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Correct bet4animal marmo (#306) + renaming default from no_mcr to env and env to _spm
1 parent f061b3a commit 1f2ceb8

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‎Dockerfile_hdbet‎

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# Generated by: Neurodocker version 0.7.0+15.ga4940e3.dirty
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# Latest release: Neurodocker version 0.7.0
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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# pull request on our GitHub repository:
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#
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# https://github.com/ReproNim/neurodocker
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#
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# Timestamp: 2020/12/02 18:33:44 UTC
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FROM macatools/macapype_env:v0.3.2
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USER root
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ARG DEBIAN_FRONTEND="noninteractive"
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MAINTAINER David Meunier "david.meunier@univ-amu.fr"
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######################## Python packages
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RUN apt-get update && apt-get install -y git libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz
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RUN python -m pip install xvfbwrapper \
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psutil \
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numpy \
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scipy \
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matplotlib \
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statsmodels \
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pandas \
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networkx\
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mock \
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prov \
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click \
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funcsigs \
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pydotplus \
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pydot \
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rdflib \
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pbr \
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nibabel \
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packaging \
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pytest
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RUN python -m pip install graphviz \
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pybids \
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nipype \
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nilearn \
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scikit-image \
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brain-slam
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RUN python -m pip install SimpleITK
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RUN python -m pip install HD-BET
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############################################# install macapype
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RUN python -m pip install --pre macapype
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RUN python -c "import macapype; print(macapype.__version__)"
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################################################## Finishing
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RUN apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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RUN rm -rf \
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/tmp/hsperfdata* \
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/var/*/apt/*/partial \
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/var/log/apt/term*

‎Dockerfile_macapype_env‎

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#
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# Timestamp: 2020/12/02 18:33:44 UTC
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FROM macatools/macapype_env:v0.3.2
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FROM debian:buster
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USER root
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RUN apt-get update -qq
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################################################## Install SPM12 as MCR
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RUN apt-get -y install unzip xorg wget
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# Install MATLAB MCR in /opt/mcr/
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ENV MATLAB_VERSION R2019b
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ENV MCR_VERSION v97
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RUN mkdir /opt/mcr_install \
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&& mkdir /opt/mcr \
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&& wget --progress=bar:force -P /opt/mcr_install https://ssd.mathworks.com/supportfiles/downloads/${MATLAB_VERSION}/Release/3/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_${MATLAB_VERSION}_Update_3_glnxa64.zip \
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&& unzip -q /opt/mcr_install/MATLAB_Runtime_${MATLAB_VERSION}_Update_3_glnxa64.zip -d /opt/mcr_install \
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&& /opt/mcr_install/install -destinationFolder /opt/mcr -agreeToLicense yes -mode silent \
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&& rm -rf /opt/mcr_install /tmp/*
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# Install SPM Standalone in /opt/spm12/
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ENV SPM_VERSION 12
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ENV SPM_REVISION r7771
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ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mcr/${MCR_VERSION}/runtime/glnxa64:/opt/mcr/${MCR_VERSION}/bin/glnxa64:/opt/mcr/${MCR_VERSION}/sys/os/glnxa64:/opt/mcr/${MCR_VERSION}/sys/opengl/lib/glnxa64:/opt/mcr/${MCR_VERSION}/extern/bin/glnxa64
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ENV MCR_INHIBIT_CTF_LOCK 1
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ENV SPM_HTML_BROWSER 0
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# Running SPM once with "function exit" tests the succesfull installation *and*
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# extracts the ctf archive which is necessary if singularity is going to be
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# used later on, because singularity containers are read-only.
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# Also, set +x on the entrypoint for non-root container invocations
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RUN wget --no-check-certificate --progress=bar:force -P /opt https://www.fil.ion.ucl.ac.uk/spm/download/restricted/bids/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip \
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&& unzip -q /opt/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip -d /opt \
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&& rm -f /opt/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip \
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&& /opt/spm${SPM_VERSION}/spm${SPM_VERSION} function exit \
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&& chmod +x /opt/spm${SPM_VERSION}/spm${SPM_VERSION}
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ENV SPM_DIR /opt/spm${SPM_VERSION}
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################################################## Neurodocker
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ENV LANG="en_US.UTF-8" \
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LC_ALL="en_US.UTF-8" \
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ND_ENTRYPOINT="/neurodocker/startup.sh"
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RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
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&& apt-get install -y -q --no-install-recommends \
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apt-utils \
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bzip2 \
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ca-certificates \
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curl \
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locales \
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unzip \
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&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
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&& dpkg-reconfigure --frontend=noninteractive locales \
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&& update-locale LANG="en_US.UTF-8" \
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&& chmod 777 /opt && chmod a+s /opt \
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&& mkdir -p /neurodocker \
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&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
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echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
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&& echo 'set -e' >> "$ND_ENTRYPOINT" \
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&& echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
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&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
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fi \
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&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
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ENTRYPOINT ["/neurodocker/startup.sh"]
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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:buster" \
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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": "2.4.3" \
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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": "6.0.7.17" \
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\n } \
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\n ], \
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\n [ \
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\n "afni", \
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\n { \
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\n "version": "latest" \
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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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################################################## Install AFNI
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ENV PATH="/opt/afni-latest:$PATH" \
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AFNI_PLUGINPATH="/opt/afni-latest"
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RUN apt-get install -y -q --no-install-recommends \
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ed \
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gsl-bin \
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libglib2.0-0 \
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libglu1-mesa-dev \
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libglw1-mesa \
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libgomp1 \
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libjpeg62 \
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libxm4 \
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multiarch-support \
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netpbm \
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tcsh \
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xfonts-base \
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xvfb
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RUN 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
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RUN dpkg -i /tmp/toinstall.deb
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RUN rm /tmp/toinstall.deb
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RUN apt-get install -f
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RUN gsl2_path="$(find / -name 'libgsl.so.23' || printf '')"
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RUN if [ -n "$gsl2_path" ]; then \
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ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0";\
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fi
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RUN ldconfig
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RUN echo "Downloading AFNI ..."
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RUN mkdir -p /opt/afni-latest
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RUN curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
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| tar -xz -C /opt/afni-latest --strip-components 1
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############################################# AFNI IsoSurface requires specifically libXp6
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#RUN echo 'deb http://security.ubuntu.com/ubuntu precise-security main' >> /etc/apt/sources.list
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#RUN apt update
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#RUN apt install libxp6
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RUN ls -l /usr/lib/x86_64-linux-gnu
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RUN ln -s /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0 /usr/lib/x86_64-linux-gnu/libXp.so.6
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################################################## Install ANTS
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ENV ANTSPATH="/opt/ants-2.4.3/" \
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PATH="/opt/ants-2.4.3:$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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ca-certificates \
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curl \
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unzip \
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&& rm -rf /var/lib/apt/lists/* \
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&& echo "Downloading ANTs ..." \
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&& curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.4.3/ants-2.4.3-centos7-X64-gcc.zip \
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&& unzip ants.zip -d /opt \
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&& mv /opt/ants-2.4.3/bin/* /opt/ants-2.4.3 \
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&& rm ants.zip
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######################## NiftiReg
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RUN apt-get update -qq
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RUN apt-get install --yes --no-install-recommends \
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ca-certificates cmake gcc g++ git make
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RUN git clone https://github.com/KCL-BMEIS/niftyreg.git /tmp/niftyreg-src \
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&& mkdir /tmp/niftyreg-build \
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&& cd /tmp/niftyreg-build \
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&& cmake -DCMAKE_INSTALL_PREFIX=/opt/niftyreg /tmp/niftyreg-src \
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&& make \
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&& make install
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ENV PATH=/opt/niftyreg/bin:$PATH
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####################### new: python 3.10
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RUN apt-get install -y -q wget build-essential libncursesw5-dev libssl-dev \
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libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev libffi-dev zlib1g-dev
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RUN wget https://www.python.org/ftp/python/3.10.8/Python-3.10.8.tgz
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RUN tar xzf Python-3.10.8.tgz
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#RUN cd Python-3.10.8
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#RUN echo $(pwd)
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RUN Python-3.10.8/configure --enable-optimizations
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#RUN Python-3.10.8/make altinstall
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RUN apt-get install zlib1g-dev
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RUN make altinstall
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RUN echo $(which python3.10)
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RUN echo $(python3.10 -V )
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RUN echo ""
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RUN echo $(which pip3.10)
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RUN echo $(pip3.10 -V )
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RUN echo $(which pip3.10)
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RUN echo $(pip3.10 -V )
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RUN echo $(which python3.10) && \
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ln -s /usr/local/bin/python3.10 /usr/bin/python && \
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ln -s /usr/local/bin/pip3.10 /usr/local/bin/pip3 && \
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ln -s /usr/local/bin/pip3 /usr/local/bin/pip && \
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ln -s /usr/local/bin/pip /usr/bin/pip
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RUN echo $(python -m ssl)
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RUN echo $(which python)
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RUN echo $(python -V )
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RUN echo $(which pip)
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# specific problems with pillow
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RUN apt-get install -y python3-pil python3-pil.imagetk
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RUN python -m pip install -U pillow
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#RUN pip install -U pillow
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RUN python -c "import PIL; print(PIL.__version__)"
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################################################## Install FSL
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ENV FSLDIR "/usr/local/fsl"
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ENV DEBIAN_FRONTEND "noninteractive"
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ENV LANG "en_GB.UTF-8"
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RUN apt update -y && \
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apt upgrade -y && \
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apt install -y \
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wget \
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file \
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bc \
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dc \
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mesa-utils \
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pulseaudio \
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libquadmath0 \
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libgtk2.0-0 \
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libgomp1
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RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
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RUN python -m pip install readline
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RUN python ./fslinstaller.py -d /usr/local/fsl/
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ENV PATH="${PATH}:${FSLDIR}/bin"\
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FSLOUTPUTTYPE="NIFTI_GZ" \
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FSLMULTIFILEQUIT="TRUE" \
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FSLTCLSH="${FSLDIR}/bin/fsltclsh" \
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FSLWISH="${FSLDIR}/bin/fslwish" \
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FSLLOCKDIR="" \
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FSLMACHINELIST="" \
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FSLREMOTECALL="" \
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FSLGECUDAQ="cuda.q"
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################################################## Finishing
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RUN apt-get clean \

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