It is recommended to install libraries and run scripts in a virtual environment to avoid version conflicts between different projects. In order to do this, follow these steps:

• virtualenv folder_name or if you have both python 2 and 3: virtualenv --python=python3 folder_name. Should virtualenv not be recognised you may need to call it as python -m virtualenv folder_name or (python -m virtualenv folder_name). If that doesn't work you may need to install virtualenv first pip install virtualenv.
• Activate the virtual environment using source folder_name/bin/activate. Simply type deactivate to exit the virtual environment at the end of a session.
• Install graphviz. On Ubuntu, this is done by running sudo apt install graphviz graphviz-dev.
• Install gcc and build essential: sudo apt-get install gcc build-essential
• Install cmake: sudo apt-get install cmake
• Install scikit-build: pip install scikit-build
• Install the markovmodels package by running pip install -e ..

To run a script execute it using Python. For example, python3 scripts/fix_wrong_param_study/fix_wrong_parameter.py --protocols sis staircase