# call parent container
#FROM r4.0.0
FROM debian:testing

# set author
MAINTAINER Lain Pavot <lain.pavot@inra.fr>

# set encoding
ENV LANG en_US.UTF-8

## we copy the installer and run it before copying the entier project to prevent
## reinstalling everything each time the project has changed

COPY ./XSeeker/install.R /tmp/

RUN mkdir -p /XSeeker/input/ /var/log/
VOLUME ["/XSeeker/input/"]

EXPOSE 8765
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV R_BASE_VERSION 4.0.3

RUN \
  apt-get update                                           \
  &&  apt-get install -y --no-install-recommends           \
    ed                                                     \
    less                                                   \
    locales                                                \
    vim-tiny                                               \
    wget                                                   \
    ca-certificates                                        \
    fonts-texgyre                                          \
  &&  echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen          \
  &&  locale-gen en_US.utf8                                \
  &&  /usr/sbin/update-locale LANG=en_US.UTF-8             \
  &&  echo "deb http://http.debian.net/debian sid main" >  \
     /etc/apt/sources.list.d/debian-unstable.list          \
  &&  echo 'APT::Default-Release "testing";' >             \
     /etc/apt/apt.conf.d/default                           \
  &&  echo 'APT::Install-Recommends "false";' >            \
     /etc/apt/apt.conf.d/90local-no-recommends             \
  &&  chmod o+r /etc/resolv.conf                           \
  &&  apt-get update                                       \
  &&  apt-get install -y --no-install-recommends           \
    file                                                   \
    gcc-9-base                                             \
    libopenblas0-pthread                                   \
    littler                                                \
    libcurl4-openssl-dev                                   \
    libxml2-dev                                            \
    libssl-dev                                             \
    libpwiz-dev                                            \
    libpwiz3                                               \
    r-cran-littler                                         \
    r-base                                                 \
    r-base-dev                                             \
    r-recommended                                          \
    r-cran-rlang                                           \
    r-cran-dt                                              \
    r-cran-magrittr                                        \
    r-cran-ncdf4                                           \
    r-cran-devtools                                        \
    r-cran-plotly                                          \
    r-cran-httpuv                                          \
    r-cran-xtable                                          \
    r-cran-sourcetools                                     \
    r-cran-fastmap                                         \
    r-cran-rcurl                                           \
    r-cran-proxy                                           \
    r-cran-htmlwidgets                                     \
    r-cran-rsqlite                                         \
    r-cran-openxlsx                                        \
    r-cran-stringr                                         \
    r-cran-dplyr                                           \
    r-cran-purrr                                           \
    r-cran-blob                                            \
    r-cran-dbscan                                          \
    r-cran-biocmanager                                     \
    r-bioc-biocgenerics                                    \
    r-bioc-biobase                                         \
    r-bioc-protgenerics                                    \
    r-bioc-zlibbioc                                        \
  &&  Rscript /tmp/install.R                               \
  &&  apt-get clean autoclean                              \
  &&  apt-get autoremove --yes                             \
  &&  rm -rf /var/lib/{apt,dpkg,cache,log}/                \
  &&  rm -rf /tmp/*                                        ;

COPY ./XSeeker /XSeeker
COPY ./XSeekerBaseModule /tmp/XSeekerBaseModule

COPY ./resources/XSeekerBaseModule/ /tmp/XSeekerBaseModule/
COPY ./resources/XSeeker/config/ /XSeeker/config/

RUN \
  cd /tmp/XSeekerBaseModule                                \
  &&  ./configure                                          \
  &&  make install                                         \
  &&  cd /XSeeker                                          \
  &&  ./configure                                          \
  &&  make all_modules install                             \
  &&  rm -rf /tmp/XSeekerBaseModule/                       ;


RUN chmod +x /XSeeker/run.sh

COPY ./resources/entrypoint.sh /
RUN chmod +x /entrypoint.sh
CMD /entrypoint.sh