--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/doc/INSTALL	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,74 @@
+
+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
+