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# 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