Docker image that packages several tools developed by the BIONF group into a single portable and reproducible environment.

The container allows users to run these tools without manually installing dependencies, making it suitable for:

• local development
• reproducible research
• HPC environments
• cloud platforms (e.g. AWS)

Currently included tools:

• FAS
• fDOG
• fCAT
• DCC2

• bionf_utilities
• Table of Contents
• Requirements
• Quick Start
• Using Apptainer (recommended)
• Using Docker
• How to Maintain the Image
• Testing Using AWS

You need one of the following container runtimes:

• Apptainer (recommended for Linux and HPC systems)
• Docker

Pull the container and run a BIONF tool immediately.

docker pull trvinh/bionf_utilities
docker run --platform linux/amd64 -it trvinh/bionf_utilities

Example:

fas.doAnno -i test_annofas.fa -o test_fas

apptainer pull docker://trvinh/bionf_utilities:latest
apptainer exec -e bionf_utilities_latest.sif fas.doAnno -i test_annofas.fa -o test_fas

Note: for Linux only

Apptainer is recommended for HPC clusters because it allows users to run containers without requiring root privileges.

Example installation using mamba:

mamba create -n apptainer apptainer
mamba activate apptainer

apptainer pull docker://trvinh/bionf_utilities:latest

This command downloads the Docker image and converts it into an Apptainer image file:

bionf_utilities_latest.sif

General syntax:

apptainer exec -e bionf_utilities_latest.sif <command>

Example:

FAS annotation

fas.doAnno -i test_annofas.fa -o test_fas

fDOG

fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@qfo24_02

The image is hosted on Docker Hub:

https://hub.docker.com/r/trvinh/bionf_utilities

Pull it using:

docker pull trvinh/bionf_utilities

docker run --platform linux/amd64 -it trvinh/bionf_utilities

Alternatively, you can run the container using the Docker Desktop dashboard and open a CLI session.

Once inside the container, the BIONF tools can be used directly.

Example:

FAS annotation

fas.doAnno -i test_annofas.fa -o test_fas

fDOG

fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@qfo24_02

• List containers

docker ps -a

• Stop a container

docker stop <container_id>

• Remove a container

docker rm <container_id>

To free disk space you can remove the Docker image.

• List images

docker image ls

• Remove image

docker rmi <image_id>

Follow these steps if you want to modify or rebuild the container.

git clone <repository_url>
cd bionf_utilities

Update the following files as needed:

Dockerfile
dependencies.txt
tools.txt

These files define:

• installed dependencies
• installed BIONF tools
• container configuration

docker build . -t trvinh/bionf_utilities[:0.1.2] --platform linux/amd64 --progress=plain

Notes:

• Replace trvinh with your Docker Hub username.
• :0.1.2 defines the image tag.
• If no tag is provided, Docker automatically assigns the latest tag.

docker push trvinh/bionf_utilities[:0.1.2]

More details are available in the Docker documentation:

https://docs.docker.com/docker-hub/repos/

Check disk usage:

docker system df

Remove unused build cache:

docker buildx prune

This helps free disk space after building and pushing images.

Or using this one-line "nuclear clean" command

docker system prune -a --volumes -f

Verify Docker is empty

docker system df

Instructions for testing this container on AWS can be found here:

https://gist.github.com/trvinh/475f66d40e13dddcb9a40292c8892d93