2 Run the installer

Run Installer

Download & execute the bootstrap script like this:

$ wget -qO install_bootstrap https://github.com/ICGC-TCGA-PanCancer/cli/releases/download/L4A_1.0.1/install_bootstrap && bash install_bootstrap

This script will install docker (you can skip this step by answering "N" if you already have docker installed), the pancancer_launcher image, and collect some basic configuration info to get the launcher started.

When the launcher asks "Would you like to run the pancancer_launcher now?", answer "Y" to begin the next step, where you will be asked to provide answers to some questions. It will need to know:

• The path to your AWS pem key file (this should be copied into ~/.ssh on your host VM before begining the installer, as per instructions above), for example: /home/ubuntu/.ssh/MyKeyFile.pem.
• The name of your AWS key. This is usually the same as the name of the key file you download from AWS. For example, an AWS key with the name "MyKey" is normally downloaded and saved as the file "MyKey.pem".
• Your AWS Key and AWS Secret Key. If you do not know these, this document might be able to help you.
• The name that you would like to give to your fleet. This will make it easier to find your VMs in the AWS EC2 Management Console. If you do not specify a fleet name, a randomly generated name will be used.
• The maximum number of VMs you want to have in your fleet (you will be able to change this later, if you want).
• The name of the security group for your fleet, which was set in this step. It needs this so that it can update the permissions of this group so that the VMs in the fleet can communicate properly with each other. This must be the same as the security group that the launcher is in. If you are not sure about the name of your security group, you can find it in the AWS EC2 console: Find your host VM, and then look for the "Security Group" column. This will show you the name of the security group of your VM.

If for some reason you need to exit this script, you can re-run it simply by executing this command:

bash install_bootstrap

Click here to read about working inside the Pancancer Launcher.