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
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