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
Currently Loaded Modules: 1) torque/5.1.3-1462984387_205d70d 3) intel/15.0.3 5) modules/au2015 2) moab/18.104.22.168-2015080516-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.