Tutorial: Network medicine-based drug repurposing

Setup

Tip

Windows

The easiest way to get the setup running on Windows is to work completely through the Windows Subsystem for Linux (WSL). Alternatively, you can work with the dependencies in environment.windows.yaml for most hands-on tasks.

Clone the repository:

git clone --recurse-submodules https://github.com/REPO4EU/network_medicine_drug_repurposing_tutorial.git

Enter the downloaded folder:

cd network_medicine_drug_repurposing_tutorial

After cloning the repository, install the required packages using conda and the environment.yaml file:

conda env create -f environment.yaml

Activate the environment:

conda activate network_medicine_tutorial

Register the environment as a jupyter kernel:

python -m ipykernel install --user --name network_medicine_tutorial --display-name "network_medicine_tutorial"

Launch the jupyter sever to start working on the hands-on projects:

jupyter lab

Nextflow pipeline setup

Activate the environment (Nextflow is already installed there):

conda activate network_medicine_tutorial

Install Docker if you do not have it already. If you are not using Linux, check the tips in the box below!

Tip

OS specifics

Nextflow works best in combination with Linux. Furthermore, some Docker images in the pipeline are natively only available for amd64 but not the arm architecture. Here are some tips to get the pipeline running with a different OS or architecture:

macOS

With macOS and Apple silicon, we had better experiences using the free version of orbstack instead of Docker Desktop for deploying the containers.

Windows

You will have to work through the Windows Subsystem for Linux (WSL).

What if it keeps failing?

Most pipeline steps are not essential. If the pipeline keeps failing because of a specific process, you may be able to just skip that one.

If you cannot produce any pipeline outputs, you can still work on most hands-on tasks by using the result files we provide.

Now, run the pipeline with the test profile to verify that the setup works:

nextflow run nf-core/diseasemodulediscovery -r dev -profile docker,test --outdir test_results

The first run may take some time because Nextflow needs to pull the software dependency containers. Subsequent runs should be significantly faster.