Installation

PETFit can be installed and run in three ways. Docker and Apptainer are the recommended approaches for most users; the R package is intended mainly for development.

Docker

Docker is the recommended approach for most users on their local computers. It bundles all dependencies and avoids package installation issues.

Pull the pre-built image

docker pull mathesong/petfit:latest

See Docker usage for more details on running the container.

Apptainer

Apptainer (formerly Singularity) is the standard container runtime on HPC clusters. PETFit’s Apptainer definition file lives in the apptainer/ directory.

Build from the Docker image

The fastest path is to convert the published Docker image directly into a SIF file:

apptainer build petfit_latest.sif docker://mathesong/petfit:latest

Prerequisites

  • Apptainer installed on your system (or Singularity, which uses the same commands)

  • sudo access for building (not required for running)

  • Internet access during the build

See Apptainer usage for more details.

R package (for development)

If you need to run PETFit outside a container — for example, during development or debugging, or if you just like using R — you can install the R package directly.

# Install remotes if needed
install.packages("remotes")

# Install petfit
remotes::install_github("mathesong/petfit")

Prerequisites

  • R >= 4.0

  • The kinfitr package (installed automatically as a dependency)

  • Standard R package build tools (Rtools on Windows, r-base-dev on Linux)