Managing AWS instances

Please read Workshops Organisation if you haven’t done so.

The environments and configurations presented in the previous lesson, Setting Up Your Cloud and Terminal Environments, comprise a base development environment to create and manage AWS services with both the AWS Console and the AWS CLI (command line interface). If you are using an AWS personal account (that you created and configured as described in that lesson), you can create and manage any service in any AWS region, as your account was configured with the AdministratorAccess permissions policy which “Provides full access to AWS services and resources”. Towards using the Scripts to create and manage AWS instances, we will first need to configure Internet access for the instances. The instances configuration and the Scripts were designed for each instance to be accessed through a domain name and with the program ssh using an encrypted login key, as outlined below. Hence, we will create a base domain name from which the Scripts will create, for each instance, a subdomain name to identify and make each instance accessible with ssh. Creating a domain name in your AWS account will incur some cost, as low as US $5.00 per year or more depending on the suffix /top-level domain (TLD) that you choose for your base domain name. Examples of TLDs include: .com, .net, .org, .link, among many others (the cheapest in AWS is .link). If you already have a domain name in place, you can use that instead. Your account will also incur costs for any service you launch that is not included in the AWS Free Tier — check the lesson AWS Costs Explained from another Cloud-SPAN course, so you know your free limits.

If you are using an AWS institutional account (that was created and configured by the IT department in your institution), you will most likely not be directly responsible for the cost of using a domain name or any other service with your account. However, you may need to ask your IT department to configure a base domain name for you, or to follow some guidelines to specify the domain name. Your account may also have restrictions as to the AWS region where you can create and manage AWS services. For instance, the AWS institutionl account of the Cloud-SPAN project can only make use of services in the eu-west-1 Ireland region, and the Cloud-SPAN base domain name was suggested and configured by our IT department. If your institutional account is restricted to use an AWS region other than Ireland, you may need to ask your IT department to make a copy, to your AWS account, of the Amazon Machine Image (AMI) template used by the Scripts to create AWS instances. Your IT department should be able to help you with this and other matters; just let them know what you need to configure in your AWS account to use the Scripts, and whenever you come accross Access Denied or similar messages when using the Scripts.


We use the Scripts to create and manage multiple AWS instances for training. When running a workshop, a number of instances is created as a copy of an AMI that is configured with ‘omics data and software analysis tools that are relevant to the workshop. Each student is granted exclusive access to one instance.

Each instance is created to be accessed through a domain name using ssh and an encrypted login key file.

For example, using the base domain name of the Cloud-SPAN project,, the (sub) domain name for an instance named instance001 would be

Using the base domain name of an AWS personal account, for example,, the domain name for the same instance name would be

Once an instance is created, the end user will access the instance csuser account with ssh providing the name of the corresponding login key file as shown below.

Using the AWS Cloud-SPAN institutional account base domain name:

$ ssh -i login-key-instance001.pem     ### -i stands for identity file

Using the personal account based domain name:

$ ssh -i login-key-instance001.pem              

Each instance domain name is mapped to an IP address. Domain names, IP addresses, and login keys are created automatically on creating the corresponding instances, and deleted likewise when the corresponding instances are deleted.

Configure Instances Internet Access

Episode 1 will guide you to configure internet access for the instances you will create with the Scripts. This involves:

Instances Management Tasks Using the Scripts

Episode 2 is the guide to using the Scripts to create and manage multiple instances for a course /workshop. The episode shows:

AMIs Management

Episode 3 is about managing Amazon Machine Images (AMIs). As AWS instances are copies of an AMI, you need to create a new AMI if the software or data used in a course change, but there are other reasons that may require creating a new AMI. The episode presents the management of AMIs that we have done as part of managing AWS instances with the Scripts.

The Scripts Design

Episode 4 presents the organisation and workings of the Scripts, how the Scripts were developed using the AWS CLI Command Reference, and a few ideas to improve the Scripts.


00:00 1. Configure Instances Internet Access What is internet access for instances created with the Scripts?
How to configure such internet access?
00:30 2. Instances Management Tasks Using the Scripts How are the Scripts configured and run?
What is involved in creating and managing instances for a course/workshop?
01:00 3. AMIs Management What is an Amazon Machine Image (AMI)?
How are AMIs created and managed?
When to create a new AMI?
01:30 4. The Scripts Design How do the Scripts work?
What is the code structure of the Scripts?
How to improve the Scripts?
02:00 Finish

The actual schedule may vary slightly depending on the number of related topics you decide to explore further.