for interfacing with the C code.

:Intallation:
   `Source Code <https://github.com/mhammell-laboratory/bamqc/archive/0.6.4.tar.gz>`_

   `Pypi <https://pypi.python.org/pypi?:action=display&name=BAMQC&version=0.6.4>`_

:Prerequisites:
    * `python2.7 <https://www.python.org/download/releases/2.7/>`_
    * `R <https://www.r-project.org/>`_
    * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_
    * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install 

:Notes:
    * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*
    * `Devtoolset-3 <https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/3/html/User_Guide/sect-Red_Hat_Developer_Toolset-Install.html>`_ for GCC compilers
    * `IUS <https://ius.io/>`_ for Python2.7
    * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)
    * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems

Setup
=====

1) Make sure that the GCC comiler is in your PATH:

::

   export PATH=/path/to/gcc:$PATH

2) Make sure that python2.7 is in your PYTHONPATH:

::

   export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH

3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup. 

From Source
~~~~~~~~~~~

1) Download source 

2) Unpack tarball and go to the directory of the package: 

::

   tar xvfz bamqc-0.6.4.tar.gz

   cd bamqc-0.6.4

3) Run make:

::

   make

From Setup.py
~~~~~~~~~~~~~

::

   python2.7 setup.py install 

From Pypi
~~~~~~~~~

::

   pip2.7 install BAMqc