INSTRUCTIONS ON HOW TO SET UP AND INSTALL PYMETHL

1. Download the PyMethyl package from the Pypi website or from GitHub.
<https://github.com/cowatson/pymethyl.git>
This can also be done by setting up python with setuptools and pip.
You can then pip install pymethyl or easy_install pymethyl.

If you run into any installation issues normally googling the error will
give you a recommendation. The most popular errors I have seen is with MySQL-python
and this can be fixed by entering
sudo apt-get install build-essential python-dev libmysqlclient-dev

The other issue I have seen is with the Python.h files. This can be solved by entering
sudo apt-get install python-dev


2. Once the package has installed itself. You will need the other tool outside of
Python, the local Blast tool. This can be downloaded from the NCBI website.
<http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
Download the ncbi-blast-2.2.29+-ia32-linux.tar.gz version
Make sure that you download the folder to your desktop. This step is extremely important!
After the folder is downloaded, double click the folder which is called ncbi-blast-2.2.29+ on my machine
and create a new folder called db.

You will also need to switch the path to look in the blast folder. Thus
these two commands are needed.
export BLASTDB=$HOME/Desktop/ncbi-blast-2.2.29+/db
export PATH=$PATH:$HOME/ncbi-blast-2.2.29+/bin

3. This process has only been verified for UNIX machines and for python 2.7 and higher.
Although I do expect compatibility for Mac I cannot be sure. It really depends on 
the packages that pymethyl depend on. Windows will not work since pysam is an essential package
that does not work in a windows system.
