Shiny Transcriptomic Aggregator

Requirements

• R (≥3.0.2)

sudo yum install R

• Shiny

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

• NGINX

Installation

Shiny server installation

Following this tutorial.

1. Install gdebi :

   sudo apt-get install gdebi-core

2. Download Shiny Server

   wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.5.6.875-amd64.deb

3. Use gdebi to install the Shiny Server package :

   sudo gdebi shiny-server-1.5.6.875-amd64.deb

4. The shiny-server service should start automatically. Check its status :

   sudo systemctl status shiny-server.service

5. In a browser, navigate to your public IP address or FQDN on port 3838 (e.g. example.com:3838). You should see the Shiny Server welcome page:

6. Give the right to the shiny user in /srv/shiny-server

    `chown -R shiny:shiny /srv/shiny-server`
   

Application installation

• Clone the application repository from https://github.com/abims-sbr/shiny_transcriptomic_aggregator_ectocarpus/ in /srv/shiny-server/ :

  cd /srv/shiny-server/

  git clone https://github.com/abims-sbr/shiny_transcriptomic_aggregator_ectocarpus.git

• Install R packages as root :

  cd shiny_transcriptomic_aggregator_ectocarpus

  Rscript packages.R

Configuration

Shiny server configuration

/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;
  }
}

Nginx configuration

Add few lines in /etc/nginx/nginx.conf for websockets

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

Create /etc/nginx/conf.d/sta.conf file

server {
        listen 80       default_server;
        listen [::]:80  default_server;
        server_name _;
    
        location /ectocarpus/ {
                proxy_pass      http://127.0.0.1:3838/shiny_transcriptomic_aggregator_ectocarpus/public/;
                proxy_redirect  off;
                proxy_set_header Upgrade $http_upgrade;
                proxy_set_header Connection $connection_upgrade;
        }

        location /ectocarpus/private/ {
                proxy_pass      http://127.0.0.1:3838/shiny_transcriptomic_aggregator_ectocarpus/private/;
                proxy_redirect  off;
                proxy_set_header Upgrade $http_upgrade;
                proxy_set_header Connection $connection_upgrade;
                
                auth_ldap "Connection to your sb-roscoff account required";
                auth_ldap_servers sb-roscoff;
        }
}

Add a /etc/shiny-server/conf.d/ldap-auth.conf file and complete it

ldap_server ldap_name {
        url ldap_url;
        group_attribute uniquemember;
        group_attribute_is_dn on;
        # list of allowed users
        require user "uid=,ou=,dc=,dc=";
}

Application configuration

2 instances provided : One public and one private.

The configuration of your app can be change in the private/conf.R and public/conf.R files.

### Shiny app configurations ###

# Name of the project
project <- "Project Name"

# Instance status ("public" OR "private")
instance_tag <- "public"

# Columns to ignore in metadata file
gene_col_blacklist <- c("description", "content")
sample_col_blacklist <- c("replicats")

# Project Files
tpms_input <- "data/TPMs.csv"
genes_data_input <- "data/Genes_data.csv"
samples_data_input <- "data/Samples_data.csv"

Note

Add the following block in the proxy conf for websockets

<VirtualHost *:443>
        ProxyPreserveHost On
        ProxyPass / http://rshiny.sb-roscoff.fr/
        ProxyPassReverse / http://rshiny.sb-roscoff.fr/
        RewriteEngine on
        RewriteCond %{HTTP:Upgrade} =websocket
        RewriteRule /(.*) ws://rshiny.sb-roscoff.fr/$1 [P,L]

Logs

Logs are available in /var/log/shiny-server

Update Shiny Transcriptomic Aggregator

Update the code

cd /srv/shiny-server/shiny_transcriptomic_aggregator_ectocarpus
git pull origin master
systemctl restart shiny-server

Update data

• Private :

scp path/to/your/data root@IP:/srv/shiny-server/shiny_transcriptomic_aggregator_ectocarpus/private/real-data/

• Public :

scp path/to/your/data root@IP:/srv/shiny-server/shiny_transcriptomic_aggregator_ectocarpus/private/real-data/

Verify tpms_input, genes_data_input and samples_data_input variables in private/conf.R and public/conf.R files have the good file path.