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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 6 hours 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 (8 months ago)
- Last Synced: 2024-04-14T07:57:04.771Z (8 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).