FROM ubuntu:18.04

MAINTAINER "Daniel Jacob" daniel.jacob@u-bordeaux.fr

ENV DEBIAN_FRONTEND=noninteractive \
    TZ=Europe/Paris
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone

# Install modules
RUN apt-get update && apt-get install -y \
    sudo ca-certificates wget curl git vim ed p7zip \
    libfreetype6-dev libmcrypt-dev libpng-dev libcurl4-gnutls-dev libcairo2-dev \
    libxt-dev libxml2-dev libv8-dev gnuplot \
    gdebi-core \
    libssl-dev openssl software-properties-common \
    libnlopt-dev && \
  # See https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04'
  #     https://rtask.thinkr.fr/fr/installation-de-r-3-5-sur-ubuntu-18-04-lts-et-astuces-pour-les-packages-de-cartographie/
    sh -c 'echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" >> /etc/apt/sources.list' && \
    apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
    add-apt-repository ppa:marutter/c2d4u3.5 && \
  # Install R / ...
    apt-get update && apt-get install -y \
    r-recommended r-base-dev r-cran-rcurl r-cran-foreach r-cran-multicore r-cran-base64enc r-cran-xml \
    r-cran-rcpp r-cran-biocmanager r-cran-base64enc r-cran-mime r-cran-inline r-cran-docopt \
    r-cran-doparallel r-cran-httpuv r-cran-xtable r-cran-rjson r-cran-jsonlite r-cran-htmltools r-cran-stringi \
    r-cran-signal r-cran-ptw r-bioc-impute r-bioc-massspecwavelet r-cran-speaq r-cran-minqa \
    r-cran-fs r-cran-rappdirs r-cran-sass r-cran-jquerylib r-cran-sourcetools r-cran-fastmap r-cran-commonmark \
    r-cran-bslib r-cran-cachem r-cran-zip r-cran-openxlsx r-cran-shiny r-cran-shinybs  r-cran-shinyjs \
  # Install Apache+PHP
    apache2 apache2-dev php libapache2-mod-php php-gd && \
  # See https://github.com/jeffreyhorner/rapache
    cd /usr/src && \
    git clone https://github.com/jeffreyhorner/rapache.git && \
    cd rapache && \
    ./configure && \
    make && make install && \
    cd /usr/src && rm -rf ./rapache && \
  # locale setting
    apt-get update && apt-get install -y locales && \
    echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && \
    locale-gen en_US.utf8 && \
    /usr/sbin/update-locale LANG=en_US.UTF-8 && \
    apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ENV LC_ALL=en_US.UTF-8 \
    LANG=en_US.UTF-8

RUN \
  # Download and install Shiny server
    wget --no-verbose http://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION -O "version.txt" && \
    VERSION=$(cat version.txt)  && \
    wget --no-verbose "http://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
    gdebi -n ss-latest.deb && \
    rm -f version.txt ss-latest.deb

ENV APACHE_RUN_USER=www-data \
    APACHE_RUN_GROUP=www-data \
    APACHE_LOG_DIR=/var/log/apache2 \
    APACHE_PID_FILE=/var/run/apache2.pid \
    APACHE_RUN_DIR=/var/run/apache2 \
    APACHE_LOCK_DIR=/var/lock/apache2 \
    APACHE_SERVERADMIN=admin@localhost \
    APACHE_SERVERNAME=localhost \
    APACHE_SERVERALIAS=docker.localhost \
    APACHE_DOCUMENTROOT=/var/www

# Metadata
LABEL base.image="nmrprocflow:latest" \
      version="1.4.04" \
      software="NMRProcFlow" \
      software.version="1.4.04" \
      description="An user-friendly tool dedicated to 1D NMR spectra processing (1H, 13C, 31P) for metabolomics" \
      website="https://nmrprocflow.org/" \
      documentation="https://nmrprocflow.org/" \
      license="http://gplv3.fsf.org/" \
      tags="metabolomics"

# Configuration
COPY ./nmrspec/conf/apache2.conf /etc/apache2/apache2.conf
COPY ./nmrspec/conf/my-site.conf /etc/apache2/sites-enabled/001-my-site.conf
COPY ./nmrspec/conf/shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY ./nmrspec/conf/launch-server.sh /usr/bin/launch-server.sh

# NMRVIEW
COPY ./nmrviewer/src /usr/src/
COPY ./nmrviewer/www /var/www/html/nv

# NMRSPEC
COPY ./nmrspec /srv/shiny-server

RUN \
  # NMRVIEW
    cd /usr/src/ && make && rm -f /usr/src/* && \
    mkdir -p /opt/data && \
    rm -f /etc/apache2/sites-enabled/000-default.conf && \
    chmod 755 /usr/bin/launch-server.sh && \
    mkdir -p /var/www/html/nv/tmp && \
    chown -R www-data.www-data /var/www/html/nv && \
    chmod 777 /var/www/html/nv/tmp && \
  # NMRSPEC
    chown -R shiny.shiny /srv/shiny-server && \
    adduser www-data shiny && \
  # Install Rnmr1D package
    cd /home && \
    echo 'library(Rcpp); Rcpp.package.skeleton(name="Rnmr1D", code_files="/srv/shiny-server/exec/libspec/Rnmr.R",  cpp_files = "/srv/shiny-server/exec/libspec/libCspec.cpp", example_code = FALSE, author="Daniel Jacob", email="djacob65@gmail.com"); ' | /usr/bin/R BATCH --vanilla && \
    cp /srv/shiny-server/exec/libspec/configure* ./Rnmr1D/ && \
    chmod 755 ./Rnmr1D/configure* && \
    cp /srv/shiny-server/exec/libspec/Makevars.in ./Rnmr1D/src && \
    echo 'install.packages("Rnmr1D", lib=c("/usr/local/lib/R/site-library/"), repos = NULL, type = "source");' | /usr/bin/R BATCH --vanilla && \
    [ -d "./Rnmr1D" ] && rm -rf ./Rnmr1D && rm -rf /srv/shiny-server/exec/libspec

# Volume as the root directory that will contain the output data
# the data will be stored within the directory /opt/data/<DATAID>
VOLUME /opt/data

WORKDIR /var/www/html

#EXPOSE 3838
EXPOSE 80

CMD ["/usr/bin/launch-server.sh"]