The Command Shell

What is a Shell

The shell is a command line interface to your computer.
The shell can be used to
- start and stop processes that run programs;
- create and delete files and directories (a.k.a folders);
- set environment variables;
- manage processes and process resources;
- automate tasks.
The most common shells on Linux and MacOS are bash and tcsh.
Windows provides the cmd shell and the Power Shell; bash is becoming available as well.
- cmd is very bare bones; Power Shell is more powerful.
- They provide similar facilities to the Linux/MacOS shells but under different names.
- If you install Git for Windows, which is recommended, you also get a light-weight version of the bash shell.
RStudio’s Tools menu provides the Terminal option for starting a shell terminal.
Terminal refers to the graphical user interface; the program running in a terminal is a shell.

hostname prints the name of the computer the shell is running on.
pwd prints the current working directory.
ls lists files in a directory:
- ls lists files in the current directory;
- ls foo lists files in a sub-directory foo;
cd changes the working directory:
- cd or cd ~ moves to your home directory;
- cd foo moves to the sub-directory foo;
- cd .. moves up to the parent directory;
mkdir foo creates a new sub-directory foo in your current working directory;
mv moves and renames files. BE CAREFUL IF THE FILES ARE UNDER VERSION CONTROL!
rm, rmdir can be used to remove files and directories; BE VERY CAREFUL WITH THESE!!!

Typing the name followed by the Enter key runs the program and waits until it finishes.
Typing the name followed by & and the Enter key runs the program in background and the shell returns immediately for your next command.
This is useful for starting GUI programs from the shell; for example, to start RStudio on a Linux machine you could use
```
rstudio &
```
Some Programs can take command line arguments, often names of files to process.
To start RStudio and open a file hw1.Rmd:
```
rstudio hw1.Rmd &
```

You can find out using the shell command
```
echo $SHELL
```
For most simple things it doesn’t matter.
On the CLAS systems you can change your default shell at https://hawkid.uiowa.edu/. You may have to do this from on campus or over a VPN connection.

You can find a bit more on the shell at