This repository includes the code for a master thesis about Defective Interfering Particles written at the Institute for Computational Systems Biology at the University of Hamburg.

To setup the repository for usage do the following steps:

1. Move into the desired folder and clone the repository using

git clone https://github.com/LohmannJens/MA_DIPs.git

2. Move into root folder and run the setup script

cd MA_DIPs
bash setup.sh

3. Download datasets here and unzip them into the root folder by using

tar -xzf PATH/TO/TARFILE/data.tar.gz

4. Move downloaded datasets into data folder

The folder structure should look like this afterwards:

├── src
|    └── [...]
├── data
|    └── [...]
├── results
├── .gitignore
├── README.md
├── setup.sh
└── env.yml

To run the scripts python version 3.9.12 including the following packages:

In the root of the repository a conda environment called env.yml is given. It includes all necessary libraries and python packages. It can be installed by the following typing the following comand:

conda env create -n <new env name> --file env.yml

For questions and suggestions open a new ticket in this repository