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Dockerfile_macapype_env_nomcr
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Dockerfile_macapype_env_nomcr
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# Generated by: Neurodocker version 0.7.0+15.ga4940e3.dirty
# Latest release: Neurodocker version 0.7.0
#
# 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
#
# Timestamp: 2020/12/02 18:33:44 UTC
FROM debian:buster
USER root
ARG DEBIAN_FRONTEND="noninteractive"
MAINTAINER David Meunier "[email protected]"
RUN apt-get update -qq
################################################## Neurodocker
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 install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip \
&& 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' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "debian:buster" \
\n ], \
\n [ \
\n "ants", \
\n { \
\n "version": "2.3.1" \
\n } \
\n ], \
\n [ \
\n "fsl", \
\n { \
\n "version": "5.0.10" \
\n } \
\n ], \
\n [ \
\n "afni", \
\n { \
\n "version": "latest" \
\n } \
\n ]\
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
################################################## Install FSL
ENV FSLDIR="/opt/fsl-5.0.10" \
PATH="/opt/fsl-5.0.10/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl-5.0.10/bin/fsltclsh" \
FSLWISH="/opt/fsl-5.0.10/bin/fslwish" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"
RUN 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 \
&& echo "Downloading FSL ..." \
&& mkdir -p /opt/fsl-5.0.10 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-5.0.10 --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' $ND_ENTRYPOINT \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-5.0.10/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.10
################################################## Install AFNI
ENV PATH="/opt/afni-latest:$PATH" \
AFNI_PLUGINPATH="/opt/afni-latest"
RUN apt-get install -y -q --no-install-recommends \
ed \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libxm4 \
multiarch-support \
netpbm \
tcsh \
xfonts-base \
xvfb
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
RUN dpkg -i /tmp/toinstall.deb
RUN rm /tmp/toinstall.deb
RUN apt-get install -f
RUN gsl2_path="$(find / -name 'libgsl.so.23' || printf '')"
RUN if [ -n "$gsl2_path" ]; then \
ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0";\
fi
RUN ldconfig
RUN echo "Downloading AFNI ..."
RUN mkdir -p /opt/afni-latest
RUN curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C /opt/afni-latest --strip-components 1
############################################# AFNI IsoSurface requires specifically libXp6
#RUN echo 'deb http://security.ubuntu.com/ubuntu precise-security main' >> /etc/apt/sources.list
#RUN apt update
#RUN apt install libxp6
RUN ls -l /usr/lib/x86_64-linux-gnu
RUN ln -s /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0 /usr/lib/x86_64-linux-gnu/libXp.so.6
################################################## Install ANTS
ENV ANTSPATH="/opt/ants-2.3.1" \
PATH="/opt/ants-2.3.1:$PATH"
RUN echo "Downloading ANTs ..." \
&& mkdir -p /opt/ants-2.3.1 \
&& curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \
| tar -xz -C /opt/ants-2.3.1 --strip-components 1
######################## NiftiReg
RUN apt-get install --yes --no-install-recommends \
ca-certificates cmake gcc g++ git make \
&& git clone https://github.com/KCL-BMEIS/niftyreg.git /tmp/niftyreg-src \
&& mkdir /tmp/niftyreg-build \
&& cd /tmp/niftyreg-build \
&& cmake -DCMAKE_INSTALL_PREFIX=/opt/niftyreg /tmp/niftyreg-src \
&& make \
&& make install
ENV PATH=/opt/niftyreg/bin:$PATH
####################### new: python 3.10
RUN apt-get install -y -q wget build-essential libncursesw5-dev libssl-dev \
libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev libffi-dev zlib1g-dev
RUN wget https://www.python.org/ftp/python/3.10.8/Python-3.10.8.tgz
RUN tar xzf Python-3.10.8.tgz
#RUN cd Python-3.10.8
#RUN echo $(pwd)
RUN Python-3.10.8/configure --enable-optimizations
#RUN Python-3.10.8/make altinstall
RUN apt-get install zlib1g-dev
RUN make altinstall
RUN echo $(which python3.10)
RUN echo $(python3.10 -V )
RUN echo ""
RUN echo $(which pip3.10)
RUN echo $(pip3.10 -V )
RUN echo $(which pip3.10)
RUN echo $(pip3.10 -V )
RUN echo $(which python3.10) && \
ln -s /usr/local/bin/python3.10 /usr/bin/python && \
ln -s /usr/local/bin/pip3.10 /usr/local/bin/pip3 && \
ln -s /usr/local/bin/pip3 /usr/local/bin/pip && \
ln -s /usr/local/bin/pip /usr/bin/pip
RUN echo $(python -m ssl)
RUN echo $(which python)
RUN echo $(python -V )
RUN echo $(which pip)
# specific problems with pillow
RUN apt-get install -y python3-pil python3-pil.imagetk
RUN python -m pip install -U pillow
#RUN pip install -U pillow
RUN python -c "import PIL; print(PIL.__version__)"
################################################## Finishing
RUN apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN rm -rf \
/tmp/hsperfdata* \
/var/*/apt/*/partial \
/var/log/apt/term*