Installation¶

Platform compatibility¶

MD-TASK should be compatible with any Linux/Unix-based platform, although installation of system dependencies may differ. It has been successfully tested on the following platforms:

Ubuntu Linux
MacOS
Windows 10 (with bash)

Install system dependencies¶

Note: package version numbers may differ depending on the OS version. For example, in Ubuntu 16.04, `libpng12-dev` must be installed. However, in Ubuntu 17.04, `libpng-dev` should be installed.

Ubuntu 16.04:

sudo apt-get install virtualenvwrapper python-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libpng12-dev libfreetype6-dev python-tk r-base

Windows 10:

Enable the Windows Subsystem for Linux (WSL) by following these instructions.
Install the system dependencies as with Ubuntu above.

MacOS:

On MacOS, Python comes installed by default, but the default version my not be ideal. Follow these instructions to install a more up-to-date version of Python.
Next, install virtualenv by following these instructions

Install Python dependencies¶

We recommend using a Python virtual environment when using MD-TASK

virtualenv venv
source venv/bin/activate
pip install --upgrade pip
pip install numpy
pip install scipy
pip install matplotlib cython networkx natsort
pip install mdtraj

Install the igraph package for R:

R
> install.packages("igraph")

Download the project¶

MD-TASK can be cloned from it’s GitHub repository

git clone https://github.com/RUBi-ZA/MD-TASK.git
cd MD-TASK

Always activate the virtual environment you created in the previous step when using MD-TASK.