FROM        base/archlinux
MAINTAINER  in-silico toxicology GmbH

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

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

RUN         mkdir -p /data/db
RUN         R -e "install.packages('Rserve', repos='http://rforge.net/')"
RUN         pip install xlsx2csv
USER        ist
WORKDIR     /home/ist


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

RUN         git clone https://github.com/opentox/lazar.git
WORKDIR     lazar 
RUN         git checkout "development"
RUN         ruby ext/lazar/extconf.rb
RUN         gem install bundler rake
RUN         bundle install
RUN         git checkout -b "mutanew"
#USER root
# set environment vars
# start mongo and R
USER        ist
WORKDIR     /home/ist
#EXPOSE      22
#ENTRYPOINT  ["/usr/bin/sshd -D"]