FROM        base/archlinux
MAINTAINER  in-silico toxicology GmbH

RUN         pacman-db-upgrade && pacman -Syyu --noconfirm && pacman -S --noconfirm \
            base-devel \
            boost-libs \
            cmake \
            eigen3 \
            fontconfig \
            gcc-fortran \
            git \
            gsl \
            jre10-openjdk-headless \
            mongodb \
            mongodb-tools \
            r \
            ruby \
            swig \
            vim \
            wget && pacman -Scc --noconfirm

RUN         useradd -ms /bin/bash ist
RUN         echo "ist ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers

RUN         mkdir -p /data/db
USER        ist
WORKDIR     /home/ist

RUN         wget http://www.rforge.net/src/contrib/Rserve_1.8-6.tar.gz -O Rserve_1.8-6.tgz
RUN         sudo R CMD INSTALL Rserve_1.8-6.tgz

RUN         echo 'gem: --user-install --no-document' > ~/.gemrc
ENV         PATH $PATH:/home/ist/.gem/ruby/2.5.0/bin
RUN         export GEM_HOME=$(ruby -e 'print Gem.user_dir')
RUN         gem install bundler
RUN         bundle config --global silence_root_warning 1

RUN         git clone https://git.in-silico.ch/lazar && \
            cd lazar && \
	          git fetch && git fetch --tags && \
            git checkout "v10-nestec" && \
            ruby ext/lazar/extconf.rb && \
            bundle install --path ~/.gem

# get models training data from private git repo, bitbucket, lazar-nestec-data

RUN         git clone https://git.in-silico.ch/toxtree && \
            cd toxtree && \
            ruby ext/toxtree/extconf.rb

RUN         git clone https://git.in-silico.ch/kazius-alerts

RUN         git clone https://git.in-silico.ch/lazar-gui && \
            cd lazar-gui && \
	          git fetch && git fetch --tags && \
            git checkout nestle-lazar-main-dg2 && \
            bundle install --path ~/.gem

COPY        start.sh /home/ist/start.sh
RUN         sudo chmod +x /home/ist/start.sh
EXPOSE      8088
ENTRYPOINT  ["/home/ist/start.sh"]