annotate ezBAMQC/doc/INSTALL @ 20:9de3bbec2479 draft default tip

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1 
2 Installation guide for ezBAMQC for from source installs
3 =====================================================
4 
5 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.
6 
7 :Intallation:
8    `Source Code <https://github.com/mhammell-laboratory/bamqc/archive/0.6.4.tar.gz>`_
9 
10    `Pypi <https://pypi.python.org/pypi?:action=display&name=BAMQC&version=0.6.4>`_
11 
12 :Prerequisites:
13     * `python2.7 <https://www.python.org/download/releases/2.7/>`_
14     * `R <https://www.r-project.org/>`_
15     * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_
16     * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install 
17 
18 :Notes:
19     * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*
20     * `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
21     * `IUS <https://ius.io/>`_ for Python2.7
22     * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)
23     * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems
24 
25 Setup
26 =====
27 
28 1) Make sure that the GCC comiler is in your PATH:
29 
30 ::
31 
32    export PATH=/path/to/gcc:$PATH
33 
34 2) Make sure that python2.7 is in your PYTHONPATH:
35 
36 ::
37 
38    export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH
39 
40 3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup. 
41 
42 From Source
43 ~~~~~~~~~~~
44 
45 1) Download source 
46 
47 2) Unpack tarball and go to the directory of the package: 
48 
49 ::
50 
51    tar xvfz bamqc-0.6.4.tar.gz
52 
53    cd bamqc-0.6.4
54 
55 3) Run make:
56 
57 ::
58 
59    make
60 
61 From Setup.py
62 ~~~~~~~~~~~~~
63 
64 ::
65 
66    python2.7 setup.py install 
67 
68 From Pypi
69 ~~~~~~~~~
70 
71 ::
72 
73    pip2.7 install BAMqc
74