Starting a Shiny Server Instance from the Preconfigured Image

Keith Mitchell (kgmitchell@ucdavis.edu)

A few general notes:

• be sure Adam has granted you an IAM account on the UC Davis Bioinformatics AWS account.
• Do not nuke the Zulip instances!
• The following has been adapted from:
  • https://towardsdatascience.com/how-to-host-a-r-shiny-app-on-aws-cloud-in-7-simple-steps-5595e7885722

Setting up an AWS account for yourself

• For the first year of your account being active AWS offers tons of free, cool services! One of which is a micro EC2 instance which might be enough for some datasets. A medium, large instance run about 30$, 60$ per month.
  • Here is more info on the pricing: https://aws.amazon.com/ec2/pricing/

How to prepare the instance for a client:

1. Go to the AWS AMI’s (Amazon Machine Images). Select the Rshiny Server Image. Go to Actions>Launch
2. Next Choose and Instance Type. This will vary in general based on the size of the data you are attempting to analyze. In general it is advised to start with a smaller instance and then move up from there if necessary.
3. Next Configure the Instance Details. The main step here is to set the “Auto-assign Public IP” to enable.
4. Keep clicking the bottom right button, “Next: Configure Security Group” until you get to “Step 6: Configure Security Group”
5. At step 6, select the Rshiny App security group.
6. Finally launch the instance. (Bottom right hand quarter)
7. Select an existing key pair or create a new key pair is the final step for starting the instance. Choose “Create a new key pair” and give the key a useful name, here we will use “tutorial”.
8. Move the downloaded key to ~/.ssh/ via mv ~/Downloads/tutorial.pem ~/.ssh/
9. chmod 700 ~/.ssh/tutorial.pem
10. Get the connection to the instance seen highlighted below “ec2-…….amazonaws.com”
11. Run the following command to upload the “experiment_merged.Rdata” object to the app:
    • scp -i ~/.ssh/tutorial.pem ec2-54-219-166-77.us-west-1.compute.amazonaws.com:/srv/shiny-server/scRNA_shiny_app/ ~/Desktop/experiment_merged.rds
12. Replace the green section with your Public IV4 DNS address from the instance that was created and used in the previous step.
    • http://ec2-54-219-166-77.us-west-1.compute.amazonaws.com:3838/scRNA_shiny_app/
13. If there are problems with this link do the following:
    • SSH into the server.
      • ssh -i ~/.ssh/tutorial.key ec2-54-219-166-77.us-west-1.compute.amazonaws.com
    • Restart the shiny service.
      • sudo systemctl restart shiny-server.service
14. Memory issues?
    • The default memory limit for R on the instance has caused me some problems in the app and it can be tricky to debug.
    • The following link was a solution for this issue but feel free to reach out if you have any other issues in regards to this.
      • https://stackoverflow.com/questions/1395229/increasing-or-decreasing-the-memory-available-to-r-processes
      • You can increase the default using this command, memory.limit(size=2500), where the size is in MB.
      • Or you can check the amount of available memory using memory.limit()