de.NBI Summer School 2023

Exercises for Python course

Installation

Jupyter Lab / Galaxy

1. Go to https://galaxy.eu and log in
2. Search for jupyter in the left menu
3. Click on PyIron Interactive Jupyter Notebook
4. In the middle panel click Run tool
5. Wait until the Job is started in the right panel (becomes orange)
6. Still in the right menu, click the little eye symbol in on the job
   You should be redirected to your Jupyter Instance
7. Open a terminal an clone the repository: git clone https://github.com/mpc-bioinformatics/denbi_summerschool2023_py_exercises
8. Install the dependencies: pip install jupyter matplotlib pandas plotly scipy sweetviz
9. In the left menu you should find your cloned folder.
10. Go there and open the Jupyter Notebool: exercises.ipynb

Happy coding!

Local

1. Install conda, mamba or micromamba
2. Install git
3. Clone the repository to your PC: git clone https://github.com/mpc-bioinformatics/denbi_summerschool2023_py_exercises
4. Go into the cloned folder: cd denbi_summerschool2023_exercises
5. conda env create -f environment.yml
6. conda activate cubimed_rub_python_course`
7. pip install -e .

Happy coding!