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Shiny App upload procedure

2019-03-28

Jacques SERIZAY

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This code has been written by Jacques SERIZAY, for the purpose of analysing datasets generated in the Ahringer lab, at the Gurdon Institute, University of Cambridge.

Steps to set up a Dashboard Shiny app:

PURPOSE: This markdown contains instructions to create and upload a Shiny app to present results obtained during my PhD on the project: Tissue-specific characteristics of the chromatin in C. elegans.
Dependencies: app_wrapper.sh is a wrapper of 3 functions (located in bin/) which aim to upload an existing Shiny App folder. The first step is to update existing data from Gurdon Institute server, which requires a password. The rest of the project is self-contained.

To deploy any app, run:

bash bin/app_release_wrapper.sh --folder "dashboard.Ahringer" --release-version "X.X.X"

This will execute the following commands (in the appropriate folder):

bash bin/import.data.sh
This script will automatically fetch the required data from the Gurdom Institute server.
Rscript bin/get.mininaldataset.R
This script will reduce the size of the original RData file to a more manageable minimal self-contained object.
bash bin/makeNewRelease.sh - ${APP_RELEASE}
This script will create a new release directory with a specified release #, and then sync the app folder with This app is backed-up on Github. To push changes to Github, run:

git add .
git commit -m "update"
git push -u origin master

Edited on 2019/03/28 to improve/streamline the process of uploading an app.

Infos on Digital Ocean hosting procedure:

I subscribed to a DigitalOcean droplet (IP address: 167.99.196.115). I followed the following steps to set up R on the server (mostly from https://deanattali.com/2015/05/09/setup-rstudio-shiny-server-digital-ocean/):

Register to DO and create a droplet. Save droplet name and IP/passowrd (sent by email).
CURRENT IP ADDRESS: 167.99.196.115
SSH to your droplet (ssh root@167.99.196.115), then enter your password (the one sent by email) then change it to a more convenient password.
Create a new user and give yourself sudo rights:

adduser jserizay ; gpasswd -a jserizay sudo
su - jserizay

Install Nginx

sudo apt-get update
sudo apt-get -y install nginx

Install R

sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" >> /etc/apt/sources.list'
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update
sudo apt-get -y install r-base

Add more RAM memory

sudo /bin/dd if=/dev/zero of=/var/swap.1 bs=1M count=1024
sudo /sbin/mkswap /var/swap.1
sudo /sbin/swapon /var/swap.1
sudo sh -c 'echo "/var/swap.1 swap swap defaults 0 0 " >> /etc/fstab'

Install devtools

sudo apt-get -y install libcurl4-gnutls-dev libxml2-dev libssl-dev
sudo su - -c "R -e \"install.packages('devtools', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"devtools::install_github('daattali/shinyjs')\""

Install Rstudio and Shiny

sudo apt-get -y install gdebi-core
wget https://download2.rstudio.org/rstudio-server-1.1.442-amd64.deb
sudo gdebi rstudio-server-1.1.442-amd64.deb
sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.5.6.875-amd64.deb
sudo gdebi shiny-server-1.5.6.875-amd64.deb

Upload Shiny app to /srv/shiny-server/ (ideally using the app_release_wrapper.sh script provided in ./bin/)
Install all the required packages directly from the server after launching R using sudo -i R!
IMPORTANT Don't forget to add a redirect link to the /etc/nginx/sites-enabled/default as follows:

location /Browser/ {
        proxy_pass http://167.99.196.115:3838/dashboard.Ahringer/releases/current/;
        rewrite ^(/Browser/[^/]+)$ $1/ permanent;
}

Then restart nging with systemctl restart nginx.

js2264/RegAtlas

Steps to set up a Dashboard Shiny app:

Infos on Digital Ocean hosting procedure: