Setup Lightsail Server with Rstudio, Shiny and Dropbox

Creating an RStudio/Shiny server using AWS Lightsail and Docker (on MacOS) This is inspired by Jordan Farrers Rstudio installation guide the script to install todo by mikegcoleman, and Mikkels guide to setup Rstudio an Shiny with a shared package directory.

Create a server

Create an account with Amazon Web Services (AWS) Lightsail
Create an instance.
- Leave the location as-is
- Under instance image Choose Linux/Unix > OS Only > Ubuntu 18.04 LTS
Do not use the Default SSH key, but upload a public key of your own (*_rsa.pub). To do this, use the SSH Key pair manager. Click on the + and upload a public key.
- SSH keys are located in ~/.ssh/. One can navigate there from Finder by pressing Shift+Command+G and typing the directory name (~/.ssh/.)
- Copy your public key to a visible directory that can be accessed by the web-interface
- Select the appropriate file
- Instructions to create a new SSH Key can be found here
Choose the free instance plan
Name the server (e.g. Rstudio)
Click Create Instance

Initial setup of the server

While the server is spinning up, a few parameters need to be set.

To make sure that the instance can be reached from outside

Click on 'Networking'
Create a Static-IP (note: this is free as long as it is coupled to an instance)
To couple the Static IP to the newly created instance click on the three dots next to the IP and select manage.
Select the newly created instance and click 'Attach'
Couple this to the newly created instance (note: this is also free)

To open the ports required for Rstudio and Shiny

Click on 'Instances' and select the newly created instance
Click on the three dots and select 'Manage'
Click on 'Networking and add to new entries under 'Firewall'
- Custom, TCP, 8787 <-- for Rstudio
- Custom, TCP, 3838 <-- for Shiny
- Click 'save'

Setting up a connection

Now it is time to configure Ubuntu Linux to run Rstudio and Shiny via an SSH session. #To set up a local SSH session:

note down the IP address of the instance.
open a terminal program (eg Iterm2) and initise an SSH-connection by typing ssh ubuntu@<AWS ip-address> (e.g. ubuntu@12.241.147.112)
you may have to type the secret sentence for the SSH key that you are using. This can be found in the keychain. Open keychain (e.g. via Spotlight Search) and search for the key that you have uploaded.
- if you have previously used the same IP-address to connect to another instance you will get a warning. This can be solved by removing the relevant entry from the known hosts file (~/.ssh/known_hosts). Look for the line starting with the IPADDRESS that you are using and remove it. Don't forget to save prior to issuing the ssh command in the terminal.
You may see a message asking if the host can be trusted. Say 'yes' to add the server to the known_hosts file. Now you should be seeing something like ubuntu@ip-212.141.47.12:~$. Note that the displayed IP adress is the internal rather than the

Further setup of the server

It is a good idea to upgrade the packages on the server prior to continuing with installation:

sudo apt-get update
sudo apt-get upgrade

When asked about SSH configuration file, choose to 'keep the local version currently installed'.

As the amount of memory is with 512K too limited for a common R tasks, it is helpful to assign swapspace:

sudo touch /var/swap.img
sudo chmod 600 /var/swap.img
sudo dd if=/dev/zero of=/var/swap.img bs=2048k count=1000
sudo mkswap /var/swap.img
sudo swapon /var/swap.img

Installing packages

To increase reproducability of analysis we will use Docker with Rocker images of Rstudio with tidyverse (Rocker/tidyverse) and Shiny (Rocker/shiny) installed. This will guaruantee consistency between different installations of R/Rstudio/Shiny and associated packages.

Install Docker and Docker Compose

curl -fsSL https://get.docker.com -o get-docker.sh
sh get-docker.sh

# to enable running docker as user ubuntu (note: this only takes effect after logging out)
sudo usermod -aG docker ubuntu

# install docker-compose
sudo curl -L "https://github.com/docker/compose/releases/download/1.24.1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
sudo chmod +x /usr/local/bin/docker-compose

# copy the docker-compose file onto the server
sudo mkdir /srv/docker
sudo curl -o /srv/docker/docker-compose.yml https://raw.githubusercontent.com/jkeuskamp/Biont_server_setup/master/docker-compose.yml

Install (Headless) Dropbox

#Download and start the deamon
cd ~ && wget -O - "https://www.dropbox.com/download?plat=lnx.x86_64" | tar xzf -
~/.dropbox-dist/dropboxd

You may see a line asking you to visit an URL to connect the dropbox to the server. If you are using iterm2 click on Command to activate the link and press enter. Otherwise copy the link manually. The process will continue after you do so. It will run dropbox and sync untill you press Control+C.

If your dropbox is large, you may be asked to run the following line prior to rerunning the above.

echo fs.inotify.max_user_watches=100000 | sudo tee -a /etc/sysctl.conf; sudo sysctl -p

This will add a line to sysctl.conf allowing dropbox to function well

to install Dropbox CLI enabling controlling dropbox via the command line:

sudo wget -O /usr/local/bin/dropbox "https://www.dropbox.com/download?dl=packages/dropbox.py
sudo chmod +x /usr/local/bin/dropbox

Check whether dropbox runs by issueing: dropbox status

Now if you do not want to sync all directories issue the command

dropbox exclude add *

to stop future syncing for all directories and remove existing local copies

Add specific directories by adding dropbox exclude remove [DIRECTORY] [DIRECTORY] with [DIRECTORY] the directories that you do want to sync eg dropbox exclude remove Biont

To make dropbox run every reboot:

sudo curl -o /etc/systemd/system/dropbox.service https://raw.githubusercontent.com/jkeuskamp/Biont_server_setup/master/dropbox.service
sudo systemctl daemon-reload
sudo systemctl enable dropbox.service
sudo systemctl start dropbox

Check whether the service is running by typing sudo systemctl status dropbox

Install Rstudio/Tidyverse and Shiny

# copy in systemd unit file and register it so our compose file runs 
# on system restart
sudo curl -o /etc/systemd/system/docker-compose-app.service https://raw.githubusercontent.com/jkeuskamp/Biont_server_setup/master/docker-compose-app.service
sudo systemctl enable docker-compose-app

# start up the application via docker-compose
sudo docker-compose -f /srv/docker/docker-compose.yml up -d

This may take a while the first time as the docker containers will to be downloaded

##Using the packages To use RStudio navigate to :8787 using a browser. Username = test and password = test. These passwords can be changed in the docker-compose.yml. To do this, type 'sudo nano /srv/docker/docker-compose.yml and change the lines starting with USER and PASSWORD.

To use Shiny navigate to :3838.