README.md

Development of an R-shiny application to quickly and easily analyze 16S data.

Online server (beta test) : http://genome.jouy.inra.fr/shiny/easy16S/

Shiny server Installation

Easy16S application actually works on a Open Source Shiny Server. For shiny server installation, we follow the Rstudio Guide.

1. Install and update R, the shiny R package and all the necessary packages

sudo yum install R
sudo su - -c "R -e \"install.packages('shiny', repos='https://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('rmarkdown')\""

2. Download Shiny Server

wget https://download3.rstudio.org/centos6.3/x86_64/shiny-server-1.5.9.923-x86_64.rpm

3. Install it with gdebi or yum according to your OS

sudo yum install --nogpgcheck shiny-server-1.5.9.923-x86_64.rpm

If necessary, you can stoping or starting the shiny server

sudo systemctl start shiny-server
sudo systemctl stop shiny-server

4. Configure shiny server

For example, this is our /etc/shiny-server/shiny-server.conf :

# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;

# Define a server that listens on port 3838
server {
	listen 3838;

	# Define a location at the base URL
	location / {

		# Host the directory of Shiny Apps stored in this directory
		site_dir /srv/shiny-server;

		# Log all Shiny output to files in this directory
		log_dir /var/log/shiny-server;

		# When a user visits the base URL rather than a particular application,
		# an index of the applications available in this directory will be shown.
		directory_index on;
	}
}

5. Deploy application with a git clone in /srv/shiny-server/

cd /srv/shiny-server/
git clone https://gitlab.irstea.fr/cedric.midoux/easy16S.git