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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-new-consensus-mutagenicity-dg3 && \
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"]
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