dockerize_MATRiX

Getting started

First make sure that you have java installed on your machine

java -version

that will display the following message:

openjdk version "1.8.0_72"
OpenJDK Runtime Environment (Zulu 8.13.0.5-linux64) (build 1.8.0_72-b15)
OpenJDK 64-Bit Server VM (Zulu 8.13.0.5-linux64) (build 25.72-b15, mixed mode)

if its not the case follow the tutorial here

You can use MATRiX locally by installing Docker on your machine.

1. Docker for Ubuntu/Debian
2. Docker for Windows/Mac

Link the docker daeomon to shinyproxy. By default ShinyProxy will do so on port 2375 of the docker host. In order to allow for connections on port 2375, the startup options need to be edited.

sudo mkdir /etc/systemd/system/docker.service.d/
touch /etc/systemd/system/docker.service.d/override.conf
sudo nano /etc/systemd/system/docker.service.d/override.conf

add the following information in the new file

[Service]
ExecStart=
ExecStart=/usr/bin/dockerd -D -H tcp://127.0.0.1:2375

for more information check the shinyproxy guide

Installation

First you need to clone the repositories

git clone https://github.com/GeT-TRiX/dockerize_MATRiX
cd dockerize_MATRiX
git clone https://github.com/GeT-TRiX/MA_Trix_App

You need to respect the following arborescence

.
+-- application.yml
+-- MA_Trix_App
|   +-- server.R
|   +-- ui.R
|   +-- ...
+-- shinyproxy-xxx.jar
+-- Rprofile.site
+-- Dockerfile

Next you must edit the file application.yml so that the parameters fit to your system (users credentials, paths, ...). Finally you can build docker image and run the app. using these commands

cd dockerize_MATRiX
sudo docker build -t openanalytics/shinyproxy-template .
java -jar shinyproxy-2.0.5.jar

In your browser connect to http://localhost:8080/
enter login and password (id:tesla, password:password) as configured in the file application.yml
and click on the last link (MATRiX)

Update application

Update MA_Trix_App with branch preprod

./preprod.sh

If you want validate your preprod commits or just update your main branch (pull first in MA_Trix_App repository)

./buildmain.sh

Contact

Here are our mail [Franck Soubès] (franck.soubes@inra.fr) or [Yannick Lippi] (yannick.lippi@inra.fr) for any questions, suggestions or if you need help to use MATRiX, dont hesitate to contact us.