Dockerfile

# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.7.0
# Timestamp: 2022/02/03 16:42:54 UTC
# 
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
# 
#     https://github.com/ReproNim/neurodocker

FROM neurodebian:stretch-non-free

USER root

ARG DEBIAN_FRONTEND="noninteractive"

ENV LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           apt-utils \
           bzip2 \
           ca-certificates \
           curl \
           locales \
           unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
    && dpkg-reconfigure --frontend=noninteractive locales \
    && update-locale LANG="en_US.UTF-8" \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir -p /neurodocker \
    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
    fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

ARG DEBIAN_FRONTEND="noninteractive"

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           gcc \
           g++ \
           make \
           graphviz \
           tree \
           tree \
           less \
           swig \
           netbase \
           git-annex-standalone \
           git-annex-remote-rclone \
           liblzma-dev \
           afni \
           ants \
           fsl-core \
           convert3d \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

ENV FORCE_SPMMCR="1" \
    SPM_HTML_BROWSER="0" \
    LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
    MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
RUN export TMPDIR="$(mktemp -d)" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libncurses5 \
           libxext6 \
           libxmu6 \
           libxpm-dev \
           libxt6 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading MATLAB Compiler Runtime ..." \
    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
    && dpkg -i /tmp/toinstall.deb \
    && rm /tmp/toinstall.deb \
    && apt-get install -f \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && curl -fsSL --retry 5 -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
    && chmod +x "$TMPDIR/MCRInstaller.bin" \
    && "$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlabmcr-2010a" \
    && rm -rf "$TMPDIR" \
    && unset TMPDIR \
    && echo "Downloading standalone SPM ..." \
    && curl -fsSL --retry 5 -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7771_R2010a.zip \
    && unzip -q /tmp/spm12.zip -d /tmp \
    && mkdir -p /opt/spm12-r7771 \
    && mv /tmp/spm12/* /opt/spm12-r7771/ \
    && chmod -R 777 /opt/spm12-r7771 \
    && rm -rf /tmp/spm* \
    && /opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
    && sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT

RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT

RUN sed -i '$iexport PATH=/usr/lib/afni/bin:$PATH' $ND_ENTRYPOINT

RUN sed -i '$iexport PATH=/usr/lib/ants:$PATH' $ND_ENTRYPOINT

RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro

WORKDIR /home/neuro

ENV CONDA_DIR="/opt/miniconda-latest" \
    PATH="/opt/miniconda-latest/bin:$PATH"
RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
    && echo "Downloading Miniconda installer ..." \
    && conda_installer="/tmp/miniconda.sh" \
    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash "$conda_installer" -b -p /opt/miniconda-latest \
    && rm -f "$conda_installer" \
    && conda update -yq -nbase conda \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && sync && conda clean -y --all && sync \
    && conda create -y -q --name neuro \
    && conda install -y -q --name neuro \
           "python=3.7" \
           "h5py=3.1" \
           "ipython=7.21" \
           "joblib=1.0" \
           "jupyter=1.0" \
           "jupyter_contrib_nbextensions=0.5" \
           "jupyterlab=3.0" \
           "matplotlib=3.3" \
           "nb_conda=2.2" \
           "nbformat=5.1" \
           "networkx=2.5" \
           "nibabel=3.2" \
           "nipy=0.4" \
           "notebook=6.2" \
           "numpy=1.20" \
           "pandas=1.2" \
           "pytest=6.2" \
           "scikit-image=0.18" \
           "scikit-learn=0.24" \
           "scipy=1.2" \
           "seaborn=0.11" \
           "sphinx=3.5" \
           "statsmodels=0.12" \
           "traits=6.2" \
    && sync && conda clean -y --all && sync \
    && bash -c "source activate neuro \
    &&   pip install --no-cache-dir  \
             "atlasreader==0.1" \
             "autopep8==1.5" \
             "datalad[full]" \
             "duecredit==0.8" \
             "nbval==0.9" \
             "nilearn==0.7" \
             "nipype==1.6.0" \
             "nistats==0.0.1rc0" \
             "nitime==0.9" \
             "pybids==0.12"" \
    && rm -rf ~/.cache/pip/* \
    && sync \
    && sed -i '$isource activate neuro' $ND_ENTRYPOINT

RUN conda create -y -q --name mvpa \
    && conda install -y -q --name mvpa \
           "python=2.7" \
           "h5py=2.8" \
           "hdf5=1.10" \
           "imageio=2.6" \
           "ipython=5.8" \
           "joblib=0.14" \
           "jupyter=1.0" \
           "jupyter_contrib_nbextensions=0.5" \
           "jupyterlab=0.33" \
           "matplotlib=2.2" \
           "nb_conda=2.2" \
           "nbconvert=5.6" \
           "nbformat=4.4" \
           "networkx=2.2" \
           "nibabel=2.5" \
           "nipy=0.4" \
           "notebook=5.7" \
           "numpy=1.16" \
           "pandas=0.24" \
           "pytest=4.6" \
           "scikit-image=0.14" \
           "scikit-learn=0.20" \
           "scipy=1.1" \
           "seaborn=0.9" \
           "shogun=6.1" \
           "statsmodels=0.10" \
    && sync && conda clean -y --all && sync \
    && bash -c "source activate mvpa \
    &&   pip install --no-cache-dir  \
             "atlasreader==0.1" \
             "autopep8==1.5" \
             "dask" \
             "datalad[full]" \
             "duecredit==0.8" \
             "nbval==0.9" \
             "nibabel" \
             "nilearn==0.5" \
             "nistats==0.0.1rc0" \
             "pprocess==0.5" \
             "pybids==0.9.5"" \
    && rm -rf ~/.cache/pip/* \
    && sync

RUN bash -c 'source activate mvpa && cd /home/neuro               && pip install -U pip              && pip install -U numpy              && git clone git://github.com/PyMVPA/PyMVPA.git              && cd PyMVPA              && make 3rd              && python setup.py build_ext              && python setup.py install              && cd ..              && rm -rf PyMVPA              && source deactivate mvpa'

USER root

RUN mkdir /data && chmod 777 /data && chmod a+s /data

RUN mkdir /workingdir && chmod 777 /workingdir && chmod a+s /workingdir

RUN mkdir /templates && chmod 777 /templates && chmod a+s /templates

RUN curl -qLO http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_asym_09c_nifti.zip \
                    && unzip mni_icbm152_nlin_asym_09c_nifti.zip -d /templates \
                    && rm mni_icbm152_nlin_asym_09c_nifti.zip \
                    && cd /templates/mni_icbm152_nlin_asym_09c \
                 && mv mni_icbm152_csf_tal_nlin_asym_09c.nii 1.0mm_tpm_csf.nii \
                    && mv mni_icbm152_gm_tal_nlin_asym_09c.nii 1.0mm_tpm_gm.nii \
                    && mv mni_icbm152_pd_tal_nlin_asym_09c.nii 1.0mm_PD.nii \
                    && mv mni_icbm152_t1_tal_nlin_asym_09c_mask.nii 1.0mm_mask.nii \
                    && mv mni_icbm152_t1_tal_nlin_asym_09c.nii 1.0mm_T1.nii \
                    && mv mni_icbm152_t2_tal_nlin_asym_09c.nii 1.0mm_T2.nii \
                    && mv mni_icbm152_wm_tal_nlin_asym_09c.nii 1.0mm_tpm_wm.nii \
                    && gzip 1.0mm_*nii \
                    && /usr/bin/fsl5.0-fslmaths 1.0mm_tpm_gm.nii.gz -add 1.0mm_tpm_wm.nii.gz -add 1.0mm_tpm_csf.nii.gz 1.0mm_brain_prob_mask.nii.gz \
                    && /usr/bin/fsl5.0-fslmaths 1.0mm_T1.nii.gz -mul 1.0mm_mask.nii.gz 1.0mm_brain.nii.gz

COPY ["notebooks", "/home/neuro/notebooks"]

COPY ["scripts/test_notebooks.py", "/home/neuro/test_notebooks.py"]

COPY ["notebooks/templates", "/reports"]

RUN chown -R neuro /home/neuro

RUN chown -R neuro /templates

RUN chown -R neuro /data

RUN rm -rf /opt/conda/pkgs/*

USER neuro

RUN bash -c 'source activate mvpa && jupyter nbextension enable exercise2/main && jupyter nbextension enable hide_input/main && jupyter nbextension enable code_prettify/autopep8 && jupyter nbextension enable hide_input_all/main && jupyter nbextension enable printview/main && jupyter nbextension enable spellchecker/main'

RUN bash -c 'source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable hide_input/main && jupyter nbextension enable code_prettify/autopep8 && jupyter nbextension enable hide_input_all/main && jupyter nbextension enable printview/main && jupyter nbextension enable spellchecker/main'

RUN bash -c 'source activate neuro && pip install -U pip && pip install -U numpy nbval'

RUN bash -c 'git config --global user.email 'you@example.com' && git config --global user.name 'Your Name''

RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py

WORKDIR /home/neuro/notebooks

CMD ["jupyter-notebook", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--NotebookApp.token=fmriflows"]

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "neurodebian:stretch-non-free" \
    \n    ], \
    \n    [ \
    \n      "arg", \
    \n      { \
    \n        "DEBIAN_FRONTEND": "noninteractive" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "install", \
    \n      [ \
    \n        "gcc", \
    \n        "g++", \
    \n        "make", \
    \n        "graphviz", \
    \n        "tree", \
    \n        "tree", \
    \n        "less", \
    \n        "swig", \
    \n        "netbase", \
    \n        "git-annex-standalone", \
    \n        "git-annex-remote-rclone", \
    \n        "liblzma-dev", \
    \n        "afni", \
    \n        "ants", \
    \n        "fsl-core", \
    \n        "convert3d" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "spm12", \
    \n      { \
    \n        "version": "r7771" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "add_to_entrypoint", \
    \n      "source /etc/fsl/fsl.sh" \
    \n    ], \
    \n    [ \
    \n      "add_to_entrypoint", \
    \n      "export PATH=/usr/lib/afni/bin:$PATH" \
    \n    ], \
    \n    [ \
    \n      "add_to_entrypoint", \
    \n      "export PATH=/usr/lib/ants:$PATH" \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "neuro" \
    \n    ], \
    \n    [ \
    \n      "workdir", \
    \n      "/home/neuro" \
    \n    ], \
    \n    [ \
    \n      "miniconda", \
    \n      { \
    \n        "version": "latest", \
    \n        "conda_install": [ \
    \n          "python=3.7", \
    \n          "h5py=3.1", \
    \n          "ipython=7.21", \
    \n          "joblib=1.0", \
    \n          "jupyter=1.0", \
    \n          "jupyter_contrib_nbextensions=0.5", \
    \n          "jupyterlab=3.0", \
    \n          "matplotlib=3.3", \
    \n          "nb_conda=2.2", \
    \n          "nbformat=5.1", \
    \n          "networkx=2.5", \
    \n          "nibabel=3.2", \
    \n          "nipy=0.4", \
    \n          "notebook=6.2", \
    \n          "numpy=1.20", \
    \n          "pandas=1.2", \
    \n          "pytest=6.2", \
    \n          "scikit-image=0.18", \
    \n          "scikit-learn=0.24", \
    \n          "scipy=1.2", \
    \n          "seaborn=0.11", \
    \n          "sphinx=3.5", \
    \n          "statsmodels=0.12", \
    \n          "traits=6.2" \
    \n        ], \
    \n        "pip_install": [ \
    \n          "atlasreader==0.1", \
    \n          "autopep8==1.5", \
    \n          "datalad[full]", \
    \n          "duecredit==0.8", \
    \n          "nbval==0.9", \
    \n          "nilearn==0.7", \
    \n          "nipype==1.6.0", \
    \n          "nistats==0.0.1rc0", \
    \n          "nitime==0.9", \
    \n          "pybids==0.12" \
    \n        ], \
    \n        "create_env": "neuro", \
    \n        "activate": true \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "miniconda", \
    \n      { \
    \n        "miniconda_version": "4.6", \
    \n        "conda_install": [ \
    \n          "python=2.7", \
    \n          "h5py=2.8", \
    \n          "hdf5=1.10", \
    \n          "imageio=2.6", \
    \n          "ipython=5.8", \
    \n          "joblib=0.14", \
    \n          "jupyter=1.0", \
    \n          "jupyter_contrib_nbextensions=0.5", \
    \n          "jupyterlab=0.33", \
    \n          "matplotlib=2.2", \
    \n          "nb_conda=2.2", \
    \n          "nbconvert=5.6", \
    \n          "nbformat=4.4", \
    \n          "networkx=2.2", \
    \n          "nibabel=2.5", \
    \n          "nipy=0.4", \
    \n          "notebook=5.7", \
    \n          "numpy=1.16", \
    \n          "pandas=0.24", \
    \n          "pytest=4.6", \
    \n          "scikit-image=0.14", \
    \n          "scikit-learn=0.20", \
    \n          "scipy=1.1", \
    \n          "seaborn=0.9", \
    \n          "shogun=6.1", \
    \n          "statsmodels=0.10" \
    \n        ], \
    \n        "pip_install": [ \
    \n          "atlasreader==0.1", \
    \n          "autopep8==1.5", \
    \n          "dask", \
    \n          "datalad[full]", \
    \n          "duecredit==0.8", \
    \n          "nbval==0.9", \
    \n          "nibabel", \
    \n          "nilearn==0.5", \
    \n          "nistats==0.0.1rc0", \
    \n          "pprocess==0.5", \
    \n          "pybids==0.9.5" \
    \n        ], \
    \n        "create_env": "mvpa", \
    \n        "activate": false \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "run_bash", \
    \n      "source activate mvpa && cd /home/neuro               && pip install -U pip              && pip install -U numpy              && git clone git://github.com/PyMVPA/PyMVPA.git              && cd PyMVPA              && make 3rd              && python setup.py build_ext              && python setup.py install              && cd ..              && rm -rf PyMVPA              && source deactivate mvpa" \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "root" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "mkdir /data && chmod 777 /data && chmod a+s /data" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "mkdir /workingdir && chmod 777 /workingdir && chmod a+s /workingdir" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "mkdir /templates && chmod 777 /templates && chmod a+s /templates" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "curl -qLO http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_asym_09c_nifti.zip \\\\n             && unzip mni_icbm152_nlin_asym_09c_nifti.zip -d /templates \\\\n             && rm mni_icbm152_nlin_asym_09c_nifti.zip \\\\n             && cd /templates/mni_icbm152_nlin_asym_09c\\n             && mv mni_icbm152_csf_tal_nlin_asym_09c.nii 1.0mm_tpm_csf.nii \\\\n             && mv mni_icbm152_gm_tal_nlin_asym_09c.nii 1.0mm_tpm_gm.nii \\\\n             && mv mni_icbm152_pd_tal_nlin_asym_09c.nii 1.0mm_PD.nii \\\\n             && mv mni_icbm152_t1_tal_nlin_asym_09c_mask.nii 1.0mm_mask.nii \\\\n             && mv mni_icbm152_t1_tal_nlin_asym_09c.nii 1.0mm_T1.nii \\\\n             && mv mni_icbm152_t2_tal_nlin_asym_09c.nii 1.0mm_T2.nii \\\\n             && mv mni_icbm152_wm_tal_nlin_asym_09c.nii 1.0mm_tpm_wm.nii \\\\n             && gzip 1.0mm_*nii \\\\n             && /usr/bin/fsl5.0-fslmaths 1.0mm_tpm_gm.nii.gz -add 1.0mm_tpm_wm.nii.gz -add 1.0mm_tpm_csf.nii.gz 1.0mm_brain_prob_mask.nii.gz \\\\n             && /usr/bin/fsl5.0-fslmaths 1.0mm_T1.nii.gz -mul 1.0mm_mask.nii.gz 1.0mm_brain.nii.gz" \
    \n    ], \
    \n    [ \
    \n      "copy", \
    \n      [ \
    \n        "notebooks", \
    \n        "/home/neuro/notebooks" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "copy", \
    \n      [ \
    \n        "scripts/test_notebooks.py", \
    \n        "/home/neuro/test_notebooks.py" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "copy", \
    \n      [ \
    \n        "notebooks/templates", \
    \n        "/reports" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "chown -R neuro /home/neuro" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "chown -R neuro /templates" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "chown -R neuro /data" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "rm -rf /opt/conda/pkgs/*" \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "neuro" \
    \n    ], \
    \n    [ \
    \n      "run_bash", \
    \n      "source activate mvpa && jupyter nbextension enable exercise2/main && jupyter nbextension enable hide_input/main && jupyter nbextension enable code_prettify/autopep8 && jupyter nbextension enable hide_input_all/main && jupyter nbextension enable printview/main && jupyter nbextension enable spellchecker/main" \
    \n    ], \
    \n    [ \
    \n      "run_bash", \
    \n      "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable hide_input/main && jupyter nbextension enable code_prettify/autopep8 && jupyter nbextension enable hide_input_all/main && jupyter nbextension enable printview/main && jupyter nbextension enable spellchecker/main" \
    \n    ], \
    \n    [ \
    \n      "run_bash", \
    \n      "source activate neuro && pip install -U pip && pip install -U numpy nbval" \
    \n    ], \
    \n    [ \
    \n      "run_bash", \
    \n      "git config --global user.email '"'"'you@example.com'"'"' && git config --global user.name '"'"'Your Name'"'"'" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py" \
    \n    ], \
    \n    [ \
    \n      "workdir", \
    \n      "/home/neuro/notebooks" \
    \n    ], \
    \n    [ \
    \n      "cmd", \
    \n      [ \
    \n        "jupyter-notebook --port=8888 --no-browser --ip=0.0.0.0 --NotebookApp.token=fmriflows" \
    \n      ] \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json