btski/octoflushow

A Shiny app for swine IAV surveillance

octoflushow

Live site on flu-crew.org

Installation

The source code for the app is available on github and can be installed with devtools:

devtools::install_github("flu-crew/octoflushow", auth_token="yourtokenhere")

octoflushow::launch_app()

or

devtools::document()
devtools::install()
octoflushow::launch_app()

Updating octoflushow on AWS

cd github/octoflushow   # This will probably be in a github folder, somewhere in home directory
git pull
sudo R

From within the R environment

devtools::install()
# When it asks if you want to update packages, choose "none" (3).

# Check if it installed correctly
octoflushow::launch_app()
#ctrl-d to stop 

From back in the shell

sudo systemctl restart shiny-server

Check the website address see if site is working.

AWS Initial Setup

• Ubuntu defaults to R v3.4 but you will need >v3.5 for several R packages to install. So follow instructions here Ubuntu packages for R

  cd /etc/apt/sources.list_d      # <= add any sources.list command here instead
  sudo emacs latestRversion.list
  

  Add the following line, or the appropriated deb command from

  deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
  

  After saving sources.list, you'll need to run the following to fetch the latest R version.

  # ! === You will also need to get the R public key from the R website, go to how to install R in ubuntu
  sudo apt-get update
  sudo apt-get install r-base
  sudo apt-get install r-base-dev
  

• Start at step 4 of this tutorial How to host a r-shiny app on aws cloud in 7 steps

  # Install R shiny package    =====   Altho better to just start R, and install pkgs using the install.packages("shiny") command
  sudo su — -c “R -e \”install.packages(‘shiny’, repos = ‘http://cran.rstudio.com/')\""     
  
  # Install shiny server
  wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.4.4.807-amd64.deb
  sudo dpkg -i shiny-server-1.4.4.807-amd64.deb
  cd /srv/shiny-server                                  # <= put your shiny app here
  
  # Start shiny server
  sudo systemctl start shiny-server      
  sudo systemctl status shiny-server                   # check if it's running  
  

• Set up a username password account using this tutorial htpasswd

  cd /var/www
  sudo htpasswd -c /var/www/.htpasswd [username]      # 1st time, otherwise this will overwrite existing users
  sudo htpasswd /var/www/.htpasswd [username]         # To add more users
  less .htpasswd                                      # check file to make sure username has been added
  

  If you've changed 000-default.conf to reference a different password location (/etc/apache2/.htpasswd):

  cd /etc/apache2
  sudo htpasswd -c /etc/apache2/.htpasswd [username]      # 1st time, otherwise this will overwrite existing users
  sudo htpasswd /etc/apache2/.htpasswd [username]         # To add more users
  less .htpasswd                                          # check file to make sure username has been added
  

• Setup shiny server, or at least reroute the ports to some form of https://yourwebsite.com/projectname/

  cd /etc/apache2/sites-available/
  sudo emacs 000-default.conf                            # <= this is the main file to configure everything
  sudo systemctl restart shiny-server                    # restart server for changes to take effect
  

  Click through the documentation for what the tags mean in 000-default.conf so you can configure it properly.