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ReproNim / neurodocker

Generate custom Docker and Singularity images, and minimize existing containers
https://www.repronim.org/neurodocker/
Apache License 2.0
330 stars 97 forks source link
apptainer containers docker dockerfile linux neuroscience nipype reproducible-research science singularity-container

readme

Neurodocker

build status docker pulls python versions DOI

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.

See our list of supported software

Installation

Use the Neurodocker Docker image (recommended):

docker run --rm repronim/neurodocker:latest --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.

Build status

You can check the status of the build of the Docker images for several of the neuroimaging software packages that are supported by Neurodocker on this page.