Dockerfile_shiny

FROM library/debian:buster


ENV SHINY_VERSION=1.5.16.958
ENV R_VERSION=4.0.3
ENV PANDOC_TEMPLATES_VERSION=2.11.3
ENV S6_VERSION=2.1.0.2
ENV S6_BEHAVIOUR_IF_STAGE2_FAILS=2


## Set locales to en_US
RUN apt-get update \
  && apt-get install -y --no-install-recommends locales \
  && sed -i '/^#.* en_US.* /s/^#//' /etc/locale.gen \
  && sed -i '/^#.* en_GB.* /s/^#//' /etc/locale.gen \
  && locale-gen en_GB.UTF-8 \
  && locale-gen en_US.UTF-8 \
  && /usr/sbin/update-locale LANG="en_US.UTF-8" \
  && /usr/sbin/update-locale LANGUAGE="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_CTYPE="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_NUMERIC="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_TIME="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_COLLATE="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_MONETARY="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_MESSAGES="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_PAPER="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_NAME="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_ADDRESS="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_TELEPHONE="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_MEASUREMENT="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_IDENTIFICATION="en_US.UTF-8" \
  && /usr/sbin/update-locale LC_ALL="en_US.UTF-8"


## Set environment variable for path and locales
ENV LC_ALL=en_US.UTF-8
ENV LANGUAGE=en_US.UTF-8
ENV LANG=en_US.UTF-8
ENV LC_COLLATE=en_US.UTF-8


## Install libraries
RUN apt-get update \
  && apt-get install -y --no-install-recommends dialog apt-utils \
  && apt-get install -y --no-install-recommends \
    autoconf \ 
    automake \ 
    bash-completion \ 
    build-essential \ 
    ca-certificates \ 
    cargo \ 
    curl \ 
    default-jdk \ 
    fastqtl \ 
    ffmpeg \ 
    file \ 
    fonts-texgyre \ 
    g++ \ 
    gdebi \
    gfortran \ 
    git \ 
    gsfonts \ 
    htop \ 
    libapparmor1 \ 
    libavfilter-dev \ 
    libblas-dev \ 
    libbz2-1.0 \ 
    libbz2-dev \ 
    libcairo2-dev \ 
    libclang-dev \ 
    libcurl4-openssl-dev \ 
    libedit2 \ 
    libgc1c2 \ 
    libgdal-dev \ 
    libgit2-dev \
    libgsl-dev \ 
    libicu-dev \ 
    libio-socket-ssl-perl \ 
    libjpeg-dev \ 
    libjpeg62-turbo \ 
    libleptonica-dev \
    liblzma-dev \ 
    liblzma5 \ 
    libmagick++-dev \ 
    libmpfr-dev \
    libobjc4 \ 
    libopenblas-dev \ 
    libopenmpi-dev \ 
    libpango1.0-dev \ 
    libpangocairo-1.0-0 \ 
    libpcre2-dev \
    libpcre3 \ 
    libpcre3-dev \ 
    libpng-dev \ 
    libpng16-16 \ 
    libpoppler-cpp-dev \
    libreadline-dev \ 
    libreadline7 \ 
    librsvg2-dev \ 
    libsasl2-dev \ 
    libsodium-dev \
    libssl-dev \ 
    libssh2-1-dev \
    libtesseract-dev \ 
    libtiff5 \ 
    libtiff5-dev \ 
    libudunits2-dev \ 
    libv8-dev \ 
    libx11-dev \ 
    libxml2-dev \ 
    libxt-dev \ 
    lmodern \ 
    lsb-release \ 
    make \ 
    man-db \ 
    multiarch-support \ 
    nano \
    openssh-client \ 
    pandoc \ 
    pandoc-citeproc \ 
    perl \ 
    plink \ 
    plink1.9 \ 
    procps \ 
    psmisc \ 
    python-setuptools \ 
    qpdf \ 
    sudo \ 
    tar \ 
    tcl8.6-dev \ 
    tesseract-ocr-eng \ 
    texinfo \ 
    tk8.6-dev \ 
    unzip \ 
    vcftools \ 
    wget \ 
    x11proto-core-dev \ 
    xauth \ 
    xclip \ 
    xfonts-base \ 
    xtail \
    xvfb \ 
    zip \ 
    zlib1g \ 
    zlib1g-dev \
  && apt-get autoremove -y \
  && apt-get autoclean -y \
  && apt-get clean -y \
  && rm -rf /var/lib/apt/lists/ \
  && rm -rf /tmp/*


## Configure git
RUN git config --system core.sharedRepository 0775 \
  && git config --system credential.helper "cache --timeout=3600" \
  && git config --system push.default simple \
  && git config --system core.editor "nano -w" \
  && git config --system color.ui auto 


## Install libraries for databases
# https://dev.mysql.com/downloads/connector/odbc/
# https://dev.mysql.com/get/Downloads/Connector-ODBC/8.0/mysql-connector-odbc-setup_8.0.22-1debian10_amd64.deb
RUN apt-get update \
  && apt-get install -y tdsodbc odbc-postgresql libsqliteodbc unixodbc unixodbc-dev \
  && wget -q -P /tmp/ https://dev.mysql.com/get/Downloads/Connector-ODBC/8.0/mysql-connector-odbc-8.0.19-linux-debian10-x86-64bit.tar.gz \
  && tar -C /tmp/ -xvf /tmp/mysql-connector-odbc-8.0.19-linux-debian10-x86-64bit.tar.gz \
  && cp /tmp/mysql-connector-odbc-8.0.19-linux-debian10-x86-64bit/bin/* /usr/local/bin \
  && cp /tmp/mysql-connector-odbc-8.0.19-linux-debian10-x86-64bit/lib/* /usr/local/lib \
  && myodbc-installer -a -d -n "MySQL ODBC 8.0 Driver" -t "Driver=/usr/local/lib/libmyodbc8w.so" \
  && rm -rf /tmp/*
  

## Install R
RUN wget -q -P /tmp/ https://cran.r-project.org/src/base/R-4/R-${R_VERSION}.tar.gz \
  ## Extract source code
  && tar -C /tmp/ -zxvf /tmp/R-${R_VERSION}.tar.gz \
  && cd /tmp/R-${R_VERSION} \
  ## Set compiler flags
  && R_PAPERSIZE=a4 \
    R_BATCHSAVE="--no-save --no-restore" \
    R_BROWSER=xdg-open \
    PAGER=/usr/bin/pager \
    PERL=/usr/bin/perl \
    R_UNZIPCMD=/usr/bin/unzip \
    R_ZIPCMD=/usr/bin/zip \
    R_PRINTCMD=/usr/bin/lpr \
    LIBnn=lib \
    AWK=/usr/bin/awk \
    CFLAGS="-g -O2 -Wall -pedantic -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" \
    CXXFLAGS="-g -O2 -Wall -pedantic -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" \
    CXX98FLAGS="-g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2" \
    CXX11FLAGS="-g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2" \
    CXX14FLAGS="-g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2" \
  ## Configure options
  ./configure --enable-R-shlib \
              --enable-memory-profiling \
              --with-readline \
              --with-blas \
              --with-tcltk \
              --disable-nls \
              --with-recommended-packages \
  ## Build and install
  && make \
  && make install \
  ## Add a default CRAN mirror
  && echo "options(repos = c(CRAN='https://cloud.r-project.org/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
  # && MRAN=https://mran.microsoft.com/snapshot/$(date +'%Y-%m-%d') \
  # && echo MRAN=$MRAN >> /etc/environment \
  # && export MRAN=$MRAN \
  # && echo "options(repos = c(CRAN='$MRAN'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
  ## Add a library directory (for user-installed packages)
  && mkdir -p /usr/local/lib/R/site-library \
  && chown root:staff /usr/local/lib/R/site-library \
  && chmod g+wx /usr/local/lib/R/site-library \
  ## Fix library path
  && echo "R_LIBS_USER=~/R/library \
    \nTZ='Etc/UTC' \
    \nR_MAX_NUM_DLLS=300 \
    \nRENV_PATHS_CACHE=/renv_cache \
    " >> /usr/local/lib/R/etc/Renviron \
  && echo "R_LIBS=\${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library'}" >> /usr/local/lib/R/etc/Renviron \
  && rm -rf /tmp/*


## Instal Shiny server
RUN Rscript -e 'remotes::install_cran(c("shiny", "renv"), upgrade = "never", dependencies = TRUE)'
RUN wget --no-verbose "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$SHINY_VERSION-amd64.deb" -O ss-latest.deb \
  && gdebi -n ss-latest.deb \
  && rm -f version.txt ss-latest.deb \
  && . /etc/environment \
  && cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/ \
  && usermod -g staff shiny \
  && usermod -a -G shiny shiny \
  && chown shiny:staff /var/lib/shiny-server \
  && echo '### set locales \
    \nexport LANG="en_US.UTF-8" \
    \nexport LANGUAGE="en_US.UTF-8" \
    \nexport LC_CTYPE="en_US.UTF-8" \
    \nexport LC_NUMERIC="en_US.UTF-8" \
    \nexport LC_TIME="en_US.UTF-8" \
    \nexport LC_COLLATE="en_US.UTF-8" \
    \nexport LC_MONETARY="en_US.UTF-8" \
    \nexport LC_MESSAGES="en_US.UTF-8" \
    \nexport LC_PAPER="en_US.UTF-8" \
    \nexport LC_NAME="en_US.UTF-8" \
    \nexport LC_ADDRESS="en_US.UTF-8" \
    \nexport LC_TELEPHONE="en_US.UTF-8" \
    \nexport LC_MEASUREMENT="en_US.UTF-8" \
    \nexport LC_IDENTIFICATION="en_US.UTF-8" \
    \nexport LC_ALL="en_US.UTF-8"' > /home/shiny/.bashrc \
  && mkdir -p /var/log/shiny-server \
  && chown shiny:staff /var/log/shiny-server
  
  
## Clean up install
RUN apt-get autoremove -y \
  && apt-get autoclean -y \
  && apt-get clean -y \
  && rm -rf /var/lib/apt/lists/ \
  && rm -rf /tmp/*
  

EXPOSE 3838


RUN echo 'echo "shiny server is starting" \
  \nif [ "$APPLICATION_LOGS_TO_STDOUT" != "false" ] \
  \nthen \
  \n    # push the "real" application logs to stdout with xtail in detached mode \
  \n    exec xtail /var/log/shiny-server/ & \
  \nfi \
  \nexec shiny-server 2>&1"' > /boot.sh && chmod 755 boot.sh


CMD ["/boot.sh"]