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josephmjejosephmje
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add Salim's updated Dockerfile
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‎Dockerfile

Lines changed: 158 additions & 127 deletions
Original file line numberDiff line numberDiff line change
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# Use Ubuntu 16.04 LTS
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FROM ubuntu:xenial-20190610
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FROM ubuntu:xenial-20161213
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# Prepare environment
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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curl \
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bzip2 \
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ca-certificates \
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xvfb \
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cython3 \
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build-essential \
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autoconf \
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libtool \
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pkg-config \
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git && \
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curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
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apt-get install -y --no-install-recommends \
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nodejs && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Used command:
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# neurodocker generate docker --base=debian:stretch --pkg-manager=apt
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# --ants version=latest method=source --mrtrix3 version=3.0_RC3
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# --freesurfer version=6.0.0 method=binaries --fsl version=6.0.1 method=binaries
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# Getting required installation tools
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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apt-utils \
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locales \
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unzip \
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bc \
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libtool \
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tar \
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dpkg \
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curl \
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wget \
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unzip \
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gcc \
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git \
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libstdc++6
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# Neurodocker Setup
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ARG DEBIAN_FRONTEND="noninteractive"
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ENV LANG="en_US.UTF-8" \
@@ -64,55 +49,73 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
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ENTRYPOINT ["/neurodocker/startup.sh"]
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# Installing ANTS v2.3.1
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ENV ANTSPATH=/opt/ants
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RUN mkdir -p $ANTSPATH && \
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curl -sSL https://github.com/ANTsX/ANTs/archive/v2.3.1.tar.gz
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| tar -xzC $ANTSPATH --strip-components 1
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ENV PATH=$ANTSPATH:$PATH
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# Installing MRtrix3
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ENV PATH="/opt/mrtrix3-3.0_RC3/bin:$PATH"
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RUN echo "Downloading MRtrix3 ..." \
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&& mkdir -p /opt/mrtrix3-3.0_RC3 \
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&& curl -fsSL --retry 5 https://dl.dropbox.com/s/2oh339ehcxcf8xf/mrtrix3-3.0_RC3-Linux-centos6.9-x86_64.tar.gz \
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| tar -xz -C /opt/mrtrix3-3.0_RC3 --strip-components 1
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# Installing Freesurfer
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ENV FREESURFER_HOME="/opt/freesurfer-6.0.0" \
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PATH="/opt/freesurfer-6.0.0/bin:$PATH"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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bc \
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libgomp1 \
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libxmu6 \
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libxt6 \
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perl \
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tcsh \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& echo "Downloading FreeSurfer ..." \
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&& mkdir -p /opt/freesurfer-6.0.0 \
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&& curl -fsSL --retry 5 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz \
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| tar -xz -C /opt/freesurfer-6.0.0 --strip-components 1 \
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--exclude='freesurfer/average/mult-comp-cor' \
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--exclude='freesurfer/lib/cuda' \
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--exclude='freesurfer/lib/qt' \
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--exclude='freesurfer/subjects/V1_average' \
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--exclude='freesurfer/subjects/bert' \
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--exclude='freesurfer/subjects/cvs_avg35' \
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--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
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--exclude='freesurfer/subjects/fsaverage3' \
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--exclude='freesurfer/subjects/fsaverage4' \
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--exclude='freesurfer/subjects/fsaverage5' \
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--exclude='freesurfer/subjects/fsaverage6' \
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--exclude='freesurfer/subjects/fsaverage_sym' \
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--exclude='freesurfer/trctrain' \
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&& sed -i '$isource "/opt/freesurfer-6.0.0/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"
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# Installing FSL
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# SETUP taken from fmriprep:latest, installs C compiler for ANTS
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# Prepare environment
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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curl \
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bzip2 \
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ca-certificates \
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xvfb \
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cython3 \
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build-essential \
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autoconf \
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libtool \
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pkg-config \
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git && \
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curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
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apt-get install -y --no-install-recommends \
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nodejs && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Install latest pandoc
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RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb" && \
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dpkg -i pandoc-2.2.2.1-1-amd64.deb && \
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rm pandoc-2.2.2.1-1-amd64.deb
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# ANTS
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# from https://github.com/kaczmarj/ANTs-builds/blob/master/Dockerfile
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# Get CMake for ANTS
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RUN mkdir /cmake_temp
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WORKDIR /cmake_temp
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RUN wget https://cmake.org/files/v3.12/cmake-3.12.2.tar.gz \
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&& tar -xzvf cmake-3.12.2.tar.gz \
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&& echo 'done tar' \
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&& ls \
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&& cd cmake-3.12.2/ \
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&& ./bootstrap -- -DCMAKE_BUILD_TYPE:STRING=Release \
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&& make -j4 \
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&& make install \
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&& cd .. \
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&& rm -rf *
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RUN cmake --version
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RUN mkdir /ants
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RUN apt-get update && apt-get -y install zlib1g-dev
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RUN git clone https://github.com/ANTsX/ANTs.git --branch v2.3.1 /ants
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WORKDIR /ants
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RUN mkdir build \
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&& cd build \
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&& git config --global url."https://".insteadOf git:// \
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&& cmake .. \
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&& make -j1 \
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&& mkdir -p /opt/ants \
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&& mv bin/* /opt/ants && mv ../Scripts/* /opt/ants \
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&& cd .. \
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&& rm -rf build
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ENV ANTSPATH=/opt/ants/ \
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PATH=/opt/ants:$PATH
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WORKDIR /
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ENV FSLDIR="/opt/fsl-6.0.1" \
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PATH="/opt/fsl-6.0.1/bin:$PATH"
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PATH="/opt/fsl-6.0.1/bin:$PATH" \
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FSLOUTPUTTYPE="NIFTI_GZ"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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bc \
@@ -130,61 +133,58 @@ RUN apt-get update -qq \
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libxrandr2 \
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libxrender1 \
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libxt6 \
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python \
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wget \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& echo "Downloading FSL ..." \
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&& mkdir -p /opt/fsl-6.0.1 \
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&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-centos6_64.tar.gz \
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| tar -xz -C /opt/fsl-6.0.1 --strip-components 1 \
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&& sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
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&& sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
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&& sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
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&& sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT
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&& wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py \
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&& chmod 775 fslinstaller.py
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RUN /fslinstaller.py -d /opt/fsl-6.0.1 -V 6.0.1 -q
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RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
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RUN apt-get install -y nodejs
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RUN npm install -g svgo
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# FSL 6.0.1
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# Freesurfer 6.0.0
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# MRtrix3
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# ANTS
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# Python 3
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# Installing bids-validator
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RUN npm install -g [email protected]
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# MRtrix3
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# from https://hub.docker.com/r/neurology/mrtrix/dockerfile
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RUN apt-get update
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RUN apt-get install -y --no-install-recommends \
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python \
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python-numpy \
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libeigen3-dev \
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clang \
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zlib1g-dev \
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libqt4-opengl-dev \
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libgl1-mesa-dev \
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git \
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ca-certificates
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RUN mkdir /mrtrix
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RUN git clone https://github.com/MRtrix3/mrtrix3.git --branch 3.0_RC3 /mrtrix
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WORKDIR /mrtrix
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# Checkout version used in the lab: 20180128
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RUN git checkout f098f097ccbb3e5efbb8f5552f13e0997d161cce
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ENV CXX=/usr/bin/clang++
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RUN ./configure
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RUN ./build
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RUN ./set_path
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ENV PATH=/mrtrix/bin:$PATH
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WORKDIR /
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RUN echo '{ \
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\n "pkg_manager": "apt", \
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\n "instructions": [ \
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\n [ \
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\n "base", \
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\n "debian:stretch" \
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\n ], \
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\n [ \
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\n "ants", \
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\n { \
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\n "version": "latest", \
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\n "method": "source" \
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\n } \
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\n ], \
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\n [ \
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\n "mrtrix3", \
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\n { \
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\n "version": "3.0_RC3" \
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\n } \
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\n ], \
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\n [ \
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\n "freesurfer", \
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\n { \
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\n "version": "6.0.0", \
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\n "method": "binaries" \
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\n } \
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\n ], \
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\n [ \
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\n "fsl", \
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\n { \
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\n "version": "6.0.1", \
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\n "method": "binaries" \
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\n } \
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\n ] \
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\n ] \
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\n}' > /neurodocker/neurodocker_specs.json
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# Installing and setting up miniconda
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RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
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bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda3-4.5.11-Linux-x86_64.sh
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# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
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ENV PATH="/usr/local/miniconda/bin:$PATH" \
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CPATH="/usr/local/miniconda/include/:$CPATH" \
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LANG="C.UTF-8" \
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LC_ALL="C.UTF-8" \
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PYTHONNOUSERSITE=1
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# add credentials on build
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RUN mkdir ~/.ssh && ln -s /run/secrets/host_ssh_key ~/.ssh/id_rsa
@@ -193,12 +193,43 @@ RUN apt-get update && \
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apt-get install -y --no-install-recommends \
194194
libopenblas-base
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# setting up an install of dmriprep (manual version) inside the container
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ADD https://api.github.com/repos/TIGRLab/dmriprep/git/refs/heads/master version.json
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RUN git clone -b master https://github.com/TIGRLab/dmriprep.git
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#RUN mkdir dmriprep
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#COPY ./ dmriprep/
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RUN cd dmriprep && ls && python setup.py install && pip list
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RUN pip install pybids==0.9.1 && pip list
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# Precaching atlases
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ENV TEMPLATEFLOW_HOME="/opt/templateflow"
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RUN mkdir -p $TEMPLATEFLOW_HOME
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RUN pip install --no-cache-dir "templateflow>=0.3.0,<0.4.0a0" && \
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python -c "from templateflow import api as tfapi; \
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tfapi.get('MNI152NLin6Asym', atlas=None); \
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tfapi.get('MNI152NLin2009cAsym', atlas=None); \
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tfapi.get('OASIS30ANTs');" && \
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find $TEMPLATEFLOW_HOME -type d -exec chmod go=u {} + && \
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find $TEMPLATEFLOW_HOME -type f -exec chmod go=u {} +
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RUN conda install -y python=3.7.3 \
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pip=19.1 \
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libxml2=2.9.8 \
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libxslt=1.1.32 \
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graphviz=2.40.1; sync && \
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chmod -R a+rX /usr/local/miniconda; sync && \
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chmod +x /usr/local/miniconda/bin/*; sync && \
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conda build purge-all; sync && \
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conda clean -tipsy && sync
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# Setting up an install of dmripreproc (manual version) inside the container
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#ADD https://api.github.com/repos/TIGRLab/dmripreproc/git/refs/heads/master version.json
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#RUN git clone -b master https://github.com/TIGRLab/dmripreproc.git dmripreproc
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RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
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RUN apt-get install -y nodejs
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RUN npm install -g svgo
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# Installing bids-validator
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RUN npm install -g [email protected]
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RUN pip install --upgrade pip
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RUN mkdir dmriprep
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COPY ./ dmriprep/
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RUN cd dmriprep && python setup.py install
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ENTRYPOINT ["dmriprep"]

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