Aegea: Amazon Web Services Operator Interface

Aegea is a command line interface (CLI) that provides a set of essential commands and terminal dashboards for operators of Amazon Web Services (AWS) accounts. Aegea lets you build AMIs and Docker images using the cloud-init config management package, manage config roles, launch and monitor instances and services, and manage AWS resources including ELB, RDS, and AWS Batch. Aegea is designed to be used in conjunction with the existing functionality of the AWS CLI and boto3. Aegea can be used in conjunction with tools like MiniWDL to orchestrate large-scale MLops and genomics workflows.

Installation

pip install aegea

Run aws configure to configure IAM access credentials that will be used by the aws and aegea commands. You can create a new IAM key at https://console.aws.amazon.com/iam/home#/users. See the AWS CLI documentation for more details.

Aegea commands

Below are some highlights from Aegea's suite of commands. Run aegea --help to see the full list of commands.

Command	Key functionality
aegea ls	List running EC2 instances
aegea launch	Launch EC2 instances and specify options such as spot tenancy, AMI, instance type, etc.
aegea ssh, aegea scp	Connect to running instances, transfer files using AWS Systems Manager or other options
aegea batch	Submit, manage and monitor AWS Batch jobs
aegea ecs	Monitor ECS clusters and run Fargate tasks
aegea build-ami	Build EC2 AMIs using cloud-init configuration scripts
aegea build-docker-image	Build AWS ECR docker images using Dockerfiles or cloud-init scripts
aegea logs	Download AWS CloudWatch Logs contents using S3 export
aegea grep	Query AWS CloudWatch Logs contents using CloudWatch Logs Insights
aegea cost	List AWS cost reports generated by AWS Cost Explorer
aegea secrets	List and manage secrets stored in AWS Secrets Manager
aegea cloudtrail	Query AWS CloudTrail events to audit the security of your AWS account

Aegea Launch

The aegea launch command launches EC2 instances. It has integrated support for AWS SSM/EC2 Instance Connect, runtime cloud-init configuration, automatic location of Aegea-built AMIs or up-to-date Ubuntu or Amazon Linux AMIs, automatic storage configuration, and other options.

Aegea SSH

The aegea ssh command (and its variant aegea scp) is an SSH configuration wrapper that integrates with the AWS Systems Manager and EC2 Instance Connect to provide SSH connectivity to your instances without opening any inbound ports (if your instance OS is not configured with SSM, use aegea ssh --no-ssm to open a direct connection). aegea ssh securely resolves instance addresses by name and pre-fetches their public keys without the Trust-On-First-Use requirement.

Visual Studio Code Remote Development integration

Visual Studio Code provides a remote development extension pack which allows your VSCode IDE to connect remotely to AWS instances. To use VSCode with aegea ssh, open the Remote.SSH plugin settings (command palette > Remote-SSH: Settings) and enter the path to the aegea-ssh executable under the "Remote.SSH: Path" setting (for example, /usr/local/bin/aegea-ssh). After doing this, you can use the "Remote-SSH: Connect to Host" palette command to connect to any aegea-launched instance by name or ID (for example, aegea launch my-test-instance followed by entering my-test-instance in the Connect to Host dialog). Note that VSCode will use the default AWS CLI profile for authentication.

Aegea Batch

The AWS Batch API lets you run non-interactive command line workflows in Docker containers, managing AWS ECS, Fargate, and EC2/Spot in your account on your behalf. Use the aegea batch family of commands to interact with AWS Batch. The key command is aegea batch submit to submit jobs.

Run aegea batch submit --command "echo 'hello world'" --memory 4096 --vcpus 2 --watch to run a Batch job that requires 4 GB RAM and 2 cores to be allocated to the Docker container, and executes the specified command.

You can also use aegea batch submit --execute FILE. This will slurp up FILE (any type of shell script or ELF executable) and execute it in the job's Docker container.

The concurrency and cost of your Batch jobs is governed by the "Max vCPUs" setting in your compute environment. To change the capacity or other settings of the default compute environment used by aegea batch, go to https://console.aws.amazon.com/batch/home?region=us-east-1#/compute-environments, select "aegea_batch", and click "Edit".

Batch and ECS Fargate

The ECS Fargate API is an interface to the AWS container-based virtualization platform, Firecracker. ECS Fargate allows you to run workloads in fully managed containers: no instances run in your account; you are billed by the second of container use, and containers start up within 10 seconds, compared to minutes for EC2 instances.

AWS Batch can run your jobs on either ECS Container Instances (EC2 instances connected to ECS that Batch manages in your account) or directly in ECS Fargate containers. While Fargate containers are much faster to start, they have lower CPU and memory limits of 4 CPUs and 30 GB RAM (compared to 96 CPUs and 768 GB RAM on EC2).

By default, aegea batch will create and use an AWS Batch compute environment and queue that uses ECS Fargate, but you can control this by setting the --compute-type option to aegea batch create-compute-environment.

Aegea also supports direct use of ECS Fargate without Batch via the aegea ecs run command. Most aegea batch semantics are applicable to aegea ecs, which interacts with ECS via the "one shot" ECS RunTask API.

Configuration management

Aegea supports ingesting configuration from a configurable array of sources. Each source is a JSON or YAML file. Configuration sources that follow the first source update the configuration using recursive dictionary merging. Sources are enumerated in the following order of priority:

Command line options (values take priority over all other sources)
Any sources listed in the colon-delimited variable AEGEA_CONFIG_FILE
User configuration source, ~/.config/aegea/config.yml
Site-wide configuration source, /etc/aegea/config.yml
Configuration defaults from base_config.yml

Array merge operators: When loading a chain of configuration sources, Aegea uses recursive dictionary merging to combine the sources. Additionally, when the original config value is a list, Aegea supports array manipulation operators, which let you extend and modify arrays defined in underlying configurations. For example, to enable full S3 access for all instances launched with aegea launch, add the following to ~/.config/aegea/config.yml:

launch:
  iam_policies:
    $append: AmazonS3FullAccess

To enable S3 and SQS access, and also list the instance private IP address and availability zone in aegea ls, add the following:

launch:
  iam_policies:
    $extend:
      - AmazonS3FullAccess
      - AmazonSQSFullAccess
ls:
  columns:
    $extend:
      - private_ip_address
      - placement.AvailabilityZone

For a listing of available configuration parameters that can be set, run aegea configure or see https://github.com/kislyuk/aegea/blob/develop/aegea/base_config.yml. See https://github.com/kislyuk/tweak#array-merge-operators for a formal description of the array merge operators.

Building AMIs and Docker images

Aegea includes a lightweight configuration management system for building machine images based on cloud-init (both Docker images and AMIs are supported).