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Dockerfile.cpu
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Dockerfile.cpu
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FROM ubuntu:focal
ENV PUBLIC=0
# Basic build setup
ENV DEBIAN_FRONTEND noninteractive
ENV CRAN_URL https://cloud.r-project.org/
ENV TZ=Europe/Warsaw
RUN chsh -s /bin/bash root && echo 'SHELL=/bin/bash' >> /etc/environment && ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && apt update && apt dist-upgrade -y && apt-get install -y pciutils libkmod-dev libgsl-dev libv8-dev mc libglu1-mesa-dev libharfbuzz-dev libfribidi-dev libgit2-dev gdebi uuid apt-transport-https screen libfontconfig1-dev build-essential libxml2-dev xorg ca-certificates cmake curl git libatlas-base-dev libcurl4-openssl-dev libjemalloc-dev liblapack-dev libopenblas-dev libopencv-dev libzmq3-dev software-properties-common sudo unzip wget && add-apt-repository -y ppa:ubuntu-toolchain-r/test && apt update && apt install -y build-essential libmagick++-dev libbz2-dev libpcre2-16-0 libpcre2-32-0 libpcre2-8-0 libpcre2-dev fort77 xorg-dev liblzma-dev libblas-dev gfortran gcc-multilib gobjc++ libreadline-dev && apt install -y pandoc texinfo texlive-fonts-extra texlive libcairo2-dev freeglut3-dev build-essential libx11-dev libxmu-dev libxi-dev libgl1-mesa-glx libglu1-mesa libglu1-mesa-dev libglfw3-dev libgles2-mesa-dev libopenblas-dev liblapack-dev libopencv-dev build-essential git gcc cmake libcairo2-dev libxml2-dev texlive-full texlive-xetex ttf-mscorefonts-installer build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev default-jre default-jdk && echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true" | debconf-set-selections
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
# Install Anaconda
ENV PATH /opt/conda/bin:$PATH
ENV SHELL /bin/bash
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
/bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda
RUN rm Miniconda3-latest-Linux-x86_64.sh &&\
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
ENV TENSORFLOW_PYTHON /opt/conda/bin/python
ENV RETICULATE_PYTHON /opt/conda/bin/python
RUN conda install -c anaconda jupyter
RUN pip install jupytext tensorflow keras numpy pandas xgboost scikit-learn tqdm pickle5
# Keras, tensorflow, jupyter
ENV OPENGL_gl_LIBRARY /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1
ENV OPENGL_glu_LIBRARY /usr/lib/x86_64-linux-gnu/libGLU.so.1
RUN apt-get update --fix-missing && \
apt-get install -y apt-utils libxml2-dev sshfs cifs-utils libffi-dev libx11-dev mesa-common-dev libfreetype6-dev libglu1-mesa-dev libssl-dev wget bzip2 ca-certificates build-essential cmake git unzip pkg-config libopenblas-dev liblapack-dev libhdf5-serial-dev libglib2.0-0 libxext6 libsm6 libxrender1 gfortran gfortran-7 gcc libglu1-mesa-dev freeglut3-dev mesa-common-dev && apt-get clean && echo "options(repos=structure(c(CRAN='http://cran.r-project.org')))" >> ~/.Rprofile
# Seperate tensorflow env
# RUN conda create -c anaconda -c conda-forge -n tensorflow tensorflow keras numpy pandas xgboost scikit-learn tqdm pickle5
# R:
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -sc)-cran40/" && apt update && apt -y dist-upgrade && apt install -y r-base-dev texlive-full texlive-xetex ttf-mscorefonts-installer r-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev default-jre default-jdk && Rscript -e "install.packages(c('remotes','devtools','BiocManager','keras','rgl','rJava'))"
# Speed up compliation in R:
# RUN mkdir $HOME/.ccache && mkdir $HOME/.R && echo -e 'CXX_STD = CXX14\n\nVER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars && echo -e 'max_size = 5.0G\nsloppiness = include_file_ctime\nhash_dir=false' > $HOME/.ccache/ccache.conf
# Setup R env
COPY vignettes/setup.R /
COPY docker/register_jupyter.R /
COPY docker/keras.R /
RUN Rscript -e "chooseCRANmirror(ind=1);" && Rscript /setup.R && echo 'root:biostat' | chpasswd
RUN Rscript /register_jupyter.R && jupyter notebook --generate-config && mkdir /OmicSelector/
# Setup keras in R env
RUN Rscript /keras.R
# Build GUI
COPY docker/jupyter_notebook_config.py /root/.jupyter/jupyter_notebook_config.py
COPY docker/logo.png /opt/conda/lib/python3.7/site-packages/notebook/static/base/images/logo.png
COPY docker/entrypoint.sh /entrypoint.sh
COPY docker/update.R /update.R
RUN chsh -s /bin/bash && echo 'export PATH="/opt/conda/bin:$PATH"' >> ~/.bashrc && apt-get install -y --reinstall build-essential apt-utils && chmod +x /entrypoint.sh && add-apt-repository -y ppa:ondrej/php && apt update && apt -y dist-upgrade && apt-get install -y nginx php7.3-fpm php7.3-common php7.3-mysql php7.3-gmp php7.3-curl php7.3-intl php7.3-mbstring php7.3-xmlrpc php7.3-gd php7.3-xml php7.3-cli php7.3-zip php7.3-soap php7.3-imap nano
COPY docker/nginx.conf /etc/nginx/nginx.conf
COPY docker/php.ini /etc/php/7.3/fpm/php.ini
COPY docker/default /etc/nginx/sites-available/default
COPY docker/www.conf /etc/php/7.3/fpm/pool.d/www.conf
# Extentions
RUN conda install -c conda-forge jupyter_contrib_nbextensions nbresuse && jupyter contrib nbextension install --sys-prefix && jupyter nbextension enable varInspector/main && jupyter nbextension install --py nbresuse --sys-prefix && jupyter nbextension enable --py nbresuse --sys-prefix && pip install -U scikit-learn xgboost
RUN pip install nbzip && jupyter serverextension enable --py nbzip --sys-prefix && jupyter nbextension install --py nbzip && jupyter nbextension enable --py nbzip
# RStudio server:
RUN apt install -y libclang-dev libssl-dev gdebi-core && wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.02.3-492-amd64.deb && gdebi -n rstudio-server-2022.02.3-492-amd64.deb && apt -f -y install && cd / && rm rstudio-server-2022.02.3-492-amd64.deb
# MXNET:
# RUN wget https://raw.githubusercontent.com/milq/milq/master/scripts/bash/install-opencv.sh && chmod +x install-opencv.sh && ./install-opencv.sh
# RUN apt-get install -y libopencv-dev && Rscript -e "install.packages('opencv')" && pip install --upgrade cmake && cd / && git clone --recursive https://github.com/apache/incubator-mxnet.git -b v1.x && cd /incubator-mxnet && mkdir build && cd build && cmake -DUSE_CUDA=ON -DUSE_MKL_IF_AVAILABLE=ON -DUSE_MKLDNN=OFF -DUSE_OPENMP=ON -DUSE_OPENCV=OFF .. && make -j $(nproc) USE_OPENCV=0 USE_BLAS=openblas && make install && cp -a . .. && cp -a . ../lib && cd /incubator-mxnet/ && make -f R-package/Makefile rpkg
# Shiny server:
RUN wget --no-verbose https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION -O "version.txt" && VERSION=$(cat version.txt) && wget --no-verbose "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && gdebi -n ss-latest.deb && rm -f version.txt ss-latest.deb
COPY docker/shiny-server.conf /etc/shiny-server/shiny-server.conf
RUN Rscript -e 'install.packages(c("shiny","rmarkdown"))' && Rscript -e 'devtools::install_github("radiant-rstats/radiant")' && echo "options(radiant.init.data = list.files(path = '/radiant-data', full.names = TRUE))" >> /root/.Rprofile
# Ensure OmicSelector is installed
RUN Rscript -e 'devtools::install_github("kstawiski/OmicSelector")'
RUN Rscript -e 'library(OmicSelector)'
# VSCODE:
RUN curl -fsSL https://code-server.dev/install.sh | sh
# Tailscale
RUN echo 'net.ipv4.ip_forward = 1' | tee -a /etc/sysctl.d/99-tailscale.conf && echo 'net.ipv6.conf.all.forwarding = 1' | tee -a /etc/sysctl.d/99-tailscale.conf && sysctl -p /etc/sysctl.d/99-tailscale.conf && curl -fsSL https://tailscale.com/install.sh | sh
# Squid
RUN apt -y install squid && rm -f /etc/squid/squid.conf && wget --no-check-certificate -O /etc/squid/squid.conf https://gist.githubusercontent.com/radenvodka/d26f13fd2f7398d31635bcf17f9330b7/raw/432fbcee54c986248168851263720852a6b11005/squid.conf && iptables -I INPUT -p tcp --dport 3128 -j ACCEPT && iptables-save
EXPOSE 8888
EXPOSE 80
EXPOSE 443
ENTRYPOINT ["/entrypoint.sh"]