ideal - Interactive Differential Expression AnaLysis in RNA-seq data - Server Edition

ideal is a Bioconductor package containing a Shiny application for analyzing RNA-Seq data in the context of differential expression. This enables an interactive and at the same time reproducible analysis, keeping the functionality accessible, and yet providing a comprehensive selection of graphs and tables to mine the dataset at hand.

This repository contains the information and the files for setting up a Shiny Server instance where ideal runs for you.

The code contained here is also released under the MIT License.

More information on ideal can be found at https://github.com/federicomarini/ideal - as well as at http://bioconductor.org/packages/ideal/

Setting up the Shiny Server

Mainly refer to this excellent reference: http://docs.rstudio.com/shiny-server/

In my case, I tested the deployment on a Ubuntu-based server. If this is your case too, please go to http://docs.rstudio.com/shiny-server/#ubuntu-12.04

If you are already familiar with Shiny Server, you can consider going directly here: http://docs.rstudio.com/shiny-server/#quick-start

Follow the indications in the main reference guide to see whether you have all packages installed, and visit the address which will refer to the address of your server (http://your.server.address:3838/sample-apps/hello/).

Setting up ideal

You need to:

• install ideal
• setup ideal on the server

Installing ideal

You need first to install Bioconductor

sudo su - -c "R -e \"install.packages('BiocManager')\""

Once that is done, you can install ideal with

sudo su - -c "R -e \"BiocManager::install('ideal')\""

You can also install the development version of ideal from GitHub with

# install devtools first
sudo su - -c "R -e \"BiocManager::install('devtools')\""
# and then ideal
sudo su - -c "R -e \"BiocManager::install('federicomarini/ideal')\""

Setup ideal on the server

You essentially need to do two things:

• in /srv/shiny-server,

git clone https://github.com/federicomarini/ideal_serveredition.git

This will clone the repository with all the files required for running

• you need to edit /etc/shiny-server/shiny-server.conf. To do this, use any text editor (e.g. vi), and add the following lines

server {
  listen 3838;

  #...

  ### FROM HERE
  location /ideal {
    # Run this location in 'app_dir' mode, which will host a single Shiny
    # Application available at '/srv/shiny-server/myApp'
    app_dir /srv/shiny-server/ideal;

    # Log all Shiny output to files in this directory
    log_dir /var/log/shiny-server/ideal;

    # 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 off;

    # recommended, to wait for the application to start
    app_init_timeout 250;
  }
  ### TO HERE

  # ...
}

This is basically as suggested in the Shiny Server reference, with the only exception of the app_init_timeout value: set this a little higher, so that you avoid that the service stops too often. Credits go to Mark Robinson for suggesting this parameter setup!

You might need to restart the Shiny Server (systemctl restart shiny-server on Ubuntu). Then you should be good to go!

Visit http://your.server.address:3838/ideal for your personal running instance.

ideal at the IMBEI

http://shiny.imbei.uni-mainz.de:3838/ideal is the address for the public instance of ideal on the Shiny Server I manage at the Institute of Medical Biostatistics, Epidemiology and Informatics.

The relevant setup of that machine is the following (in case you are asking what specs you need):

• 4 cores
• 8 GB RAM

lsb_release -a

    No LSB modules are available.
    Distributor ID: Ubuntu
    Description:    Ubuntu 16.04.2 LTS
    Release:    16.04
    Codename:   xenial

Contact

For additional details regarding the functions of ideal, please consult the package documentation or write an email to marinif@uni-mainz.de.

For questions regarding the deployment on your Shiny Server, please use https://github.com/federicomarini/ideal_serveredition/issues

Bug reports/Issues/New features

Please use https://github.com/federicomarini/ideal/issues for reporting bugs, issues or for suggesting new features to be implemented.