Command-line Interface#
Neurodocker provides the command-line program neurodocker.
This program has two subcommands: generate and minify.
neurodocker#
Usage: neurodocker [OPTIONS] COMMAND [ARGS]...
Generate custom containers, and minify existing containers.
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
generate Generate a container.
genfromjson Generate a container from a ReproEnv JSON file.
minify Minify a container.
neurodocker generate#
Usage: neurodocker generate [OPTIONS] COMMAND [ARGS]...
Generate a container.
Options:
--template-path DIRECTORY Path to directories with templates to register
[env var: REPROENV_TEMPLATE_PATH]
--help Show this message and exit.
Commands:
docker Generate a Dockerfile.
singularity Generate a Singularity recipe.
The neurodocker generate command has two subcommands: docker and singularity.
Most of the arguments for these subcommands are identical, but please check the details below.
neurodocker generate docker#
Usage: neurodocker generate docker [OPTIONS]
Generate a Dockerfile.
Options:
-p, --pkg-manager [yum|apt] System package manager [required]
-b, --base-image TEXT Base image [required]
--arg KEY=VALUE Build-time variables (do not persist after
container is built)
--copy TUPLE Copy files into the container. Provide at least
two paths. The last path is always the
destination path in the container.
--add TUPLE Extract a tar file as a layer in the container.
Provide a source and destination path.
--env KEY=VALUE Set persistent environment variables
--entrypoint TUPLE Set entrypoint of the container
--install TUPLE Install packages with system package manager
--label KEY=VALUE Set labels on the container
--run TEXT Run commands in /bin/sh
--run-bash TEXT Run commands in a bash shell
--user TEXT Switch to a different user (create user if it
does not exist)
--workdir TEXT Set the working directory
--yes Reply yes to all prompts.
--json Output instructions as JSON. This can be used
to generate Dockerfiles or Singularity recipes
with Neurodocker.
--_header KEY=VALUE Add _header
method=[source]
options for method=source
--afni KEY=VALUE Add afni
method=[binaries|source]
options for method=binaries
- install_path [default: /opt/afni-{{ self.version }}]
- version [default: latest]
- install_r_pkgs [default: false]
- install_python3 [default: false]
options for method=source
- version [required]
- repo [default: https://github.com/afni/afni.git]
- install_path [default: /opt/afni-{{ self.version }}]
- install_r_pkgs [default: false]
- install_python3 [default: false]
--ants KEY=VALUE Add ants
method=[binaries|source]
options for method=binaries
- version [required]
version=[2.4.3|2.4.2|2.4.1|2.3.4|2.3.2|2.3.1|2.3.0|2.2.0|2.1.0|2.0.3|2.0.0]
- install_path [default: /opt/ants-{{ self.version }}]
options for method=source
- version [required]
- repo [default: https://github.com/ANTsX/ANTs.git]
- install_path [default: /opt/ants-{{ self.version }}]
- cmake_opts [default: -DCMAKE_INSTALL_PREFIX={{ self.install_path }} -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF]
- make_opts [default: -j1]
--bids_validator KEY=VALUE Add bids_validator
method=[binaries]
options for method=binaries
- version [required]
version=[1.9.0|1.13.0|1.12.0|1.11.0|1.10.0]
- node_version [default: 20]
--cat12 KEY=VALUE Add cat12
method=[binaries]
options for method=binaries
- version [required]
version=[r2166_R2017b|r1933_R2017b]
- install_path [default: /opt/CAT12-{{ self.version }}]
--convert3d KEY=VALUE Add convert3d
method=[binaries]
options for method=binaries
- version [required]
version=[nightly|1.0.0]
- install_path [default: /opt/convert3d-{{ self.version }}]
--dcm2niix KEY=VALUE Add dcm2niix
method=[binaries|source]
options for method=binaries
- version [required]
version=[v1.0.20201102|v1.0.20200331|v1.0.20190902|latest]
- install_path [default: /opt/dcm2niix-{{ self.version }}]
options for method=source
- version [required]
- repo [default: https://github.com/rordenlab/dcm2niix]
- install_path [default: /opt/dcm2niix-{{ self.version }}]
- cmake_opts [default: ]
- make_opts [default: -j1]
--freesurfer KEY=VALUE Add freesurfer
method=[binaries]
options for method=binaries
- version [required]
version=[7.4.1|7.3.2|7.3.1|7.3.0|7.2.0|7.1.1-min|7.1.1|7.1.0|6.0.1|6.0.0-min|6.0.0]
- install_path [default: /opt/freesurfer-{{ self.version }}]
- exclude_paths [default: average/mult-comp-cor
lib/cuda
lib/qt
subjects/V1_average
subjects/bert
subjects/cvs_avg35
subjects/cvs_avg35_inMNI152
subjects/fsaverage3
subjects/fsaverage4
subjects/fsaverage5
subjects/fsaverage6
subjects/fsaverage_sym
trctrain
]
--fsl KEY=VALUE Add fsl
method=[binaries]
options for method=binaries
- version [required]
version=[6.0.7.4|6.0.7.1|6.0.6.4|6.0.6.3|6.0.6.2|6.0.6.1|6.0.6|6.0.5.2|6.0.5.1|6.0.5|6.0.4|6.0.3|6.0.2|6.0.1|6.0.0|5.0.9|5.0.8|5.0.11|5.0.10]
- install_path [default: /opt/fsl-{{ self.version }}]
- exclude_paths [default: ]
**Note**: FSL is non-free. If you are considering commercial use of FSL, please consult the relevant license(s).
--jq KEY=VALUE Add jq
method=[binaries|source]
options for method=binaries
- version [required]
version=[1.6|1.5]
options for method=source
- version [required]
--matlabmcr KEY=VALUE Add matlabmcr
method=[binaries]
options for method=binaries
- version [required]
version=[2023b|2023a|2022b|2022a|2021b|2021a|2020b|2020a|2019b|2019a|2018b|2018a|2017b|2017a|2016b|2016a|2015b|2015aSP1|2015a|2014b|2014a|2013b|2013a|2012b|2012a|2010a]
- curl_opts [default: ]
- install_path [default: /opt/MCR-{{ self.version }}]
--minc KEY=VALUE Add minc
method=[binaries]
options for method=binaries
- version [required]
version=[1.9.18|1.9.17|1.9.16|1.9.15]
- install_path [default: /opt/minc-{{ self.version }}]
--miniconda KEY=VALUE Add miniconda
method=[binaries]
options for method=binaries
- version [required]
version=[latest|*]
- install_path [default: /opt/miniconda-{{ self.version }}]
- installed [default: false]
- env_name [default: base]
- env_exists [default: true]
- conda_install [default: ]
- pip_install [default: ]
- conda_opts [default: ]
- pip_opts [default: ]
- yaml_file [default: ]
- mamba [default: false]
--mricron KEY=VALUE Add mricron
method=[binaries]
options for method=binaries
- version [required]
version=[1.0.20190902|1.0.20190410|1.0.20181114|1.0.20180614|1.0.20180404|1.0.20171220]
- install_path [default: /opt/mricron-{{ self.version }}]
--mrtrix3 KEY=VALUE Add mrtrix3
method=[binaries|source]
options for method=binaries
- version [required]
version=[3.0.4|3.0.3|3.0.2|3.0.1|3.0.0]
- install_path [default: /opt/mrtrix3-{{ self.version }}]
- build_processes [default: 1]
options for method=source
- version [required]
- repo [default: https://github.com/MRtrix3/mrtrix3.git]
- install_path [default: /opt/mrtrix3-{{ self.version }}]
- build_processes [default: 1]
--ndfreeze KEY=VALUE Add ndfreeze
method=[source]
options for method=source
- date [required]
- opts [default: ]
--neurodebian KEY=VALUE Add neurodebian
method=[binaries]
options for method=binaries
- os_codename [required]
- version [required]
version=[usa-tn|usa-nh|usa-ca|japan|greece|germany-munich|germany-magdeburg|china-zhejiang|china-tsinghua|china-scitech|australia]
- full_or_libre [default: full]
--niftyreg KEY=VALUE Add niftyreg
method=[source]
options for method=source
- version [required]
- repo [default: https://github.com/KCL-BMEIS/niftyreg]
- install_path [default: /opt/niftyreg-{{ self.version }}]
- cmake_opts [default: -DCMAKE_INSTALL_PREFIX={{ self.install_path }} -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF]
- make_opts [default: -j1]
--petpvc KEY=VALUE Add petpvc
method=[binaries]
options for method=binaries
- version [required]
version=[1.2.4|1.2.2|1.2.1|1.2.0-b|1.2.0-a|1.1.0|1.0.0]
- install_path [default: /opt/petpvc-{{ self.version }}]
--spm12 KEY=VALUE Add spm12
method=[binaries]
options for method=binaries
- version [required]
version=[r7771|r7487|r7219|r6914|r6685|r6472|r6225]
- install_path [default: /opt/spm12-{{ self.version }}]
- matlab_install_path [default: /opt/matlab-compiler-runtime-2010a]
--vnc KEY=VALUE Add vnc
method=[source]
options for method=source
- passwd [required]
--help Show this message and exit.
neurodocker generate singularity#
Usage: neurodocker generate singularity [OPTIONS]
Generate a Singularity recipe.
Options:
-p, --pkg-manager [apt|yum] System package manager [required]
-b, --base-image TEXT Base image [required]
--arg KEY=VALUE Build-time variables (do not persist after
container is built)
--copy TUPLE Copy files into the container. Provide at least
two paths. The last path is always the
destination path in the container.
--add TUPLE Extract a tar file as a layer in the container.
Provide a source and destination path.
--env KEY=VALUE Set persistent environment variables
--entrypoint TUPLE Set entrypoint of the container
--install TUPLE Install packages with system package manager
--label KEY=VALUE Set labels on the container
--run TEXT Run commands in /bin/sh
--run-bash TEXT Run commands in a bash shell
--user TEXT Switch to a different user (create user if it
does not exist)
--workdir TEXT Set the working directory
--yes Reply yes to all prompts.
--json Output instructions as JSON. This can be used
to generate Dockerfiles or Singularity recipes
with Neurodocker.
--_header KEY=VALUE Add _header
method=[source]
options for method=source
--afni KEY=VALUE Add afni
method=[binaries|source]
options for method=binaries
- install_path [default: /opt/afni-{{ self.version }}]
- version [default: latest]
- install_r_pkgs [default: false]
- install_python3 [default: false]
options for method=source
- version [required]
- repo [default: https://github.com/afni/afni.git]
- install_path [default: /opt/afni-{{ self.version }}]
- install_r_pkgs [default: false]
- install_python3 [default: false]
--ants KEY=VALUE Add ants
method=[binaries|source]
options for method=binaries
- version [required]
version=[2.4.3|2.4.2|2.4.1|2.3.4|2.3.2|2.3.1|2.3.0|2.2.0|2.1.0|2.0.3|2.0.0]
- install_path [default: /opt/ants-{{ self.version }}]
options for method=source
- version [required]
- repo [default: https://github.com/ANTsX/ANTs.git]
- install_path [default: /opt/ants-{{ self.version }}]
- cmake_opts [default: -DCMAKE_INSTALL_PREFIX={{ self.install_path }} -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF]
- make_opts [default: -j1]
--bids_validator KEY=VALUE Add bids_validator
method=[binaries]
options for method=binaries
- version [required]
version=[1.9.0|1.13.0|1.12.0|1.11.0|1.10.0]
- node_version [default: 20]
--cat12 KEY=VALUE Add cat12
method=[binaries]
options for method=binaries
- version [required]
version=[r2166_R2017b|r1933_R2017b]
- install_path [default: /opt/CAT12-{{ self.version }}]
--convert3d KEY=VALUE Add convert3d
method=[binaries]
options for method=binaries
- version [required]
version=[nightly|1.0.0]
- install_path [default: /opt/convert3d-{{ self.version }}]
--dcm2niix KEY=VALUE Add dcm2niix
method=[binaries|source]
options for method=binaries
- version [required]
version=[v1.0.20201102|v1.0.20200331|v1.0.20190902|latest]
- install_path [default: /opt/dcm2niix-{{ self.version }}]
options for method=source
- version [required]
- repo [default: https://github.com/rordenlab/dcm2niix]
- install_path [default: /opt/dcm2niix-{{ self.version }}]
- cmake_opts [default: ]
- make_opts [default: -j1]
--freesurfer KEY=VALUE Add freesurfer
method=[binaries]
options for method=binaries
- version [required]
version=[7.4.1|7.3.2|7.3.1|7.3.0|7.2.0|7.1.1-min|7.1.1|7.1.0|6.0.1|6.0.0-min|6.0.0]
- install_path [default: /opt/freesurfer-{{ self.version }}]
- exclude_paths [default: average/mult-comp-cor
lib/cuda
lib/qt
subjects/V1_average
subjects/bert
subjects/cvs_avg35
subjects/cvs_avg35_inMNI152
subjects/fsaverage3
subjects/fsaverage4
subjects/fsaverage5
subjects/fsaverage6
subjects/fsaverage_sym
trctrain
]
--fsl KEY=VALUE Add fsl
method=[binaries]
options for method=binaries
- version [required]
version=[6.0.7.4|6.0.7.1|6.0.6.4|6.0.6.3|6.0.6.2|6.0.6.1|6.0.6|6.0.5.2|6.0.5.1|6.0.5|6.0.4|6.0.3|6.0.2|6.0.1|6.0.0|5.0.9|5.0.8|5.0.11|5.0.10]
- install_path [default: /opt/fsl-{{ self.version }}]
- exclude_paths [default: ]
**Note**: FSL is non-free. If you are considering commercial use of FSL, please consult the relevant license(s).
--jq KEY=VALUE Add jq
method=[binaries|source]
options for method=binaries
- version [required]
version=[1.6|1.5]
options for method=source
- version [required]
--matlabmcr KEY=VALUE Add matlabmcr
method=[binaries]
options for method=binaries
- version [required]
version=[2023b|2023a|2022b|2022a|2021b|2021a|2020b|2020a|2019b|2019a|2018b|2018a|2017b|2017a|2016b|2016a|2015b|2015aSP1|2015a|2014b|2014a|2013b|2013a|2012b|2012a|2010a]
- curl_opts [default: ]
- install_path [default: /opt/MCR-{{ self.version }}]
--minc KEY=VALUE Add minc
method=[binaries]
options for method=binaries
- version [required]
version=[1.9.18|1.9.17|1.9.16|1.9.15]
- install_path [default: /opt/minc-{{ self.version }}]
--miniconda KEY=VALUE Add miniconda
method=[binaries]
options for method=binaries
- version [required]
version=[latest|*]
- install_path [default: /opt/miniconda-{{ self.version }}]
- installed [default: false]
- env_name [default: base]
- env_exists [default: true]
- conda_install [default: ]
- pip_install [default: ]
- conda_opts [default: ]
- pip_opts [default: ]
- yaml_file [default: ]
- mamba [default: false]
--mricron KEY=VALUE Add mricron
method=[binaries]
options for method=binaries
- version [required]
version=[1.0.20190902|1.0.20190410|1.0.20181114|1.0.20180614|1.0.20180404|1.0.20171220]
- install_path [default: /opt/mricron-{{ self.version }}]
--mrtrix3 KEY=VALUE Add mrtrix3
method=[binaries|source]
options for method=binaries
- version [required]
version=[3.0.4|3.0.3|3.0.2|3.0.1|3.0.0]
- install_path [default: /opt/mrtrix3-{{ self.version }}]
- build_processes [default: 1]
options for method=source
- version [required]
- repo [default: https://github.com/MRtrix3/mrtrix3.git]
- install_path [default: /opt/mrtrix3-{{ self.version }}]
- build_processes [default: 1]
--ndfreeze KEY=VALUE Add ndfreeze
method=[source]
options for method=source
- date [required]
- opts [default: ]
--neurodebian KEY=VALUE Add neurodebian
method=[binaries]
options for method=binaries
- version [required]
version=[usa-tn|usa-nh|usa-ca|japan|greece|germany-munich|germany-magdeburg|china-zhejiang|china-tsinghua|china-scitech|australia]
- os_codename [required]
- full_or_libre [default: full]
--niftyreg KEY=VALUE Add niftyreg
method=[source]
options for method=source
- version [required]
- repo [default: https://github.com/KCL-BMEIS/niftyreg]
- install_path [default: /opt/niftyreg-{{ self.version }}]
- cmake_opts [default: -DCMAKE_INSTALL_PREFIX={{ self.install_path }} -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF]
- make_opts [default: -j1]
--petpvc KEY=VALUE Add petpvc
method=[binaries]
options for method=binaries
- version [required]
version=[1.2.4|1.2.2|1.2.1|1.2.0-b|1.2.0-a|1.1.0|1.0.0]
- install_path [default: /opt/petpvc-{{ self.version }}]
--spm12 KEY=VALUE Add spm12
method=[binaries]
options for method=binaries
- version [required]
version=[r7771|r7487|r7219|r6914|r6685|r6472|r6225]
- install_path [default: /opt/spm12-{{ self.version }}]
- matlab_install_path [default: /opt/matlab-compiler-runtime-2010a]
--vnc KEY=VALUE Add vnc
method=[source]
options for method=source
- passwd [required]
--help Show this message and exit.
neurodocker minify#
Note
Minifying images requires additional dependencies installed with :code: pip. Please install neurodocker with
pip install neurodocker[minify]
Usage: neurodocker minify [OPTIONS] COMMAND...
Minify a container.
Trace COMMAND... in the container, and remove all files in `--dirs-to-prune`
that were not used by the commands.
Examples
--------
docker run --rm -itd --name to-minify python:3.9-slim bash
neurodocker minify \
--container to-minify \
--dir /usr/local \
"python -c 'a = 1 + 1; print(a)'"
Options:
-c, --container TEXT ID or name of running Docker container [required]
-d, --dir TEXT Directories in container to prune. Data will be lost
in these directories [required]
--yes Reply yes to all prompts.
--help Show this message and exit.