---
title: "Installation"
date: 2021-09-07T13:42:31-04:00
draft: false
weight: 20
---

## 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](https://github.com/aws/amazon-genomics-cli/releases) 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:

```shell
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
```

```shell
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.

![image of cannot open popup](agc-cannot-open-popup.png)

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.

![image of cannot verify developer popup](agc-cannot-verify-developer-popup.png)

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:

```shell
 agc completion <shell>
``` 

where "shell" is one of:

### Bash

```shell
source <(agc completion bash)
```

To load completions for each session, execute once:
#### Linux:
```shell
agc completion bash > /etc/bash_completion.d/agc
```

#### macOS:

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

```shell
brew install bash-completion
```

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

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

Once bash completion is installed

```shell
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:

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

To load completions for each session, execute once:

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

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

### fish:

```shell
agc completion fish | source
```

To load completions for each session, execute once:
```shell
agc completion fish > ~/.config/fish/completions/agc.fish
```
PowerShell:

```shell
agc completion powershell | Out-String | Invoke-Expression
```

To load completions for every new session, run:

```shell
agc completion powershell > agc.ps1
```

and source this file from your PowerShell profile.