phenopipe postprocess setup

Phenopipe Postprocessing Server Setup

This page describes setting the application up on CentOS 7.

First you need to install MongoDb 3.4.

Install full java if only the headless version is installed:

sudo yum install java-1.8.0-openjdk java-1.8.0-openjdk-devel

Additionally we need Xvfb (X virtual frame buffer).

sudo yum groupinstall "X Window System"
sudo yum install xorg-x11-server-Xvfb

System Configuration

To run xvfb on startup we create a systemd service (/etc/systemd/system/xvfb.service):

[Unit]
Description=virtual frame buffer X server for display 99
After=network.target

[Service]
ExecStart=/usr/bin/Xvfb :99 

[Install]
WantedBy=multi-user.target

Open the necessary port for accessing the service:

sudo firewall-cmd --zone=public --permanent --add-port=50052/tcp 

Now create a new user and group for running the phenopipe application:

sudo adduser -r -s /sbin/nologin phenopipe

Next create the directory to which we want to install the application and give our user access:

sudo mkdir /var/www/phenopipe
sudo chown phenopipe:phenopipe /var/www/phenopipe/

If you don't have git installed already run:

yum install git

Building the application

To build and install the application you have to download the source code to your server via

git clone https://github.com/Gregor-Mendel-Institute/PhenoBox-System.git

Now you have to create/adapt some configuration files in order to build it successfully. Under 'PhenoBox-System/phenopipe-postprocess-server/src/main/resources/' you have to add a file called 'shared_folder_map.properties'. This file should contain the mapping from your smb file share (its SMB URL) to the local mount point. It should look like the following.

smb\://url.of.your.server/share=/your/local/mountpoint/

Afterwards you have to run the following commands:

cd PhenoBox-System/phenopipe-postprocess-server
./gradlew build
sudo tar -xvf build/distributions/phenopipe-postprocess-server.tar -C /var/www/phenopipe
sudo chown -R phenopipe:phenopipe /var/www/phenopipe/phenopipe-postprocess-server/

Now that the application has been built and installed we have to create a service to start it automatically

Installation and Autostart

Now that the application is built we have to create a service to start it automatically Using systemd we can do the following: Create the service description at /etc/systemd/system/phenopipe-postprocess-server.service This file should look like this:

[Unit]
Description=Phenopipe Postprocessing service
Wants=network-online.target
After=network-online.target

[Service]
Environment="DISPLAY=:99"
ExecStart=/var/www/phenopipe/phenopipe-postprocess-server/bin/phenopipe-postprocess-server

User=phenopipe
Group=phenopipe

[Install]
WantedBy=multi-user.target

To start and enable the service do the following:

sudo systemctl daemon-reload
sudo sytemctl enable phenopipe-postprocess-server

Now the server should start everytime you restart the system.