Getting Comfortable on the Command Line

Learning objectives

• Set up and customize your machine’s command line
• Access a server via SSH (secure socket shell)

Command Line

Why use Command Line?

• On a server, administrative interaction is via the command line
  
• Many tasks are quicker and easier

Admin via GUI

In some organizations, server admin tasks are done via a graphical tool, but this is a red flag.

It means that the organization is either trying to find relatively low-paid (and probably low-skilled) admins or are using a graphical tool to limit what IT/Admins can do. Either way, it’s going to be harder to get things done.

Getting the command line you want

• The terminal is the GUI where you’ll type in commands
  

• RStudio, Positron, and VS Code have built-in terminals
  

• Author recommends iTerm2 for MacOS

• The shell takes the commands you type and runs them
  

• Matches the commands you type to actual programs on your system, e.g. Rscript, positron, code, git, etc.

• MacOS and Linux have bash and zsh, while Windows comes with Command Shell (cmd) and the PowerShell. Also, git bash on Windows
  

• Windows Subsystem for Linux (WSL) is another option

Configuration management

Customization tools for window/tab behavior and text theme/plugins:

• MacOS: Prezto or OhMyZsh. Three places to configure:
  • iTerm2 preferences
    
  • the zsh configuration file .zshrc
    
  • Prezto configuration file .zpreztorc
• Author recommends looking into Git plugins, auto-completion and command history search functionality
  
• Windows: Oh My Posh for PowerShell

Text editors

• IDE (RStudio, Positron, o VS Code)
  
• Standalone: Sublime or Notepad++ (Windows only)

SSH

Secure server connections with SSH

• Remotely accessing a server from the command line on your machine
• SSH (Secure Socket Shell) is a tool for making a secure connection to another computer over an unsecured network
  
• SSH requires invoking the ssh command line interface from a local host (your computer) with a username and the remote host’s (server’s) address.

For example, connecting to the server at server.example.com as the user alex would look like:

> ssh alex@server.example.com

Understanding SSH Keys

• Configure your SSH keypair (public key and private key)
  • Public key: Register anywhere you’re trying to SSH into.
  • Private key: Secret
    
• Public key is the lock and private key is the key

Public Key Cryptography

• Public key cryptography is the underlying technology
  
• Never move the private key from the computer where it was created and never share it

Practical SSH usage

• Step 1: Create a keypair on the machine you are SSHing from. Public key has .pub suffix. id_<encryption type> is the standard way to name the key
• Step 2: Register a public key to SSH into a server
  • Add the public key to the end of your .ssh/authorized_keys file in your home directory
    
  • Ensure the permissions on the authorized_keys file are correct
    
• Step 3: To use SSH, type ssh <user>@<host>
  • You can specify a particular key with the -i flag
    
  • Set up an SSH config file if you use SSH a lot. That would shorten ssh -i my-ssh-key alex@server.example.com to ssh alex-server

Continuous connection and debugging

• SSH blocks the terminal it’s using and the connection will break when your computer goes to sleep
  
• Use tmux command line utility to:
  • Put sessions into the background
    
  • Make sessions durable through sleeps and other operations
• For debugging SSH: Add a -v to your command for verbose mode
  • Add another v for more verbosity with -vv, and if that’s not enough, add another v for super verbose mode