How to Install MACS2 on OSC

How to Install MACS2 on the Ohio Supercomputer Center’s Oakley Cluster

MACS2 requires Python 2.7 and a GCC complier for installation. You can read more about the installation requirements here

In bash, run

module list

This gives

Currently Loaded Modules:
  1) torque/5.1.3-1462984387_205d70d       3) intel/15.0.3   5) modules/au2015
  2) moab/8.1.1.2-2015080516-eb28ad0-el6   4) mvapich2/2.1

We now load the Anaconda module to install the dependencies. Now since Oakley loads the Anaconda3 distribution by default, we create a self-contained Conda Python 2 enviornment. Let’s call the enviroment py2k

module load anaconda
conda create -n py2k python=2 anaconda

Next we activate the enviroment

source activate py2k

Note that the path to Python 2 gets prepended

discarding /usr/local/anaconda/anaconda3/bin from PATH
prepending /users/PAS1129/osu9535/envs/py2k/bin to PATH

A great way to install bioinformatics package dependencies effortlessly is to use Bioconda, a distribution of bioinformatics software which can be accessed through the Conda package manager. To add the Bioconda and R channels, which several packages depend on, run

conda config --add channels r
conda config --add channels bioconda

Next we swap the intel compilers with the GNU GCC compiler

module load gnu/5.2.0

You should get this message

Lmod is automatically replacing "intel/15.0.3" with "gnu/5.2.0"

We are almost ready to install MACS2, but first we need to install pip and setuptools so MACS2 is able to install Python packages from PyPI.

conda install pip
conda install setuptools

Next we install MACS2

conda install MACS2

Next time you log in or when submitting a batch job, just load the anaconda distribution and activate the Python 2 Conda enviornment

module load anaconda
source activate py2k

You should be able to use MACS2 now.