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endseq

Pipeline for endseq analysis and plots

Instructions for installing endseq

Update Python and base packages by downloading a python release from: http://continuum.io/downloads

Once the installation is complete, download and install the following python modules by entering the following commands:

	sudo conda install numpy --upgrade
	sudo conda install matplotlib --upgrade
	sudo conda install pandas --upgrade
	sudo conda install seaborn
	sudo pip install brewer2mpl

Installing HTSeq module on Mac OS X
Install Xcode from the Mac App store to install llvm-gcc and llvm-g++
You can check if these are installed by checking gcc --version in a terminal

After installing Xcode, install HTSeq by entering the following command:

	sudo pip install HTSeq

git clone https://github.com/mohanbolisetty/endseq.git

In a terminal change directory to endseq download folder and enter the following command:

sudo python setup.py install

This should check for all dependencies and install endseq on your computer within PYTHONPATH

To check endseq installation, in a terminal in any directory enter:

	endseq --version
	
	This should print:
	endseq 0.1.0

Download bowtie-1.0.0 binary and add it to your PATH