class: title-slide, middle, center # Unix and the command line ## Robert Castelo [robert.castelo@upf.edu](mailto:robert.castelo@upf.edu) ### Dept. of Medicine and Life Sciences ### Universitat Pompeu Fabra <br> ## Fundamentals of Computational Biology ### BSc on Human Biology ### UPF School of Medicine and Life Sciences ### Academic Year 2024-2025 --- ## The Unix operating system .pull-left[ * An _operating system_ (OS) is a software that enables the use and manipulation of the different physical devices forming a computer. &nbsp;&nbsp; * The Unix OS ([Ritchie and Thompson, 1974](https://doi.org/10.1145/361011.361061); [Kernighan and Pike, 1984](https://en.wikipedia.org/wiki/The_Unix_Programming_Environment)) was born on 1969 as a result of a research project at [Bell-Labs](http://www.bell-labs.com/history/unix), USA. ] .pull-right[  ] .footer[ Ken Thompson (seated) types as Dennis Ritchie (standing) looks on in 1972, shortly after they and their Bell Labs colleagues invented Unix. Image and caption taken from [The strange birth and long life of Unix. _IEEE Spectrum_, 2011.](https://spectrum.ieee.org/tech-history/cyberspace/the-strange-birth-and-long-life-of-unix) ] --- ## The Unix operating system * The group of engineers that developed Unix already made other attempts to develop an OS in the 60s, such as [Multics](https://en.wikipedia.org/wiki/Multics). &nbsp;&nbsp; * However, only after they developed the [B programming language](https://en.wikipedia.org/wiki/B_%28programming_language%29) they succeeded to develop the first version of Unix, which was written in this language. &nbsp;&nbsp; * The [B programming language](https://en.wikipedia.org/wiki/B_%28programming_language%29) was the precursor of the widely-used [C programming language](https://en.wikipedia.org/wiki/C_%28programming_language%29) ([Kernighan and Ritchie, 1978)](https://en.wikipedia.org/wiki/The_C_Programming_Language). &nbsp;&nbsp; * There are many [variants](https://www.levenez.com/unix) of Unix, one of the most popular ones is [Linux](https://en.wikipedia.org/wiki/Linux) but also [Android](https://en.wikipedia.org/wiki/Android_%28operating_system%29), [iOS](https://en.wikipedia.org/wiki/IOS) and [macOS](https://en.wikipedia.org/wiki/MacOS) are based on a Unix OS. &nbsp;&nbsp; * Did they use the Unix OS 50 years ago in the same way we use it now? --- background-image: url(data:image/png;base64,#img/Computers60s_2500x2010.jpg) background-position: center background-color: white background-size: cover ## The Unix operating system <div class="footer"> <p style="color:white">Big computers, big hair: the women of Bell Labs in the 1960s - in pictures.<br> <a href="https://www.theguardian.com/technology/gallery/2016/feb/13/future-women-the-bell-lab-computer-operators-of-the-1960s-in-pictures-women-in-computing" target="_blank">The Guardian, Sat 13 Feb 2016</a> </p> </div> --- ## The Unix operating system .pull-left[  ] .pull-right[ "Twenty years ago, a girl could be a secretary, a schoo teacher ... maybe a librarian, a social worker or a nurse. If she was really ambitious, she could go into the professions and compete with men ... usually working harder and longer to earn less pay for the same job. Now have come the big, dazzling computers -and **a whole new kind of work for women: programming.**" See [The Computer Girls: 1967 Cosmo article highlights women in technology](https://www.siliconrepublic.com/people/women-in-technology-the-computer-girls-cosmopolitan) ] <div class="footer"> <p>The Computer Girls. <a href="https://archive.org/details/the-computer-girls-cosmopolitan-magazine-april-1967/The%20Computer%20Girls%20-%20Cosmopolitan%20magazine%20%28April%201967%29%20%5Bocr%5D/" target="_blank">Cosmopolitan magazine, April 1967.</a> </p> </div> --- ## The Unix operating system * The Unix OS is organized into **layers**.  * The [_graphical user interface_ (GUI)](https://en.wikipedia.org/wiki/Graphical_user_interface) layer appeared later and the Unix OS was conceived to be used through the shell layer. &nbsp;&nbsp; * The [_shell_](https://en.wikipedia.org/wiki/Unix_shell) layer is a [_command-line user interface_ (CLI)](https://en.wikipedia.org/wiki/Command-line_interface) that allows the user to interact with the computer by writing commands through a [_computer terminal_](https://en.wikipedia.org/wiki/Computer_terminal) or a [_terminal emulator_](https://en.wikipedia.org/wiki/Terminal_emulator). --- ## The computer terminal  .footer[ A DEC VT100 computer terminal. Image taken from [Wikipedia](https://en.wikipedia.org/wiki/Computer_terminal). ] --- ## The terminal window  --- ## The terminal window * Nowadays, every OS (Windows, macOS or Linux) starts up with a GUI. &nbsp;&nbsp; * The terminal window is just an application with an icon similar to this one:  * In Linux is located next to every other application. &nbsp;&nbsp; * In macOS is located in `Applications -> Utilities`. &nbsp;&nbsp; * In Windows you need to install some Unix emulator such as [Git for Windows](https://gitforwindows.org) (using its Git Bash application). &nbsp;&nbsp; * Other options for Windows in increasing order of complexity are: * Running a Unix system in the [cloud](https://en.wikipedia.org/wiki/Cloud_computing) and access it through the browser. You require a stable internet connection and you normally have to pay for it. * Running a [virtual machine](https://en.wikipedia.org/wiki/Virtual_machine) and installing in it a Linux system. * [Partitioning the hard drive disk](https://en.wikipedia.org/wiki/Disk_partitioning) and install Windows in one of the partitions, and Linux in the other one. --- ## The terminal window * At this point, you may ask yourself why do we want to work with a Unix command-line in a terminal window. &nbsp;&nbsp; * The answer is because the command-line allows you to use computing in a modular, efficient and reproducible way: * Modularity: reusing and chaining computations. * Efficiency: automatizing workflows. * Reproducibility: recording computing steps. * In summary, the command-line facilitates the release of your full potential as a computational biologist.. -- <img style="float:left; margin-left:40px;" src="data:image/png;base64,#img/captainmarvel.gif" height=137/> <img style="float:right; margin-right:80px;" src="data:image/png;base64,#img/hulk.gif"/> --- ## The Unix filesystem * A fundamental component of any OS is the [filesystem](https://en.wikipedia.org/wiki/File_system) that the OS uses to store data. &nbsp;&nbsp; * The filesystem determines the way in which files are organized and the GUIs in currently available OSs provide a graphical interface to this organisation. &nbsp;&nbsp; * We want to learn here how to work with the filesystem through the Unix command-line: * High-level understanding about how the filesystem stores files in the computer. &nbsp;&nbsp; * Learn filesystem commands and the syntax to specify them in the shell. --- ## The Unix filesystem * A graphical representation of the Unix file system is through a [hierarchy](https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard), sometimes referred to as a tree.  * We have two main types of files in the filesystem: regular files and directories. &nbsp;&nbsp; * Directories can store regular files and other directories. &nbsp;&nbsp; * On top of the hierarchy we have the [root directory](https://en.wikipedia.org/wiki/Root_directory), which can be likened to the trunk of a tree, as the starting point where all branches originate from. --- ## The Unix filesystem * [Path](https://en.wikipedia.org/wiki/Path_%28computing%29): unique location in the filesystem represented by a sequence of directories, optionally ending with a regular file, separated by the slash character `/`, for instance, `/home/professor/notes`  * When we start the shell in a terminal window, we have by default access to a specific working directory in the filesystem: our [home directory](https://en.wikipedia.org/wiki/Home_directory), which can be coded in a path by writing the tilde character (`~`), e.g., `~/notes` --- ## The Unix filesystem * [Current working directory (CWD)](https://en.wikipedia.org/wiki/Working_directory): directory where we have default access, which can be coded in a path by writing a dot (`.`), for instance, `./notes`  * **Previous directory**: directory containing the CWD, which can be coded in a path by two consecutive dots (`..`): `../examens` &nbsp;&nbsp; * **Absolute path**: path starting at the root directory: `/home/professor/notes` &nbsp;&nbsp; * **Relative path**: path starting at some given CWD: `./notes`, `../examens`, etc. --- ## Unix commands The syntax of Unix commands is the following: `$ command [options] [arguments]` where * **$**: is the [command prompt](https://en.wikipedia.org/wiki/Command-line_interface#Command_prompt), which we **should not** write and merely indicates that the rest of the line should be written in the shell. &nbsp;&nbsp; * **command**: is the name of the instruction that we want to execute. For instance, to copy a file we should use the command `cp`. &nbsp;&nbsp; * **options**: one or more words starting with a hyphen (`-`) separated by spaces, i.e., `-r` or `-lha`, that tune the behavior of the command. &nbsp;&nbsp; * **arguments**: one or more words separated by spaces that specify input information that the command needs to perform its task. The (square) brackets `[` and `]` are used above to indicate that not all commands have options and arguments. --- ## Unix file commands Examples of Unix commands that manipulate files: * listing files: &nbsp;&nbsp; `$ ls` &nbsp;&nbsp; * copying files: &nbsp;&nbsp; `$ cp ~/Downloads/data.zip .` &nbsp;&nbsp; * removing files: &nbsp;&nbsp; `$ rm data.zip` &nbsp;&nbsp; * showing CWD: &nbsp;&nbsp; `$ pwd` &nbsp;&nbsp; * changing CWD: &nbsp;&nbsp; `$ cd data` --- ## Unix commands to explore file contents Examples of Unix commands that explore the contents of [text files](https://en.wikipedia.org/wiki/Text_file): * beginning of a text file: &nbsp;&nbsp; `$ head filename` &nbsp;&nbsp; * end of a text file: &nbsp;&nbsp; `$ tail filename` &nbsp;&nbsp; * whole text file: &nbsp;&nbsp; `$ cat filename` &nbsp;&nbsp; * paging text files: &nbsp;&nbsp; `$ more filename` --- ## Redirecting terminal output to a file * Unix offers a mechanism to [redirect](https://en.wikipedia.org/wiki/Redirection_%28computing%29) to a file, the output printed in the terminal window. `$ command > file`  --- ## Concluding remarks * Most Unix filesystems are case-sensitive, a wrong upper-case letter may lead to an error. Syntax must be precise and the [devil is in the detail](https://en.wikipedia.org/wiki/The_devil_is_in_the_detail). &nbsp;&nbsp; -- * The shell interprets commands by reading words separated by space characters. Using space characters in filenames becomes problematic in the command line. &nbsp;&nbsp; -- * **.red[DO NOT]** use spaces or any other non-standard [ASCII](https://en.wikipedia.org/wiki/ASCII) character such as `ñ`, `ç`, accents, etc., in filenames. &nbsp;&nbsp; -- * **.red[DO NOT]** use spaces or any other non-standard [ASCII](https://en.wikipedia.org/wiki/ASCII) character such as `ñ`, `ç`, accents, etc., in filenames. &nbsp;&nbsp; -- * Use [snake case](https://en.wikipedia.org/wiki/Snake_case) (e.g., `raw_data.csv`) or [camel case](https://en.wikipedia.org/wiki/Camel_case) (e.g., `rawData.csv`) instead of spaces to specify meaningful filenames. &nbsp;&nbsp; -- * You do not learn Unix and the command line by only reading through these slides. **You need to do the practicals and the assignments** to actually learn how to do stuff.