MØD is a software package for cheminformatics, that is developed at SDU. It is traditionally available for Linux using the CONDA package manager. For anyone not using Linux, the software can be installed and used using Docker.
For Windows, this requires Windows Subsystem for Linux (WSL), while Mac can do it natively.
MØD is mostly used through the command line of a unix system. To be able to run it on Windows, some prerequisites need to be fulfilled. After this short chapter, you should be able to follow the rest of the tutorial with no problems on your Windows PC. If you already have WSL2 and Docker installed on your Windows machine, you can directly jump to “Installing MØD” and continue there.
On Windows, the only option to install MØD is to pull a docker container. This requires docker on your machine, which in turn requires WSL2. Following the next steps ensures that all prerequisites for the installation on Windows are met.
First, you need PowerShell or some other Windows terminal on your machine. This should be present by default.
To run docker, you need a virtual machine that allows you to run a Linux distribution on your Windows system. To this end, WSL2 is installed, which essentially gives a Linux terminal. Type the command into the PowerShell command line
wsl --install
For a more detailed description of the installation process, see the documentation by Microsoft: https://learn.microsoft.com/en-us/windows/wsl/install. Here, it is also explained how to set up any different settings from the default.
Follow the link to install Docker for Windows on your machine. It details using either the interactive mode or the command line for installation.
https://docs.docker.com/desktop/install/windows-install/
Further information about wsl and Docker interaction can be found in the following link:
https://docs.docker.com/desktop/wsl/
Download latest MØD Docker Image in the terminal with the following command:
docker pull jakobandersen/mod:25-alife
Open Docker Desktop and import Docker Image.
Open Code Editor of Choice.
Copy the testing code from the Resources section on this website into a new file and save it as a Python file.
Start a linux terminal and navigate to the location / directory / folder where you want to save the output files that MØD will generate. If you want to use your “normal” windows locations, like Documents, you need to use the following command in the linux terminal (replacing YourUsername with your Windows username):
cd /mnt/c/Users/YourUsername/Documents
This navigates to the mounting point, where the wsl distribution overlaps with the filesystem of Windows and enters said filesystem.
In the linux terminal, run the following command to open a docker container that runs MØD, deletes the container when closing it, but also creates a summary and out folder in the directory from which the container was opened.
docker run -it --rm -v $(pwd):/workdir -u $(id -u):$(id -g) jakobandersen/mod:25-alife
When using the above command to start MØD, after running it, you can access the /summary and /out directory by either using the file explorer and navigating to the directory you started the docker container from, or using powershell or a second linux terminal and navigating to said directory.
If you use a different command to start the Docker container, the /summary and /out folders might be created and deleted when closing the container.
Install Docker Desktop: https://www.docker.com/products/docker-desktop/
Download latest MØD Docker Image in the terminal with the following command:
docker pull jakobandersen/mod:25-alife
Open Docker Desktop and import Docker Image.
Open Code Editor of Choice.
Copy the testing code from the Resources section on this website into a new file and save it as a Python file.
In the terminal, navigate to the location of your file.
Start the Docker Container with:
docker run -it --rm -v $(pwd):/workdir -u $(id -u):$(id -g) jakobandersen/mod:25-alife
Run the file with:
mod -f filename.py
Congratulations, you are running MØD!