Neurodocker tutorial

This page covers the steps to create containers with Neurodocker.

Neurodocker is a command-line program that enables users to generate Docker containers and Singularity images that include neuroimaging software.

Requirements:

• Docker or Singularity
• Internet connection

Usage

To view the Neurodocker help message

docker run --rm kaczmarj/neurodocker:0.4.0 generate [docker|singularity] --help

Note: choose between docker and singularity in [docker|singularity].

1. Users must specify a base Docker image and the package manager. Any Docker image on DockerHub can be used as your base image. Common base images include debian:stretch, ubuntu:16.04, centos:7, and the various neurodebian images. If users would like to install software from the NeuroDebian repositories, it is recommended to use a neurodebian base image. The package manager is apt or yum, depending on the base image.
2. Next, users should configure the container to fit their needs. This includes installing neuroimaging software, installing packages from the chosen package manager, installing Python and Python packages, copying files from the local machine into the container, and other operations. The list of supported neuroimaging software packages is available in the neurodocker help message.
3. The neurodocker command will generate a Dockerfile or Singularity recipe. The Dockerfile can be used with the docker build command to build a Docker image. The Singularity recipe can be used to build a Singularity container with the singularity build command.

Create a Dockerfile or Singularity recipe with FSL, Python 3.6, and Nipype

This command prints a Dockerfile (the specification for a Docker image) or a Singularity recipe (the specification for a Singularity container) to the terminal.

$ docker run --rm kaczmarj/neurodocker:0.4.0 generate [docker|singularity] \
  --base debian:stretch --pkg-manager apt \
  --fsl version=5.0.10 \
  --miniconda create_env=neuro \
              conda_install="python=3.6 traits" \
              pip_install="nipype"

Build the Docker image

The Dockerfile can be saved and used to build the Docker image

$ docker run --rm kaczmarj/neurodocker:0.4.0 generate docker \
  --base debian:stretch --pkg-manager apt \
  --fsl version=5.0.10 \
  --miniconda create_env=neuro \
              conda_install="python=3.6 traits" \
              pip_install="nipype" > Dockerfile
$ docker build --tag my_image .
$ # or
$ docker build --tag my_image - < Dockerfile

Build the Singularity container

The Singularity recipe can be saved and used to build the Singularity container

$ docker run --rm kaczmarj/neurodocker:0.4.0 generate singularity \
  --base debian:stretch --pkg-manager apt \
  --fsl version=5.0.10 \
  --miniconda create_env=neuro \
              conda_install="python=3.6 traits" \
              pip_install="nipype" > Singularity
$ singularity build my_nipype.simg Singularity

Use NeuroDebian

This example installs AFNI and ANTs from the NeuroDebian repositories. It also installs git and vim.

$ docker run --rm kaczmarj/neurodocker:0.4.0 generate [docker|singularity] \
  --base neurodebian:stretch --pkg-manager apt \
  --install afni ants git vim

Note: the --install option will install software using the package manager. Because the NeuroDebian repositories are enabled in the chosen base image, AFNI and ANTs may be installed using the package manager. git and vim are available in the default repositories.

Other examples

Create a container with dcm2niix, Nipype, and jupyter notebook. Install Miniconda as a non-root user, and activate the Miniconda environment upon running the container.

$ docker run --rm kaczmarj/neurodocker:0.4.0 generate docker \
  --base centos:7 --pkg-manager yum \
  --dcm2niix version=master method=source \
  --user neuro \
  --miniconda create_env=neuro conda_install="jupyter traits nipype" \
  > Dockerfile
$ docker build --tag my_nipype - < Dockerfile

Copy local files into a container.

$ docker run --rm kaczmarj/neurodocker:0.4.0 generate [docker|singularity] \
  --base ubuntu:16.04 --pkg-manager apt \
  --copy relative/path/to/source.txt /absolute/path/to/destination.txt

See the Neurodocker examples page for more.