Installation

Download and install Amazon Genomics CLI

Download the Amazon Genomics CLI zip, unzip its contents, and run the install.sh script:

To download a specific release, see releases page of our Github repo.

To download the latest release navigate to https://github.com/aws/amazon-genomics-cli/releases/

Once you have downloaded a release, type the following to install:

The latest nightly build can be accessed here: s3://healthai-public-assets-us-east-1/amazon-genomics-cli/nightly-build/amazon-genomics-cli.zip

You can download the nightly by running the following:

aws s3api get-object --bucket healthai-public-assets-us-east-1 --key amazon-genomics-cli/nightly-build/amazon-genomics-cli.zip amazon-genomics-cli.zip

unzip amazon-genomics-cli-<version>.zip
cd amazon-genomics-cli/ 
./install.sh

This will place the agc command in $HOME/bin.

The Amazon Genomics CLI is a statically compiled Go binary. It should run in your environment natively without any additional setup. Test the CLI with:

$ agc --help

🧬 Launch and manage genomics workloads on AWS.

Commands
  Getting Started 🌱
    account     Commands for AWS account setup.
                Install or remove AGC from your account.

  Contexts
    context     Commands for contexts.
                Contexts specify workflow engines and computational fleets to use when running a workflow.

  Logs
    logs        Commands for various logs.

  Projects
    project     Commands to interact with projects.

  Workflows
    workflow    Commands for workflows.
                Workflows are potentially-dynamic graphs of computational tasks to execute.

  Settings ⚙️
    configure   Commands for configuration.
                Configuration is stored per user.

Flags
      --format string   Format option for output. Valid options are: text, table, json (default "text")
  -h, --help            help for agc
      --silent          Suppresses all diagnostic information.
  -v, --verbose         Display verbose diagnostic information.
      --version         version for agc
Examples
  Displays the help menu for the specified sub-command.
  `$ agc account --help`

If this doesn’t work immediately, try:

• start a new terminal shell
• modifying your $HOME/.bashrc (or equivalent file) appending the following line and restarting your shell:

export PATH=$HOME/bin:$PATH

If you are running this on MacOS, you may see this below popup window when you initially run any agc commands due to Apple’s security restrictions.

Click Cancel and navigate to Apple’s System Preferences, click Security & Privacy, then click General. Near the bottom, you will see a line indicating "agc" was blocked from use because it is not from an identified developer. To the right, click Allow Anyway.

Now go back to the terminal and run agc --help again. You will see this new popup window below asking you to override the system security.

Click Open and now your agc is correctly installed.

Verify that you have the latest version of Amazon Genomics CLI with:

agc --version

If you do not, you may need to uninstall any previous versions of Amazon Genomics CLI and reinstall the latest.

Command Completion

Amazon Genomics CLI can generate shell completion scripts that enable ‘Tab’ completion of commands. Command completion is optional and not required to use Amazon Genomics CLI. To generate a completion script you can use:

 agc completion <shell>

where “shell” is one of:

Bash

source <(agc completion bash)

To load completions for each session, execute once:

Linux:

agc completion bash > /etc/bash_completion.d/agc

macOS:

If you haven’t already installed bash-completion, execute the following once

brew install bash-completion

and then, add the following line to your ~/.bash_profile:

[[ -r "/usr/local/etc/profile.d/bash_completion.sh" ]] && . "/usr/local/etc/profile.d/bash_completion.sh"

Once bash completion is installed

agc completion bash > /usr/local/etc/bash_completion.d/agc

Zsh:

If shell completion is not already enabled in your environment, you will need to enable it. You can execute the following once:

echo "autoload -U compinit; compinit" >> ~/.zshrc

To load completions for each session, execute once:

agc completion zsh > "${fpath[1]}/_agc"

You will need to start a new shell for this setup to take effect.

fish:

agc completion fish | source

To load completions for each session, execute once:

agc completion fish > ~/.config/fish/completions/agc.fish

PowerShell:

agc completion powershell | Out-String | Invoke-Expression

To load completions for every new session, run:

agc completion powershell > agc.ps1

and source this file from your PowerShell profile.