Installation guide for RSeQC
==============================


Use pip to install RSeQC
------------------------

You must first install pip following the instructions: https://pypi.python.org/pypi/pip
Then type:
pip install RSeQC


Install RSeQC from source code (Not recommended)
------------------------------------------------

Prerequisite:
   * gcc
   * python2.7
   * numpy
   * If your computer can not connnect to internet, nose>= 0.10.4 and distribute-0.6.10 are also required. 

Below is an example of installing RSeQC on Linux system using BASH. You need to change '--root' directory, PYTHONPATH and PATH accordingly

    1) tar zxf RSeQC-VERSION.tar.gz
    2) cd RSeQC-VERSION
    3) python setup.py install 					#will install RSeQC in system level. require root previledge
    4) python setup.py install --root=/home/user/RSeQC 		#will install RSeQC at user specified location
    5) export PYTHONPATH=/home/user/RSeQC/usr/local/lib/python2.7/site-packages:$PYTHONPATH. #setup PYTHONPATH, so that RSeQC knows where to import modules
    6) export PATH=/home/user/RSeQC/usr/local/bin:$PATH 	#setup PATH, so that system knows where to find executable file 

NOTE:
    * To install RSeQC on MAC OSX, user need to download and install Xcode beforehand.
    * To produce graphical outputs, R must be installed.
    * If the installation failed with error like: /usr/bin/ld: cannot find -lz, you may need to install a shared zlib library on your system. 


Online Manual:
http://rseqc.sourceforge.net/

