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====== Intro to using Linux via a command-line interface ======

The CLI, or command-line interface, is a very powerful way to interact with any computer. In Linux especially, the CLI is often the primary way to perform tasks. Additionally, you can write scripts to automate tasks over the command-line. So even when there is a GUI option, if you want to automate a task, learning how to do it using the command-line is essential.

A terminal is the actual application that you use (i.e. Terminal.app, cmd.exe, PowerShell, PuTTY, etc); it is the command-line environment on your computer from which you can use SSH to access the remote linux server.

===== SSH =====

SSH stands for "Secure SHell" and it is both a tool to open a connection to a remote server and the protocol that is used for the connection. A Shell is the actual command-line interface that you use; it is an interactive program where you can run commands to do things like navigate the file system ande run other programs (i.e. stata). I'll review basic commands below, and provide a link to further self-paced training.

The SSH protocol is Secure because it encrypts the communication channel. No one listening on the network can see any data or information about the connection other than where you are coming from and where you are connecting. Using SSH to encrypt communication is the backbone of many data security agreements.

==== Using SSH on Windows ====

Windows does not have a built-in SSH client application. You will need to install a command-line environment, such as the **Windows Subsystem for Linux**, or an SSH connection tool, such as **PuTTY.exe**

  * [[https://www.putty.org/|PuTTY]] (Recommended)
  * [[https://learn.microsoft.com/en-us/windows/wsl/install|Windows Subsytem for Linux (WSL)]]

If you use PuTTY, then simply download and run the PuTTY.exe program, then fill in the Host Name (or IP Address) field and click Open.

If you use WSL, then you would open the WSL terminal and type the following command to connect to the linux server:<code>
ssh username@server
</code>
  * where ''username'' is your user account name on the server
  * where ''server'' is the FQDN of the server

==== Using SSH on Mac ====

There is already a built-in application you can use on Mac. Simply open **/Applications/Utilities/Terminal.app**

And then run the command:<code>
ssh username@server
</code>
  * where ''username'' is your user account name on the server
  * where ''server'' is the FQDN of the server

===== List of Basic Commands =====

^ Command ^ Description ^
| <code>passwd</code> | Change your password  |
| <code>ls
ls -l </code> | List files/folders in the current directory((''-l'' is an option to show a detailed listing, with information such as file size, permissions, and timestamp))  |
| <code>cd myfolder/
cd ../</code> | Change directory to another folder in your current folder or go up one directory to the parent folder  |
| <code>cd /data/my/example/folder/</code> | Change directory to another folder outside your current directory. Notice the leading ''/'' indicating an absolute path(([[https://swcarpentry.github.io/shell-novice/02-filedir/index.html|see this link]] for more information about absolute vs relative paths and how to navigate directories))  |
| <code>cd</code> | Change directory back to your home directory  |
| <code>pwd</code> | Print your current working directory  |
| <code>mkdir newname</code> | Make a directory named "newname"  |
| <code>rmdir newname</code> | Remove an empty directory named "newname" (only works if it is empty)  |
| <code>rm myfile</code> | Delete a file "myfile"  |
| <code>rm file*
rm -f file*</code> | Delete all files matching the pattern "file*" - be very careful with this!((It is a good idea to test a pattern with ''ls file*'' to make sure you are erasing what you intend. There is NO RECYCLE BIN in Linux, but it will ask you to confirm deleting each file. If you are sure you want to erase all matching files, and you don't want to confirm each one by pressing "y", then you can use the option ''-f'' to force the deletion))  |
| <code>cp myfile myfile2</code> | Copy a file named "myfile" to a new file named "myfile2"  |
| <code>mv myfile myfile2</code> | Move a file named "myfile" to a new file named "myfile2"  |
| <code>cat somedata.txt
less somedata.txt</code> | Display the contents of a file named "somedata.txt"((cat prints to the screen, less is interactive and you use arrow keys or j/k keys to move down/up, respectively))  |
| <code>grep "string" myfiles*</code> | Search for the word "string" in all files with filenames matching the pattern "myfiles*"((read more about pattern matching [[https://swcarpentry.github.io/shell-novice/aio/index.html#using-wildcards-for-accessing-multiple-files-at-once|here]])), then print matching results  |
| <code>man grep</code> | Read a manual page (help page) about the command "grep" or any command you specify  |
| <code>stata</code> | Run stata, if stata is installed  |

=== Tab Completion ===
You can also use tab-completion by typing a command and hitting the "tab" key twice to show potential commands that match what you have typed. For example, if there are multiple versions of stata installed, type "stata" and hit tab twice to see all matching commands.

===== Self-paced online lessons =====

There is a lot more you can do. This brief overview is just an idea to get you started. I highly recommend the links below for additional resources. They have lessons that you can work through on your own to become more familiar with all the above commands and go even more in depth:

  * [[https://swcarpentry.github.io/shell-novice/|Software Carpentry - Shell Novice]]
  * [[https://ubuntu.com/tutorials/command-line-for-beginners#3-opening-a-terminal|Ubuntu - The Linux command line for beginners]]