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ARG CUDA_VERSION=11.6.1-runtime-ubuntu20.04
FROM nvcr.io/nvidia/cuda:${CUDA_VERSION}
WORKDIR /workspace
ARG DEBIAN_FRONTEND="noninteractive"
ARG mne_v=v0.23.0
ARG MNE_USER="mne_user"
ARG HOME_DIR="/home/${MNE_USER}"
ENV MNE_USER=${MNE_USER}
ENV HOME_DIR=${HOME_DIR}
RUN chmod 777 -R /opt
VOLUME /var/mne_test
ENV FSLDIR="/opt/fsl-6.0.5.1" \
PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl-6.0.5.1/bin/fsltclsh" \
FSLWISH="/opt/fsl-6.0.5.1/bin/fslwish" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"
RUN export DEBIAN_FRONTEND=noninteractive && apt-get update && \
apt-get install --no-install-recommends --yes \
wget \
unzip \
ca-certificates \
software-properties-common && \
apt-get clean && apt-get autoremove
RUN apt-key del 7fa2af80 && \
apt-get install -y wget && \
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb && \
dpkg -i cuda-keyring_1.0-1_all.deb
RUN sed -i '/developer\.download\.nvidia\.com\/compute\/cuda\/repos/d' /etc/apt/sources.list && \
rm /etc/apt/sources.list.d/cuda.list
RUN add-apt-repository ppa:deadsnakes/ppa
RUN apt install -y python3.9
RUN apt install -y python3.9-distutils
RUN apt install -y python3.10
RUN apt install -y python3.10-distutils
RUN add-apt-repository -y ppa:ubuntu-toolchain-r/test
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
libopenblas-dev \
bzip2 \
ca-certificates \
cmake \
curl \
dcm2niix \
locales \
unzip \
bc \
dc \
file \
git \
subversion \
cmake \
build-essential \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
libglu1-mesa-dev \
libglu1-mesa \
libgomp1 \
libice6 \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
tcsh \
nano \
vim \
libfontconfig \
libfreetype6:amd64 \
libx11-dev \
libxxf86vm-dev \
libxcursor-dev \
libxrandr-dev \
libxinerama-dev \
libegl-dev \
libwayland-dev \
wayland-protocols \
libxkbcommon-dev \
libdbus-1-dev \
linux-libc-dev \
libxi-dev \
libxmu-dev \
libxext6 \
libxcb-randr0-dev \
libxcb-xtest0-dev \
libxcb-xinerama0-dev \
libxcb-shape0-dev \
libxcb-xkb-dev \
libqt5gui5 \
libxss1 \
libxft2 \
python-tk \
libvtk6-dev \
libjpeg62 \
libffi-dev \
sudo \
wget \
xvfb \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN 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
RUN echo "Downloading FSL ..." \
&& mkdir -p /opt/fsl-6.0.5.1 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-6.0.5.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.5.1
RUN wget https://bootstrap.pypa.io/get-pip.py
RUN python3.9 get-pip.py
RUN python3.10 get-pip.py
RUN pip3.9 install --no-cache-dir -U install setuptools
RUN pip3.9 install cytoolz && \
pip3.9 install dask && \
pip3.9 install lz4 && \
pip3.9 install pandas && \
pip3.9 install tini && \
pip3.9 install numpy && \
pip3.9 install scipy && \
pip3.9 install matplotlib && \
pip3.9 install numba && \
pip3.9 install xlrd && \
pip3.9 install scikit-learn && \
pip3.9 install h5py && \
pip3.9 install pillow && \
pip3.9 install statsmodels && \
pip3.9 install jupyter && \
pip3.9 install joblib && \
pip3.9 install psutil && \
pip3.9 install numexpr && \
pip3.9 install imageio && \
pip3.9 install tqdm && \
pip3.9 install spyder-kernels && \
pip3.9 install imageio-ffmpeg && \
pip3.9 install vtk && \
pip3.9 install pyvista && \
pip3.9 install pyvistaqt && \
pip3.9 install qdarkstyle && \
pip3.9 install pyqt5 && \
pip3.9 install darkdetect && \
pip3.9 install mayavi && \
pip3.9 install PySurfer && \
pip3.9 install dipy && \
pip3.9 install nibabel && \
pip3.9 install nilearn && \
pip3.9 install python-picard && \
pip3.9 install mne && \
pip3.9 install mffpy && \
pip3.9 install ipywidgets && \
pip3.9 install s3fs && \
pip3.9 install bokeh && \
pip3.9 install ipyvtklink && \
pip3.9 install nipype && \
pip3.9 install scikit-image && \
pip3.9 install fslpy
RUN pip3.10 install --no-cache-dir -U install setuptools
RUN pip3.10 install cytoolz && \
pip3.10 install dask && \
pip3.10 install lz4 && \
pip3.10 install pandas && \
pip3.10 install tini && \
pip3.10 install numpy && \
pip3.10 install scipy && \
pip3.10 install matplotlib && \
pip3.10 install numba && \
pip3.10 install xlrd && \
pip3.10 install scikit-learn && \
pip3.10 install h5py && \
pip3.10 install pillow && \
pip3.10 install statsmodels && \
pip3.10 install jupyter && \
pip3.10 install joblib && \
pip3.10 install psutil && \
pip3.10 install numexpr && \
pip3.10 install imageio && \
pip3.10 install tqdm && \
pip3.10 install spyder-kernels && \
pip3.10 install imageio-ffmpeg && \
pip3.10 install pyvista && \
pip3.10 install pyvistaqt && \
pip3.10 install qdarkstyle && \
pip3.10 install darkdetect && \
pip3.10 install dipy && \
pip3.10 install nibabel && \
pip3.10 install nilearn && \
pip3.10 install python-picard && \
pip3.10 install mffpy && \
pip3.10 install ipywidgets && \
pip3.10 install s3fs && \
pip3.10 install bokeh && \
pip3.10 install ipyvtklink && \
pip3.10 install nipype && \
pip3.10 install scikit-image && \
pip3.10 install bpy
ENV NVIDIA_DISABLE_REQUIRE=1