Installation instruction for ‘Introduction to solving biological problems with Python’ course

Dependencies

This only needs to be done once. To run the course, first download and install these dependencies:

Python3: install Python 3 by downloading the latest version from https://www.python.org/
Git: install Git by downloading the latest version from https://git-scm.com/downloads

Now clone the GitHub repository to copy the course materials onto your computer:

Clone the GitHub repo python-basic:

git clone https://github.com/pajtraining/python-basic.git
cd python-basic/

Create a virtual environment to install the python dependencies:

python3 -m venv venv
# activate your virtual environment
source venv/bin/activate
# update pip if needed
pip install --upgrade pip
# install jupyter
pip install jupyter

Usage

Go to the directory where you’ve cloned this repository, activate your virtual environment and run jupyter.

Your web browser should automatically open with this url http://localhost:8888/tree where you see the directory tree of the course with all the jupyter notebooks.

cd python-basic
source venv/bin/activate
jupyter notebook

You are now setup to run the course and start your python journey! Congratulations

Click on the first notebook python_basic_1_intro.ipynb and start reading.

To shutdown jupyter, type ctrl-C into the terminal you’ve ran jupyter notebook, answer y and press enter.

You may wish to deactivate the virtual environment, by entering into the terminal:

deactivate

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