https://github.com/ReproNim/neurodocker

Generate custom Docker and Singularity images, and minimize existing containers
https://github.com/ReproNim/neurodocker

apptainer containers docker dockerfile linux neuroscience nipype reproducible-research science singularity-container

Last synced: about 2 months ago
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Generate custom Docker and Singularity images, and minimize existing containers

• Host: GitHub
• URL: https://github.com/ReproNim/neurodocker
• Owner: ReproNim
• License: apache-2.0
• Created: 2017-04-18T18:00:49.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-04-13T17:08:31.000Z (5 months ago)
• Last Synced: 2024-04-14T07:57:04.771Z (5 months ago)
• Topics: apptainer, containers, docker, dockerfile, linux, neuroscience, nipype, reproducible-research, science, singularity-container
• Language: Python
• Homepage: https://www.repronim.org/neurodocker/
• Size: 6.14 MB
• Stars: 319
• Watchers: 18
• Forks: 96
• Open Issues: 32
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

        
# Neurodocker

[![build status](https://github.com/ReproNim/neurodocker/actions/workflows/pull-request.yml/badge.svg)](https://github.com/ReproNim/neurodocker/actions/workflows/pull-request.yml)

[![docker pulls](https://img.shields.io/docker/pulls/repronim/neurodocker.svg)](https://hub.docker.com/r/repronim/neurodocker/)

[![python versions](https://img.shields.io/pypi/pyversions/neurodocker.svg)](https://pypi.org/project/neurodocker/)

[![DOI](https://zenodo.org/badge/88654995.svg)](https://zenodo.org/badge/latestdoi/88654995)

_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](https://www.repronim.org/neurodocker/user_guide/examples.html#supported-software)

# Installation

Use the _Neurodocker_ Docker image (recommended):

```shell

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

```

The Docker images were moved to [repronim/neurodocker](https://hub.docker.com/r/repronim/neurodocker) from [kaczmarj/neurodocker](https://hub.docker.com/r/kaczmarj/neurodocker).

This project can also be installed with `pip`:

```shell

pip install neurodocker

neurodocker --help

```

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

```shell

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](https://github.com/ReproNim/neurodocker/blob/test_docker_build/docs/README.md).