OVO Containers¶

OVO supports multiple execution environments through the use of containers. Containers provide a consistent and reproducible environment for running workflows, ensuring that all dependencies and software versions are correctly managed.

Configuring OVO to use containers¶

By default, OVO uses Conda to manage execution environments. You can customize the scheduler profile to run using Singularity, Apptainer, Docker, or other container platform by modifying the OVO configuration file, typically located at ~/ovo/config.yml:

schedulers:
  local:
    name: Local with Conda   # <-- Choose a descriptive name
    type: NextflowScheduler
    workdir: ./workdir
    submission_args:
      profile: conda,cpu_env # <--- Change 'conda' to 'singularity', 'apptainer', 'docker', ...
      config: ./nextflow_local.config # <--- Customize advanced Nextflow config if needed

Container types¶

OVO containers are defined in the ovo-containers GitHub repository.

Conda environments are defined directly in the envs directory of the OVO repository or plugin repositories like OVO promb and are automatically created by Nextflow during workflow execution.

Singularity and Apptainer (recommended)¶

For Singularity and Apptainer, OVO will automatically download the required containers during workflow execution from http://ovo.dichlab.org/public/singularity. The downloaded containers will be stored in $OVO_HOME/workdir/work/singularity/. If you wish to build the containers yourself, you will need to first build the Docker images using instructions below. save them into a Docker archive (docker save -o image.tar image), and then convert them to Singularity/Apptainer format (singularity build image-name docker-archive://image.tar).

Example configuration for Singularity:

schedulers:
  local:
    name: Local with Singularity
    type: NextflowScheduler
    workdir: ./workdir
    submission_args:
      profile: singularity,cpu_env
      config: ./nextflow_local.config

See Scheduler documentation for more details on configuring OVO to use Singularity or Apptainer on HPC clusters with grid schedulers like SLURM or PBS Pro.

Docker¶

For Docker, please build all required images using the provided docker-compose file in the ovo-containers repository:

# Clone the ovo-containers repository
git clone https://github.com/MSDLLCpapers/ovo-containers
# Navigate to cloned repo
cd ovo-containers
# Build all Docker images
docker compose build