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generated-full.Dockerfile
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# Generated by Neurodocker v0.3.1-20-gb8c8f73.
#
# 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/kaczmarj/neurodocker
#
# Timestamp: 2017-11-07 11:35:34
FROM debian:stretch
ARG DEBIAN_FRONTEND=noninteractive
#----------------------------------------------------------
# Install common dependencies and create default entrypoint
#----------------------------------------------------------
ENV LANG="en_US.UTF-8" \
LC_ALL="C.UTF-8" \
ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN apt-get update -qq && apt-get install -yq --no-install-recommends \
apt-utils bzip2 ca-certificates curl locales unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& localedef --force --inputfile=en_US --charmap=UTF-8 C.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 +x' >> $ND_ENTRYPOINT \
&& echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
#--------------------
# Install AFNI latest
#--------------------
ENV PATH=/opt/afni:$PATH
RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin libglu1-mesa-dev libglib2.0-0 libglw1-mesa \
libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb \
&& libs_path=/usr/lib/x86_64-linux-gnu \
&& if [ -f $libs_path/libgsl.so.19 ]; then \
ln $libs_path/libgsl.so.19 $libs_path/libgsl.so.0; \
fi \
&& echo "Install libxp (not in all ubuntu/debian repositories)" \
&& apt-get install -yq --no-install-recommends libxp6 \
|| /bin/bash -c " \
curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb" \
&& echo "Install libpng12 (not in all ubuntu/debian repositories" \
&& apt-get install -yq --no-install-recommends libpng12-0 \
|| /bin/bash -c " \
curl -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
&& dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb" \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo "Downloading AFNI ..." \
&& mkdir -p /opt/afni \
&& curl -sSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar zx -C /opt/afni --strip-components=1
#-------------------
# Install ANTs 2.2.0
#-------------------
RUN echo "Downloading ANTs ..." \
&& curl -sSL --retry 5 https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz \
| tar zx -C /opt
ENV ANTSPATH=/opt/ants \
PATH=/opt/ants:$PATH
#------------------------
# Install Convert3D 1.0.0
#------------------------
RUN echo "Downloading C3D ..." \
&& mkdir /opt/c3d \
&& curl -sSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
| tar -xzC /opt/c3d --strip-components=1
ENV C3DPATH=/opt/c3d \
PATH=/opt/c3d/bin:$PATH
#------------------------
# Install dcm2niix master
#------------------------
WORKDIR /tmp
RUN deps='cmake g++ gcc git make pigz zlib1g-dev' \
&& apt-get update -qq && apt-get install -yq --no-install-recommends $deps \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& mkdir dcm2niix \
&& curl -sSL https://github.com/rordenlab/dcm2niix/tarball/master | tar xz -C dcm2niix --strip-components 1 \
&& mkdir dcm2niix/build && cd dcm2niix/build \
&& cmake .. && make \
&& make install \
&& rm -rf /tmp/* \
&& apt-get purge -y --auto-remove $deps
#--------------------------
# Install FreeSurfer v6.0.0
#--------------------------
# Install version minimized for recon-all
# See https://github.com/freesurfer/freesurfer/issues/70
RUN apt-get update -qq && apt-get install -yq --no-install-recommends bc libgomp1 libxmu6 libxt6 tcsh perl \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo "Downloading minimized FreeSurfer ..." \
&& curl -sSL https://dl.dropbox.com/s/nnzcfttc41qvt31/recon-all-freesurfer6-3.min.tgz | tar xz -C /opt \
&& sed -i '$isource $FREESURFER_HOME/SetUpFreeSurfer.sh' $ND_ENTRYPOINT
ENV FREESURFER_HOME=/opt/freesurfer
#-----------------------------------------------------------
# Install FSL v5.0.10
# FSL is non-free. If you are considering commerical use
# of this Docker image, please consult the relevant license:
# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
#-----------------------------------------------------------
RUN apt-get update -qq && apt-get install -yq --no-install-recommends bc dc libfontconfig1 libfreetype6 libgl1-mesa-dev libglu1-mesa-dev libgomp1 libice6 libmng1 libxcursor1 libxft2 libxinerama1 libxrandr2 libxrender1 libxt6 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo "Downloading FSL ..." \
&& curl -sSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
| tar zx -C /opt \
&& /bin/bash /opt/fsl/etc/fslconf/fslpython_install.sh -q -f /opt/fsl \
&& sed -i '$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' $ND_ENTRYPOINT
ENV FSLDIR=/opt/fsl \
PATH=/opt/fsl/bin:$PATH
#--------------------
# Install MINC 1.9.15
#--------------------
RUN apt-get update -qq && apt-get install -yq --no-install-recommends libgl1-mesa-dev libice6 libsm6 libx11-6 libxext6 libxi6 libxmu6 libgomp1 libjpeg62 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo " Downloading MINC, BEASTLIB, and MODELS..." \
&& curl -sSL --retry 5 https://dl.dropbox.com/s/40hjzizaqi91373/minc-toolkit-1.9.15-20170529-CentOS_6.9-x86_64.tar.gz \
| tar zx -C /opt \
&& curl -sSL --retry 5 http://packages.bic.mni.mcgill.ca/tgz/beast-library-1.1.tar.gz \
| tar zx -C /opt/minc/share \
&& curl -sSL --retry 5 -o /tmp/mni_90a.zip http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09a_minc2.zip \
&& unzip /tmp/mni_90a.zip -d /opt/minc/share/icbm152_model_09a \
&& curl -sSL --retry 5 -o /tmp/mni_90c.zip http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_minc2.zip \
&& unzip /tmp/mni_90c.zip -d /opt/minc/share/icbm152_model_09c \
&& rm -r /tmp/mni_90* \
&& sed -i '$isource /opt/minc/minc-toolkit-config.sh' $ND_ENTRYPOINT
# Create new user: neuro
RUN useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro
#------------------
# Install Miniconda
#------------------
ENV CONDA_DIR=/opt/conda \
PATH=/opt/conda/bin:$PATH
RUN echo "Downloading Miniconda installer ..." \
&& miniconda_installer=/tmp/miniconda.sh \
&& curl -sSL -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& /bin/bash $miniconda_installer -b -p $CONDA_DIR \
&& rm -f $miniconda_installer \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& conda clean -tipsy && sync
#-------------------------
# Create conda environment
#-------------------------
RUN conda create -y -q --name neuro --channel vida-nyu python=3.5.1 \
numpy \
pandas \
reprozip \
traits \
&& sync && conda clean -tipsy && sync \
&& /bin/bash -c "source activate neuro \
&& pip install -q --no-cache-dir nipype" \
&& sync \
&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
#-------------------------
# Update conda environment
#-------------------------
RUN /bin/bash -c "source activate neuro \
&& pip install -q --no-cache-dir pylsl" \
&& sync
#-------------------------
# Create conda environment
#-------------------------
RUN conda create -y -q --name py27 python=2.7 \
&& sync && conda clean -tipsy && sync
USER root
#----------------
# Install MRtrix3
#----------------
RUN echo "Downloading MRtrix3 ..." \
&& curl -sSL --retry 5 https://dl.dropbox.com/s/2g008aaaeht3m45/mrtrix3-Linux-centos6.tar.gz \
| tar zx -C /opt
ENV PATH=/opt/mrtrix3/bin:$PATH
#--------------------------------------------------
# Add NeuroDebian repository
# Please note that some packages downloaded through
# NeuroDebian may have restrictive licenses.
#--------------------------------------------------
RUN apt-get update -qq && apt-get install -yq --no-install-recommends dirmngr gnupg \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& curl -sSL http://neuro.debian.net/lists/stretch.us-nh.full \
> /etc/apt/sources.list.d/neurodebian.sources.list \
&& curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg \
| apt-key add - \
&& (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true) \
&& apt-get update
# Install NeuroDebian packages
RUN apt-get update -qq && apt-get install -yq --no-install-recommends dcm2niix git-annex-standalone \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
#--------------------
# Install PETPVC 1.2.0-b
#--------------------
RUN echo "Downloading PETPVC..." \
&& mkdir /opt/petpvc \
&& curl --retry 5 -sSL https://github.com/UCL/PETPVC/releases/download/v1.2.0-b/PETPVC-1.2.0-b-Linux.tar.gz| tar zx --strip-components=1 -C /opt/petpvc
ENV PATH=/opt/petpvc/bin:$PATH
#----------------------
# Install MCR and SPM12
#----------------------
# Install MATLAB Compiler Runtime
RUN apt-get update -qq && apt-get install -yq --no-install-recommends libxext6 libxt6 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo "Downloading MATLAB Compiler Runtime ..." \
&& curl -sSL -o /tmp/mcr.zip https://www.mathworks.com/supportfiles/downloads/R2017a/deployment_files/R2017a/installers/glnxa64/MCR_R2017a_glnxa64_installer.zip \
&& unzip -q /tmp/mcr.zip -d /tmp/mcrtmp \
&& /tmp/mcrtmp/install -destinationFolder /opt/mcr -mode silent -agreeToLicense yes \
&& rm -rf /tmp/*
# Install standalone SPM
RUN echo "Downloading standalone SPM ..." \
&& curl -sSL -o spm.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2017a.zip \
&& unzip -q spm.zip -d /opt \
&& chmod -R 777 /opt/spm* \
&& rm -rf spm.zip \
&& /opt/spm12/run_spm12.sh /opt/mcr/v92/ quit \
&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12/run_spm12.sh /opt/mcr/v92/ script\"' $ND_ENTRYPOINT
ENV MATLABCMD=/opt/mcr/v92/toolbox/matlab \
FORCE_SPMMCR=1 \
LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:/opt/mcr/v92/runtime/glnxa64:/opt/mcr/v92/bin/glnxa64:/opt/mcr/v92/sys/os/glnxa64:$LD_LIBRARY_PATH
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends git \
vim \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
USER neuro
WORKDIR /home/neuro
#--------------------------------------
# Save container specifications to JSON
#--------------------------------------
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "check_urls": false, \
\n "instructions": [ \
\n [ \
\n "base", \
\n "debian:stretch" \
\n ], \
\n [ \
\n "afni", \
\n { \
\n "version": "latest" \
\n } \
\n ], \
\n [ \
\n "ants", \
\n { \
\n "version": "2.2.0" \
\n } \
\n ], \
\n [ \
\n "c3d", \
\n { \
\n "version": "1.0.0" \
\n } \
\n ], \
\n [ \
\n "dcm2niix", \
\n { \
\n "version": "latest" \
\n } \
\n ], \
\n [ \
\n "freesurfer", \
\n { \
\n "version": "6.0.0", \
\n "min": true \
\n } \
\n ], \
\n [ \
\n "fsl", \
\n { \
\n "version": "5.0.10" \
\n } \
\n ], \
\n [ \
\n "minc", \
\n { \
\n "version": "1.9.15" \
\n } \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "conda_opts": "--channel vida-nyu", \
\n "conda_install": "python=3.5.1 numpy pandas reprozip traits", \
\n "pip_install": "nipype", \
\n "activate": "true" \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "pip_install": "pylsl" \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "py27", \
\n "conda_install": "python=2.7" \
\n } \
\n ], \
\n [ \
\n "user", \
\n "root" \
\n ], \
\n [ \
\n "mrtrix3", \
\n {} \
\n ], \
\n [ \
\n "neurodebian", \
\n { \
\n "os_codename": "stretch", \
\n "download_server": "usa-nh", \
\n "pkgs": "dcm2niix git-annex-standalone" \
\n } \
\n ], \
\n [ \
\n "petpvc", \
\n { \
\n "version": "1.2.0-b" \
\n } \
\n ], \
\n [ \
\n "spm", \
\n { \
\n "version": "12", \
\n "matlab_version": "R2017a" \
\n } \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "git", \
\n "vim" \
\n ] \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "workdir", \
\n "/home/neuro" \
\n ] \
\n ], \
\n "generation_timestamp": "2017-11-07 11:35:34", \
\n "neurodocker_version": "0.3.1-20-gb8c8f73" \
\n}' > /neurodocker/neurodocker_specs.json