#shinyNAP #Setting up ShinyNAP

Using Ubuntu 18.04 on Amazon AWS EC2

The purpose of this markdown file is to reproduce the R (Shiny) application shinyNAP, or shiny NeoAntigenPortal deployed onto an Amazon AWS EC2 server instance (or other LINUX/UNIX-based systems). ShinyNAP is an application designed to provide oncology researchers with a visualization tool for protein immunogenicity.

Using AWS EC2

For general setup using Amazon AWS:

• Log into [Amazon] (https://signin.aws.amazon.com/signin?redirect_uri=https%3A%2F%2Fus-east-2.console.aws.amazon.com%2Fec2%2Fv2%2Fhome%3Fregion%3Dus-east-2%26state%3DhashArgs%2523Instances%253Asort%253DkeyName%26isauthcode%3Dtrue&client_id=arn%3Aaws%3Aiam%3A%3A015428540659%3Auser%2Fec2&forceMobileApp=0)

  1. Click create instance
  2. Click launch screen
  3. Select Ubuntu18.04 (free instance)
  4. Select General Purpose - t2.micro
  5. Click Review and Launch in the bottom-left

• Change security settings for instance

  1. in the SSH row, change source to My IP

  2. Click Add Rule to add custom TCP rule

  3. Under Port Range enter 3838 (port for R shiny server)

  4. Under Port Range enter 8787 (port for Rstudio Server)

  5. Change Source to Anywhere

  6. Click Review and Launch in the bottom left

  7. Click Launch to get the private key to SSH into the EC2 instance

  8. Create new key pair NAPkey to download NAPkey.pem and save to an easily accessible directory

     • Secure the key by using chmod 400 NAPkey.pem

  9. Copy address to instance under Public DNS (IPv4)

     -Ex. ec2-18-223-112-142.us-east-2.compute.amazonaws.com

####Connect using SSH In AWS console, select connect, and copy the path in the dialogue box with the SAME directory the Key file is in: sudo ssh -i "NAPkey.pem" [email protected]

###Install R, etc. on server

You have now successfully logged into the server instance you created!!! Let's use it. The following instructions/commands are adapted from [Kimberly Coffee] (http://www.kimberlycoffey.com/blog/2016/2/13/mlz90wjw0k76446xkg262prvjp0l8u). You can also follow a useful video from [Youtube] (https://www.youtube.com/watch?v=hglgkFfRqyQ) that also uses Kimberly's commands.

sudo su -c "echo 'deb http://archive.linux.duke.edu/cran/bin/linux/ubuntu trusty/' >> /etc/apt/sources.list"

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

sudo apt-get update

sudo apt-get upgrade -y #when receiving warning here, click continue!

udo apt-get dist-upgrade -y

sudo apt-get install r-base -y

Install R packages here:

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

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

sudo su -c "R -e \"install.packages('ggplot2', repos='https://cran.rstudio.com/')\""

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

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

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

For other packages... sudo su -c "R -e \"install.packages('PACKAGE NAME HERE', repos='https://cran.rstudio.com/')\""

####Install shiny server Use the most-updated shiny server [link] (https://www.rstudio.com/products/shiny/download-server/) and use the following commands in the server. sudo apt-get install gdebi-core

sudo gdebi shiny-server-1.5.9.923-amd64.deb

Test the above by using your server's IP address (found in the console)

http://18.223.112.142/3838

####Install Rstudio server Use the most-updated Rstudio server [link] (https://www.rstudio.com/products/rstudio/download-server/)

wget https://download2.rstudio.org/rstudio-server-1.1.463-amd64.deb

sudo gdebi rstudio-server-1.1.463-amd64.deb

####Add user for login to Rstudio You can obviously choose your own login. It will also prompt you to enter your own password... sudo adduser shinynapadmin

####Add sudo user priveleges sudo vim /etc/sudoers

Scroll down to **allow members of group sudo to execute any command. Press "i" to insert:

%shinynapadmin ALL=(ALL:ALL) ALL

Check sudoers:

sudo cat /etc/sudoers

##Transfer NetMHC files from LOCAL to server In the folder where the key is located, enter the following command to transer R scripts to the server (you can do this, or git clone from the repo. ShinyNAP should already have a configured version of NetMHC included in the app.

scp -i NAPkey.pem *.R

Now, download netMHC to a local location. You will be transferring the unlocked version from the DTU Bioinformatics [website] (http://www.cbs.dtu.dk/services/NetMHC/). You will be prompted to enter a .edu email address in order to download.

Once you have the netMHC files, transfer them to the server using the ubuntu/server address from your EC2 console. sudo scp -i NAPkey.pem -r netMHC-4.0 [email protected]:~

####Configure NetMHC software on server

Install tsch to execute netMHC:

sudo apt-get install csh

sudo apt-get install tcsh

Set shortcut to "data" folder for netMHC. In the netMHC-4.0 directory, change the path from its default to /home/ubuntu/netmhc_files/netMHC-4.0 using the following command

sudo pico netMHC

Download "test" data from server using the link provided in netMHC's download [email] (http://www.cbs.dtu.dk/services/NetMHC-4.0/data.tar.gz).

Transfer gzipped files to server:

sudo scp -i NAPkey.pem -r data.tar.gz [email protected]:~/netMHC-4.0/

Unzip the files:

gunzip -c data | tar xvf -

Test netMHC per instructions:

sudo ../netMHC test.fsa > test.fsa.myout

sudo ../netMHC -p test.pep > test.pep.myout

Once netMHC is configured, move (or copy) netMHC to the www directory in the shinyNAP app directory www (netMHC should already be configured when the repo is cloned).

####Restart server after installation of all updates

sudo reboot

sudo apt-get update

#Clone ShinyNAP git repo ####in Rstudio Before we get started, enable sudoer permissions for your usernames/shiny's usernames so shiny can read/write/execute. sudo pico /etc/sudoers

• add %shinynapadmin ALL=(ALL:ALL) ALL
• add %ubuntu ALL=(ALL:ALL) ALL
• add %shiny ALL=(ALL:ALL) ALL

The moment you've all been waiting for...

Once you're logged into Rstudio by entering your.IP.address/8787:

1. Click new project
2. Click version control
3. Click git
4. Enter address https://github.com/miosisoniii/shinyNAP
5. Enter your git username
6. Enter password

The app should run when using Rstudio on the server to run the app, with NetMHC.

If there are any questions please email at [email protected] or slack me at miosisoniii.