Installation Guide

This page provides instructions to install and run the FAMP pipeline. You can either build the required Docker containers yourself using the provided Dockerfiles, or install FAMP directly using pip in a local Python environment (Linux only).

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Installation via Docker (recommended)

FAMP includes Dockerfiles to build containerized environments for modeling, simulation, and data analysis. These Dockerfiles allow reproducible and portable setups across systems, including GPU support for MD simulations.

Note

We do not publish pre-built Docker images. You must build all containers locally from the provided Dockerfiles.

Prerequisites

• Docker Desktop (recommended for inexperienced users)

• Docker Engine (alternative for experienced users or server setups)

Step-by-step instructions

1. Install Docker Desktop (if not yet installed)

   • Docker Desktop for Linux

   • Docker Desktop for macOS

   • Docker Desktop for Windows

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2. Download FAMP and the Docker files

3. Build the container

   • Start the Docker Desktop application on your system.

   • In the left sidebar, go to Images, then click on >_ Terminal to open an integrated terminal.

   • Use the cd command to move into the folder where the Dockerfile is located. For example:

cd ~/Downloads/FAMP_rna/docker_files

• Run the following command to build the image. This process may take several minutes, especially on first run:

docker build -t /famp_rna:gpu famp_placeholder

• After the build finishes, you will see the new image famp_rna:gpu listed under the Images section in Docker Desktop.

3. Run a container

   • Click on Containers

   • Use the docker terminal to run:

 docker run -p 8888:8888 -v .\:/src/data/ --rm felix/pipeline 

Option	Description
docker run	Starts a new container from a Docker image
-p 8888:8889	Maps port 8888 in the container to port 8889 on your host
-v $(pwd):/src/data	Mounts the current working directory into the container at /src/data
--rm	Automatically removes the container after it stops
famp_rna:gpu	Name of the Docker image you built

4. Access the running container If the container starts successfully, a link to a Jupyter Notebook will be displayed in the terminal output. You can open this link in your web browser.

Alternatively, if the default settings are used, you can try opening the following link directly in your browser: http://localhost:8889/TOKEN

Installing FAMP without Docker (Linux only)

Required Dependencies

To use the FAMP pipeline outside of Docker, the following software tools must be pre-installed on your system:

• RNAfold (https://www.tbi.univie.ac.at/RNA/)

• Rosetta (https://www.rosettacommons.org/software/license-and-download)

• GROMACS (https://www.gromacs.org)

These tools are used for RNA structure prediction (2D and 3D) and molecular dynamics simulations.
The following sections provide basic installation steps for each dependency on Linux systems.
For detailed information, please consult the official documentation linked above each section.

GROMACS

sudo apt update
sudo apt install gromacs

Ensure GROMACS is available in your terminal:

gmx --version

If GROMACS was built from source (installation guide): Add the GROMACS binary to your PATH:

echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bashrc
source ~/.bashrc

RNAfold (from ViennaRNA)

sudo apt install vienna-rna

Test the installation:

RNAfold --version

Rosetta (requires academic license)

1. Register and download from: https://rosettacommons.org/software/download/

2. Unpack and build according to their documentation

3. Add the binary to your PATH:

echo "export PATH=/path/to/rosetta/main/source/bin:$PATH" >> ~/.bashrc
source ~/.bashrc

• Install FAMP_rna using pip

pip install famp