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FROM archlinux/base
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 \
r \
ruby \
swig \
python-pip \
catdoc \
wget
RUN pacman -Scc --noconfirm
RUN R -e "install.packages('Rserve', repos='http://rforge.net/')"
RUN pip install xlsx2csv
RUN useradd -ms /bin/bash ist
# mongodb has been removed from main repositories
USER ist
WORKDIR /home/ist
RUN mkdir data
RUN mkdir src
WORKDIR /home/ist/src
RUN wget https://aur.archlinux.org/cgit/aur.git/snapshot/mongodb-bin.tar.gz
RUN tar -xvzf mongodb-bin.tar.gz
WORKDIR /home/ist/src/mongodb-bin
RUN makepkg -s --noconfirm
# installation requires root
USER root
RUN pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz
# install lazar-gui gem
RUN echo 'gem: --no-document' > /etc/gemrc
#RUN gem install lazar-gui
RUN gem install lazar
RUN gem install qsar-report
RUN gem install sinatra haml sass rdiscount unicorn
USER ist
WORKDIR /home/ist
RUN rm -r src
# lazar-gui
RUN git clone https://git.in-silico.ch/lazar-gui
WORKDIR lazar-gui
RUN git checkout prerelease
# SWAGGER for API
WORKDIR /home/ist
RUN git clone https://github.com/swagger-api/swagger-ui.git
COPY swagger.html /home/ist/swagger-ui/dist/index.html
# TODO adjust to lazar-gui gem path
RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js /home/ist/lazar-gui/public/swagger-ui-bundle.js
RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js /home/ist/lazar-gui/public/swagger-ui-standalone-preset.js
RUN ln -s /home/ist/swagger-ui/dist/swagger-ui.css /home/ist/lazar-gui/public/swagger-ui.css
# start script
COPY start.sh /home/ist/start.sh
ENTRYPOINT ["/home/ist/start.sh"]
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