Restoring Dockerfile

Dockerfile

@@ -1,5 +1,319 @@
-FROM nipype/nipype:py38
-COPY . /work
+# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
+# Latest release: Neurodocker version 0.7.0
+# Timestamp: 2021/11/09 11:04:47 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
-RUN /bin/bash -c "source activate neuro && pip install /work"
+
+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' >> "$ND_ENTRYPOINT"; \
+    fi \
+    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           git \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+ENV FSLDIR="/opt/fsl-6.0.3" \
+    PATH="/opt/fsl-6.0.3/bin:$PATH" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    FSLTCLSH="/opt/fsl-6.0.3/bin/fsltclsh" \
+    FSLWISH="/opt/fsl-6.0.3/bin/fslwish" \
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    FSLREMOTECALL="" \
+    FSLGECUDAQ="cuda.q"
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bc \
+           dc \
+           file \
+           libfontconfig1 \
+           libfreetype6 \
+           libgl1-mesa-dev \
+           libgl1-mesa-dri \
+           libglu1-mesa-dev \
+           libgomp1 \
+           libice6 \
+           libxcursor1 \
+           libxft2 \
+           libxinerama1 \
+           libxrandr2 \
+           libxrender1 \
+           libxt6 \
+           sudo \
+           wget \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && echo "Downloading FSL ..." \
+    && mkdir -p /opt/fsl-6.0.3 \
+    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
+    | tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \
+    && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
+    && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
+    && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
+    && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
+    && echo "Installing FSL conda environment ..." \
+    && bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3
+
+ENV PATH="/opt/afni-latest:$PATH" \
+    AFNI_PLUGINPATH="/opt/afni-latest"
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           ed \
+           gsl-bin \
+           libglib2.0-0 \
+           libglu1-mesa-dev \
+           libglw1-mesa \
+           libgomp1 \
+           libjpeg62 \
+           libnlopt-dev \
+           libxm4 \
+           netpbm \
+           python \
+           python3 \
+           r-base \
+           r-base-dev \
+           tcsh \
+           xfonts-base \
+           xvfb \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && 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 \
+    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
+    && dpkg -i /tmp/toinstall.deb \
+    && rm /tmp/toinstall.deb \
+    && apt-get install -f \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
+    && if [ -n "$gsl2_path" ]; then \
+         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
+    fi \
+    && ldconfig \
+    && echo "Downloading AFNI ..." \
+    && mkdir -p /opt/afni-latest \
+    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
+    | tar -xz -C /opt/afni-latest --strip-components 1 \
+    && PATH=$PATH:/opt/afni-latest rPkgsInstall -pkgs ALL
+
+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\"' $ND_ENTRYPOINT
+
+RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
 USER neuro
+
+WORKDIR /home
+
+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 "$conda_installer" \
+    && conda update -yq -nbase conda \
+    && conda config --system --prepend channels conda-forge \
+    && conda config --system --set auto_update_conda false \
+    && conda config --system --set show_channel_urls true \
+    && sync && conda clean -y --all && sync \
+    && conda create -y -q --name neuro \
+    && conda install -y -q --name neuro \
+           "python=3.8" \
+           "traits" \
+           "jupyter" \
+           "nilearn" \
+           "graphviz" \
+           "nipype" \
+           "scikit-image" \
+    && sync && conda clean -y --all && sync \
+    && bash -c "source activate neuro \
+    &&   pip install --no-cache-dir  \
+             "matplotlib"" \
+    && rm -rf ~/.cache/pip/* \
+    && sync \
+    && sed -i '$isource activate neuro' $ND_ENTRYPOINT
+
+ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:"
+
+RUN bash -c 'source activate neuro'
+
+USER root
+
+RUN chmod 777 -Rf /home
+
+RUN chown -R neuro /home
+
+USER neuro
+
+RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
+
+RUN echo '{ \
+    \n  "pkg_manager": "apt", \
+    \n  "instructions": [ \
+    \n    [ \
+    \n      "base", \
+    \n      "neurodebian:stretch-non-free" \
+    \n    ], \
+    \n    [ \
+    \n      "install", \
+    \n      [ \
+    \n        "git" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "fsl", \
+    \n      { \
+    \n        "version": "6.0.3" \
+    \n      } \
+    \n    ], \
+    \n    [ \
+    \n      "afni", \
+    \n      { \
+    \n        "version": "latest", \
+    \n        "method": "binaries", \
+    \n        "install_r": "true", \
+    \n        "install_r_pkgs": "true", \
+    \n        "install_python2": "true", \
+    \n        "install_python3": "true" \
+    \n      } \
+    \n    ], \
+    \n    [ \
+    \n      "spm12", \
+    \n      { \
+    \n        "version": "r7771", \
+    \n        "method": "binaries" \
+    \n      } \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "neuro" \
+    \n    ], \
+    \n    [ \
+    \n      "workdir", \
+    \n      "/home" \
+    \n    ], \
+    \n    [ \
+    \n      "miniconda", \
+    \n      { \
+    \n        "create_env": "neuro", \
+    \n        "conda_install": [ \
+    \n          "python=3.8", \
+    \n          "traits", \
+    \n          "jupyter", \
+    \n          "nilearn", \
+    \n          "graphviz", \
+    \n          "nipype", \
+    \n          "scikit-image" \
+    \n        ], \
+    \n        "pip_install": [ \
+    \n          "matplotlib" \
+    \n        ], \
+    \n        "activate": true \
+    \n      } \
+    \n    ], \
+    \n    [ \
+    \n      "env", \
+    \n      { \
+    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:" \
+    \n      } \
+    \n    ], \
+    \n    [ \
+    \n      "run_bash", \
+    \n      "source activate neuro" \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "root" \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "chmod 777 -Rf /home" \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "chown -R neuro /home" \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "neuro" \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py" \
+    \n    ] \
+    \n  ] \
+    \n}' > /neurodocker/neurodocker_specs.json