From cf80891415b530fc9fa52fc1e593c949c463d7da Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 18 Sep 2019 20:56:34 +0200
Subject: added docker

---
 docker/Dockerfile | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 docker/start.sh   |  7 +++++++
 2 files changed, 69 insertions(+)
 create mode 100644 docker/Dockerfile
 create mode 100644 docker/start.sh

(limited to 'docker')

diff --git a/docker/Dockerfile b/docker/Dockerfile
new file mode 100644
index 0000000..53b4032
--- /dev/null
+++ b/docker/Dockerfile
@@ -0,0 +1,62 @@
+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"]
diff --git a/docker/start.sh b/docker/start.sh
new file mode 100644
index 0000000..46246c7
--- /dev/null
+++ b/docker/start.sh
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+sudo mongod &
+R CMD Rserve --vanilla & 
+#ruby $HOME/lazar/test/all.rb
+cd $HOME/lazar-gui &&
+unicorn -p 8088 -c unicorn.rb -E production
-- 
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