How to set up a shinyapp

based on source

AWS setup

• AMI = Ubuntu 20 (certbot has no explicit support for ubuntu 22)
• Architecture = x86
• Instance type = t2.small (t2.micro is not enough to install the shiny package)
• Storage = 22GiB

Libraries and dependencies for neccesary r packages

sudo apt update -qq
sudo apt install build-essential
sudo apt install zlib1g-dev

Add cran to apt and install r

sudo apt install --no-install-recommends software-properties-common dirmngr
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
sudo apt install --no-install-recommends r-base

based on source

Instal shiny r package

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

this way of installing is to make sure packages are installed for all users, including the shiny user which runs the shiny app

sudo apt-get install gdebi-core
wget https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.21.1012-amd64.deb
sudo gdebi shiny-server-1.5.21.1012-amd64.deb

based on source

Open a port on the firewall on AWS so the app can be accessed (can be found under inbound security)

• type = Custom TCP Rule
• port = 3838

Note

By now you can access the default shiny app on [IPADRESS]:3838

Rsync the app to the server

rsync -av --progress -e "ssh -i [MYKEY].pem" app.R ubuntu@[MYSERVER]:/home/ubuntu/[MYFOLDER]

Make a link to the app in the shiny server folder where shiny looks for apps

cd /srv/shiny-server
sudo ln -s ~/[MYFOLDER] .

Edit the shiny conf file

sudo vim /etc/shiny-server/shiny-server.conf

• add preserve_logs true; to the top
• change directory_index on; to directory_index off;
• change site_dir to app_dir
• add the correct location of the app

Install additional R packages needed for the app

sudo su - -c "R -e \"install.packages(c('data.table', 'magrittr', 'ggplot2', 'stringr', 'patchwork', 'R.utils'), repos='https://cran.rstudio.com/')\""

Restart the shiny server

sudo systemctl reload shiny-server

Note

Before continuing setup a domain name at a domain name registrar, for example godaddy

Install and setup nginx

sudo apt install nginx

make a config file for the app so nginx will pick it up

cd /etc/nginx/sites-available
sudo vim shiny.conf

fill in the default nginx shiny setup see bottom of this page

cd ../sites-enabled
sudo ln -s ../sites-available/shiny.conf .
sudo nginx -t

most likely nginx will say there are settings missing, if it says all ok than skip the next steps and restart

sudo vim /etc/nginx/nginx.conf

add snippet to the nginx config see bottom of this page

sudo nginx -t

now the message should say ok

sudo systemctl restart nginx

Open a port on the firewall on AWS for nginx (can be found under inbound security)

• type = Custom TCP Rule
• port = 80

Install certbot

sudo snap install --classic certbot
sudo ln -s /snap/bin/certbot /usr/bin/certbot
sudo certbot --nginx --register-unsafely-without-email

based on source

Open a port on the firewall on AWS for https (can be found under inbound security)

• type = Custom TCP Rule
• port = 443

default nginx shiny setup

server {
    # listen 80 means the Nginx server listens on the 80 port.
    listen 80;
    listen [::]:80;
    # Replace it with your (sub)domain name.
    server_name [MYDOMAIN];
    # The reverse proxy, keep this unchanged:
    location / {
        proxy_pass http://localhost:3838;
        proxy_redirect http://localhost:3838/ $scheme://$host/;
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection $connection_upgrade;
        proxy_read_timeout 20d;
        proxy_buffering off;
    }
}

snippet

map $http_upgrade $connection_upgrade {
    default upgrade;
    '' close;
}