Neurodocker

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

Installation

Use the Neurodocker Docker image (recommended):

$ docker run --rm kaczmarj/neurodocker:0.4.3 --help

Note: Do not use the -t/--tty flag with docker run or non-printable characters will be a part of the output (see moby/moby#8513 (comment)).

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.

Supported software

software	argument	description
AFNI	version*	latest
	method	binaries (default), source. Install pre-compiled binaries or build form source.
	install_path	Installation path. Default `/opt/afni-{version}`.
	install_r	If true, install R.
	install_r_pkgs	If true, install R and AFNI's R packages.
	install_python2	If true, install Python 2.
	install_python3	If true, install Python 3.
ANTs	version*	2.3.1, 2.3.0, 2.2.0, 2.1.0, 2.0.3, or 2.0.0. If `method=source`, version can be a git commit hash or branch.
	method	binaries (default), source.
	install_path	Installation path. Default `/opt/ants-{version}`.
	cmake_opts	If `method=source`, options for `cmake`.
	make_opts	If `method=source`, options for `make`.
Convert3D	version*	1.0.0 or nightly.
	method	binaries (default)
	install_path	Installation path. Default `/opt/convert3d-{version}`.
dcm2niix	version*	latest, git commit hash or branch.
	method	source (default)
	install_path	Installation path. Default `/opt/dcm2niix-{version}`.
	cmake_opts	If `method=source`, options for `cmake`.
	make_opts	If `method=source`, options for `make`.
FreeSurfer	version*	6.0.0-min
	method	binaries (default)
	install_path	Installation path. Default `/opt/freesurfer-{version}`.
	exclude_paths	Sequence of space-separated path(s) to exclude when inflating the tarball.
	license_path	Relative path to license file. If provided, this file will be copied into the Docker image. Must be within the build context.
FSL**	version*	5.0.11, 5.0.10, 5.0.9, 5.0.8
	method	binaries (default)
	install_path	Installation path. Default `/opt/fsl-{version}`.
	exclude_paths	Sequence of space-separated path(s) to exclude when inflating the tarball.
Matlab Compiler Runtime	version*	2018a, 2012-17[a-b], 2010a
	method	binaries (default)
	install_path	Installation path. Default `/opt/matlabmcr-{version}`.
MINC	version*	1.9.15
	method	binaries (default)
	install_path	Installation path. Default `/opt/minc-{version}`.
Miniconda	version	latest (default), all other hosted versions.
	install_path	Installation path. Default `/opt/miniconda-{version}`.
	create_env	Name of conda environment to create.
	use_env	Name of previously installed environment.
	conda_install	Packages to install with `conda`. E.g., `conda_install="python=3.6 numpy traits"`
	pip_install	Packages to install with `pip`.
	activate	If true (default), activate this environment in container entrypoint.
MRtrix3	version*	3.0
	method	binaries (default)
	install_path	Installation path. Default `/opt/mrtrix3-{version}`.
NeuroDebian	os_codename*	Codename of the operating system (e.g., stretch, zesty).
	server*	Server to download NeuroDebian packages from. Choose the one closest to you. See `neurodocker generate docker --help` for the full list of servers.
	full	If true (default), use non-free sources. If false, use libre sources.
PETPVC	version*	1.2.2, 1.2.1, 1.2.0-b, 1.2.0-a, 1.1.0, 1.0.0
	method	binaries (default)
	install_path	Installation path. Default `/opt/petpvc-{version}`.
SPM12	version*	r7219, r6914, r6685, r6472, r6225
	install_path	Installation path. Default `/opt/spm12-{version}`.
		Note: Matlab Compiler Runtime is installed when SPM12 is installed.
VNC	passwd*	Choose a password for this VNC server.
	start_at_runtime	If true, start the VNC server at container runtime. False by default.
	geometry	The geometry of the VNC session (e.g., `1920x1080`).

* required argument. ** FSL is non-free. If you are considering commercial use of FSL, please consult the relevant license.

Generate Dockerfile

usage: neurodocker generate docker [-h] [-b BASE] [-p {apt,yum}]
                                   [--add-to-entrypoint ADD_TO_ENTRYPOINT]
                                   [--copy COPY [COPY ...]]
                                   [--install INSTALL [INSTALL ...]]
                                   [--entrypoint ENTRYPOINT]
                                   [-e ENV [ENV ...]] [-r RUN]
                                   [--run-bash RUN_BASH] [-u USER]
                                   [-w WORKDIR] [-f FILE] [-o OUTPUT]
                                   [--no-print] [--afni  [...]]
                                   [--ants  [...]] [--convert3d  [...]]
                                   [--dcm2niix  [...]] [--freesurfer  [...]]
                                   [--fsl  [...]] [--matlabmcr  [...]]
                                   [--minc  [...]] [--miniconda  [...]]
                                   [--mrtrix3 [[...]]] [--neurodebian  [...]]
                                   [--petpvc  [...]] [--spm12  [...]]
                                   [--vnc  [...]] [--add ADD [ADD ...]]
                                   [--arg ARG [ARG ...]] [--cmd CMD [CMD ...]]
                                   [--expose EXPOSE [EXPOSE ...]]
                                   [--label LABEL [LABEL ...]]
                                   [--volume VOLUME [VOLUME ...]]

optional arguments:
  -h, --help            show this help message and exit
  -b BASE, --base BASE  Base Docker image. E.g., debian:stretch
  -p {apt,yum}, --pkg-manager {apt,yum}
                        Linux package manager.
  --add-to-entrypoint ADD_TO_ENTRYPOINT
                        Add a command to the file /neurodocker/startup.sh,
                        which is the container's default entrypoint.
  --copy COPY [COPY ...]
                        Copy files into container. Use format <src>... <dest>
  --install INSTALL [INSTALL ...]
                        Install system packages with apt-get or yum, depending
                        on the package manager specified.
  --entrypoint ENTRYPOINT
                        Set the container's entrypoint (Docker) / append to
                        runscript (Singularity)
  -e ENV [ENV ...], --env ENV [ENV ...]
                        Set environment variable(s). Use the format KEY=VALUE
  -r RUN, --run RUN     Run a command when building container
  --run-bash RUN_BASH   Run a command in bash
  -u USER, --user USER  Switch current user (creates user if necessary)
  -w WORKDIR, --workdir WORKDIR
                        Set working directory
  -f FILE, --file FILE  Generate file from JSON. Overrides other `generate`
                        arguments
  -o OUTPUT, --output OUTPUT
                        If specified, save Dockerfile to file with this name.
  --no-print            Do not print the generated file
  --add ADD [ADD ...]   Dockerfile ADD instruction. Use format <src>... <dest>
  --arg ARG [ARG ...]   Dockerfile ARG instruction. Use format
                        KEY[=DEFAULT_VALUE] ...
  --cmd CMD [CMD ...]   Dockerfile CMD instruction.
  --expose EXPOSE [EXPOSE ...]
                        Dockerfile EXPOSE instruction.
  --label LABEL [LABEL ...]
                        Dockerfile LABEL instruction.
  --volume VOLUME [VOLUME ...]
                        Dockerfile VOLUME instruction.

Generate Singularity recipe

usage: neurodocker generate singularity [-h] [-b BASE] [-p {yum,apt}]
                                        [--add-to-entrypoint ADD_TO_ENTRYPOINT]
                                        [--copy COPY [COPY ...]]
                                        [--install INSTALL [INSTALL ...]]
                                        [--entrypoint ENTRYPOINT]
                                        [-e ENV [ENV ...]] [-r RUN]
                                        [--run-bash RUN_BASH] [-u USER]
                                        [-w WORKDIR] [-f FILE] [-o OUTPUT]
                                        [--no-print] [--afni  [...]]
                                        [--ants  [...]] [--convert3d  [...]]
                                        [--dcm2niix  [...]]
                                        [--freesurfer  [...]] [--fsl  [...]]
                                        [--matlabmcr  [...]] [--minc  [...]]
                                        [--miniconda  [...]]
                                        [--mrtrix3 [[...]]]
                                        [--neurodebian  [...]]
                                        [--petpvc  [...]] [--spm12  [...]]
                                        [--vnc  [...]]

optional arguments:
  -h, --help            show this help message and exit
  -b BASE, --base BASE  Base Docker image. E.g., debian:stretch
  -p {apt,yum}, --pkg-manager {apt,yum}
                        Linux package manager.
  --add-to-entrypoint ADD_TO_ENTRYPOINT
                        Add a command to the file /neurodocker/startup.sh,
                        which is the container's default entrypoint.
  --copy COPY [COPY ...]
                        Copy files into container. Use format <src>... <dest>
  --install INSTALL [INSTALL ...]
                        Install system packages with apt-get or yum, depending
                        on the package manager specified.
  --entrypoint ENTRYPOINT
                        Set the container's entrypoint (Docker) / append to
                        runscript (Singularity)
  -e ENV [ENV ...], --env ENV [ENV ...]
                        Set environment variable(s). Use the format KEY=VALUE
  -r RUN, --run RUN     Run a command when building container
  --run-bash RUN_BASH   Run a command in bash
  -u USER, --user USER  Switch current user (creates user if necessary)
  -w WORKDIR, --workdir WORKDIR
                        Set working directory
  -f FILE, --file FILE  Generate file from JSON. Overrides other `generate`
                        arguments
  -o OUTPUT, --output OUTPUT
                        If specified, save Dockerfile to file with this name.
  --no-print            Do not print the generated file

Examples

Please see the examples directory.

Canonical examples

The canonical examples install ANTs version 2.3.1 on Debian 9 (Stretch).

Note: Do not use the -t/--tty flag with docker run or non-printable characters will be a part of the output (see moby/moby#8513 (comment)).

Docker

$ docker run --rm kaczmarj/neurodocker:0.4.3 generate docker \
    --base debian:stretch --pkg-manager apt --ants version=2.3.1

# Build image by piping Dockerfile to `docker build`
$ docker run --rm kaczmarj/neurodocker:0.4.3 generate docker \
    --base debian:stretch --pkg-manager apt --ants version=2.3.1 | docker build -

Singularity

Install ANTs on Debian 9 (Stretch).

$ docker run --rm kaczmarj/neurodocker:0.4.3 generate singularity \
    --base debian:stretch --pkg-manager apt --ants version=2.3.1

Minimize existing Docker image

Neurodocker must be pip installed for container minimization.

In the following example, a Docker image is built with ANTs version 2.3.1 and a functional scan. The image is minified for running antsMotionCorr. The original ANTs Docker image is 1.85 GB, and the "minified" image is 365 MB.

# Create a Docker image with ANTs, and download a functional scan.
$ download_cmd="curl -sSL -o /home/func.nii.gz http://psydata.ovgu.de/studyforrest/phase2/sub-01/ses-movie/func/sub-01_ses-movie_task-movie_run-1_bold.nii.gz"
$ neurodocker generate docker -b centos:7 -p yum --ants version=2.3.1 --run="$download_cmd" | docker build -t ants:2.3.1 -

# Run the container in the background.
# The option --security-opt=seccomp:unconfined is important. Without this,
# the trace will not be able to run in the container.
$ docker run --rm -itd --name ants-container --security-opt=seccomp:unconfined ants:2.3.1

# Output a ReproZip pack file in the current directory with the files
# necessary to run antsMotionCorr.
$ cmd="antsMotionCorr -d 3 -a /home/func.nii.gz -o /home/func_avg.nii.gz"
$ neurodocker reprozip trace ants-container "$cmd"
# Create a Docker container with the contents of ReproZip's trace.
$ reprounzip docker setup neurodocker-reprozip.rpz test

Known issues

Using the -t/--tty option in docker run produces non-printable characters in the generated Dockerfile or Singularity recipe (see moby/moby#8513 (comment)).
- Solution: do not use the -t/--tty flag, unless using the container interactively.
Attempting to rebuild into an existing Singularity image may raise an error.
- Solution: remove the existing image or build a new image file.
The default apt --install option "--no-install-recommends" (that aims at minimizing container sizes) can cause a strange behaviour for cython inside the container
- Solution: use "--install apt_opts=--quiet "
- more information: examples

Name		Name	Last commit message	Last commit date
Latest commit History 947 Commits
.circleci		.circleci
examples		examples
neurodocker		neurodocker
.coveragerc		.coveragerc
.dockerignore		.dockerignore
.gitignore		.gitignore
Dockerfile		Dockerfile
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
codecov.yml		codecov.yml
requirements-dev.txt		requirements-dev.txt
requirements.txt		requirements.txt
setup.py		setup.py

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Neurodocker

Installation

Supported software

Generate Dockerfile

Generate Singularity recipe

Examples

Canonical examples

Docker

Singularity

Minimize existing Docker image

Known issues

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Neurodocker

Installation

Supported software

Generate Dockerfile

Generate Singularity recipe

Examples

Canonical examples

Docker

Singularity

Minimize existing Docker image

Known issues

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