Add another option to use Docker container: Dockerfile provided and w…

…ays to personalize it

Dockerfile

@@ -0,0 +1,319 @@
+# 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
+
+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

README.md

@@ -48,8 +48,9 @@ Instructions to download data are available [below](#download-data).
 
 To use the notebooks and launch the pipelines, you need to install the [NiPype](https://nipype.readthedocs.io/en/latest/users/install.html) Python package but also the original software package used in the pipeline (SPM, FSL, AFNI...). 
 
-To facilitate this step, we created a Docker container based on [Neurodocker](https://github.com/ReproNim/neurodocker) that contains the necessary Python packages and software packages. To install the Docker image, use the command below: 
+To facilitate this step, we created a Docker container based on [Neurodocker](https://github.com/ReproNim/neurodocker) that contains the necessary Python packages and software packages. To install the Docker image, two options are available.
 
+#### Option 1: Using Dockerhub
 ```bash
 docker pull elodiegermani/open_pipeline:latest
 ```
@@ -60,6 +61,37 @@ The image should install itself. Once it's done you can check available images o
 docker images
 ```
 
+#### Option 2: Using a Dockerfile 
+The Dockerfile used for the image stored on Dockerhub is available on the GitHub repository. But you might want to personalize your Dockerfile to install only the necessary software packages. To do so, modify the command below to modify the Dockerfile: 
+
+```bash
+docker run --rm repronim/neurodocker:0.7.0 generate docker \
+           --base neurodebian:stretch-non-free --pkg-manager apt \
+           --install git \
+           --fsl version=6.0.3 \
+           --afni version=latest method=binaries install_r=true install_r_pkgs=true install_python2=true install_python3=true \
+           --spm12 version=r7771 method=binaries \
+           --user=neuro \
+           --workdir /home \
+           --miniconda create_env=neuro \
+                       conda_install="python=3.8 traits jupyter nilearn graphviz nipype scikit-image" \
+                       pip_install="matplotlib" \
+                       activate=True \
+           --env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:$LD_LIBRARY_PATH" \
+           --run-bash "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' > Dockerfile
+```
+
+When you are satisfied with your Dockerfile, just build the image:
+
+```bash
+docker build --tag [name_of_the_image] - < Dockerfile
+```
+
 When the installation is finished, you have to build a container using the command below:
 
 ```bash