djoerch / neurodocker

Generate custom Docker and Singularity images, and minimize existing containers

Neurodocker

Neurodocker is a command-line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers.

Please see our website https://www.repronim.org/neurodocker for more information.

Installation

Use the Neurodocker Docker image (recommended):

docker run --rm repronim/neurodocker:0.7.0 --help

The Docker images were moved to repronim/neurodocker from kaczmarj/neurodocker.

This project can also be installed with pip:

pip install neurodocker
neurodocker --help

If the pip install command above gives a permissions error, install as a non-root user:

pip install --user neurodocker

Note: it is not yet possible to minimize Docker containers using the Neurodocker Docker image.

Developer installation

Clone the repository and install in editable mode.

git clone https://github.com/ReproNim/neurodocker
cd neurodocker
python -m pip install --no-cache-dir --editable .[all]

Before committing changes, initialize pre-commit with pre-commit install. This will format code with each commit to keep the style consistent. Neurodocker uses black for formatting.