Documentation/ Instructions for use of IGBA-AMI-1

This AMI launches the following servers on startup: (1) Xrdp (2) Postgres (3) Sshd

In addition you can manually launch: (1) Rserve (2) Shiny

To connect with ssh:

(1) Create a security group in your AWS account allowing ssh (port 22) connections. To connect to the Xrdp remote desktop server, also allow rdp (port 3389) connections in the security group.

(2) Create if you have not already done so, a “.pem” authentication file based on your AWS credentials and download it to your local machine.

(3) Change the permissions of the *pem file to owner-only access (chmod 600).

(4) Make sure your VPC setup assigns a public IP address to access the instance through your VPC. The AWS defaults should permit this. Note the public IP address assigned to the launched AMI instance.

(5) Connect by “ssh –I <your pem file name> ubuntu@<your instance public IP address> “.

To connect to the remote desktop server:

(6) Create a new user with “sudo adduser <your user name>” from within the “ubuntu” user account.

(7) Your Xrdp server should now be ready to accept connections through a remote desktop client. Make sure your security group allows connections through port 3389, the default RDP connection port. Upon logging into the MATE desktop, make sure to add a “Main Menu” panel for convenient use, or consult the MATE documentation to set up an Xrdp profile in your user directory.

(8) The Firefox browser is installed and ready for use in this server.

(9) There is a listing of all installed R packages in the ubuntu user directory. If you’re looking particularly for one, please consult the associated documentation at bioconductor.org . All packages have been updated to work with the R 3.5.1 installation in the AMI. You can add others as necessary with “BiocManager::install()” in the R console.

(10)A sample R script is included for an example use of this R installation at: “https://geisr-docs.s3.amazonaws.com/exH-LGG.txt” . Save this file to your user directory in your AWS instance and from the R console,and enter:

“source <path to sample script filename”. This example will import a low-grade glioma TCGA RNA-seq dataset and launch pcaExplorer for visualization. You can also try “Load the demo airway data” in this tool. Consult the “ExperimentHub” Bioconductor docs to work with other TCGA datasets for visualization. The SEQprocess package should also be usable to generate RNA-seq files for use with this tool.