diff options
| author | Christoph Helma <helma@in-silico.ch> | 2019-09-03 13:06:00 +0200 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2019-09-03 13:06:00 +0200 |
| commit | a84d9eabf1b921086a688f81df28b0f21ba4df19 (patch) | |
| tree | 8ca3d6c2a0bc8d22821212af2eada21cce2ea1e0 /docker | |
| parent | c9f8cd864a2b72e7330b8095691fa5c16fea83aa (diff) | |
docker installation as gem, links with port numbers, version 1.4.0prerelease
Diffstat (limited to 'docker')
| -rw-r--r-- | docker/Dockerfile | 46 | ||||
| -rwxr-xr-x | docker/start.sh | 4 |
2 files changed, 20 insertions, 30 deletions
diff --git a/docker/Dockerfile b/docker/Dockerfile index a606b9a..b7ba3c1 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -23,12 +23,17 @@ RUN pacman -Scc --noconfirm RUN R -e "install.packages('Rserve', repos='http://rforge.net/')" RUN pip install xlsx2csv + +# install lazar-gui gem +RUN echo 'gem: --no-document' > /etc/gemrc +RUN gem install lazar-gui + RUN useradd -ms /bin/bash ist -# mongodb has been removed from main repositories USER ist WORKDIR /home/ist RUN mkdir data +# mongodb has been removed from main repositories, AUR installation RUN mkdir src WORKDIR /home/ist/src RUN wget https://aur.archlinux.org/cgit/aur.git/snapshot/mongodb-bin.tar.gz @@ -36,38 +41,23 @@ 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 +# rest api swagger gui 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 +# mongodb installation requires root +USER root +RUN pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz + +# swagger links +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui-bundle.js +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui-standalone-preset.js +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui.css $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui.css + +USER ist +RUN rm -r /home/ist/src ENTRYPOINT ["/home/ist/start.sh"] diff --git a/docker/start.sh b/docker/start.sh index ad40a0e..07fefde 100755 --- a/docker/start.sh +++ b/docker/start.sh @@ -5,8 +5,8 @@ mongod --bind_ip 127.0.0.1 --dbpath ~/data & R CMD Rserve --vanilla & # import data -ruby -e "require 'lazar'; include OpenTox; Import.public_data" +ruby -e "require 'lazar'; include OpenTox; Import.public_data if Model::Validation.all.empty?" # start lazar service -cd $HOME/lazar-gui +cd $(gem which lazar-gui|sed 's#/lib/lazar-gui.rb/##') unicorn -p 8088 -E production |