Unix

2025-09-03

Naming conventions

  • In general you want to name your files in a way that is related to their contents and specifies how they relate to other files.

  • The Smithsonian Data Management Best Practices has “Five precepts of file naming and organization”

Five precepts of file naming and organization

  • Have a distinctive, human-readable name that describes the content.
  • Follow a consistent pattern that is machine-friendly.
  • Organize files into directories (when necessary) that follow a consistent pattern.
  • Avoid repetition of semantic elements among file and directory names.
  • Have a file extension that matches the file format (no changing extensions!)

For specific recommendations we highly recommend you follow The Tidyverse Style Guide

The System

  • Instead of clicking, dragging, and dropping to organize our files and folders, we will be typing Unix commands into the terminal.

  • The way we do this is similar to how we type commands into the R console, but instead of generating plots and statistical summaries, we will be organizing files on our system.

  • The file system is hierarchical, you create directories (folders) in other folders

  • When you log in to a Unix computer you are in your home directory

  • the command line has a prompt that is configurable and is printed on screen to let you know that the terminal is ready for input

  • Environment variables control your computing environment and many are customizable by users

  • LLMs are useful tools for finding commands and getting help navigating through your first exposure to Unix and the ideas it is based on

The terminal

  • The terminal is integrated into Mac and Linux systems, but Windows users will have to install an emulator.

  • Once you have a terminal open, you can start typing commands.

  • You should see a blinking cursor at the spot where what you type will show up. This position is called the command line.

The filesystem

Files and permissions

  • within each directory you can create files and other directories

  • files whose names start with a period . are hidden by default; use ls -a to view them

  • files have permissions: use ls -lh to view details

drwxr-xr-x    4 robert  staff   128B Aug  8 10:03 bin
-rw-r--r--@   1 robert  staff    20M Jun 24 09:11 boots.png
-rw-r--r--@   1 robert  staff    26M Jun 23 15:23 boots1.pdf
  • you can read, write, or execute files and control who can see or use them by changing permissions

Working directory

  • The working directory is the directly you are currently in.

  • Commands you issue will generally take effect in this directory

  • You can see your working directory using the Unix command pwd

  • You can list the contents of the directory (files and other directories) using ls

  • You can find out about how ls works by issuing the command: man ls

Paths

  • The string returned by pwd command is the full path to the working directory.

  • The full path to your home directory is stored in an environment variable.

  • You can see it like this echo $HOME

Paths

  • In Unix, we use the shorthand ~ as a nickname for your home directory

    • Example: the full path for docs (image in prev. slides) can be written like this ~/docs.

  • A common default for the prompt is to show the path to the working directory (that path might be long, but you can change it)

  • Let’s open a terminal window and see what the prompt is.

  • you have an environment variable called PATH which you can display using echo

    • that variable is a set of individual paths, separated by : (colon) and it tells your Unix shell where to look for commands

    • you can modify that path, so that you can have it look for commands in other, non-standard places (eg make your own bin directory)

Unix commands

  • ls: Listing directory content

  • mkdir and rmdir: make and remove a directory

  • cd: navigating the filesystem by changing directories

  • pwd: see your workding directory

  • mv: moving files

  • cp: copying files

  • rm: removing files

  • more and less: display the contents of a file

Autocomplete

  • In Unix you can auto-complete by hitting tab.

  • This means that we can type cd d then hit tab.

  • Unix will either auto-complete if docs is the only directory/file starting with d or show you the options.

  • Try it out! Using Unix without auto-complete will make it unbearable.

Text editors

Command-line text editors are essential tools, especially for system administrators, developers, and other users who frequently work in a terminal environment. Here are some of the most popular command-line text editors:

  • Nano
  • Pico
  • Vi or Vim
  • Emacs

Other useful commands

  • curl - download data from the internet.

  • tar - archive files and directories into one file.

  • gzip - and other compression tools - make big files small

  • ssh - connect to another computer.

  • find - search for files by filename in your system.

  • grep - search for patterns in a file.

  • awk/sed - These are two very powerful commands that permit you to find specific strings in files and change them.

A deeper dive

  • The shell you use helps to organize and facilitate your interactions with the operating system

  • echo $SHELL will display the shell you are using

  • many software tools use hidden files and directories to provide customization e.g. .gitconfig or .ssh

  • most shells have two files that are commonly used to provide user level customization .zsh, and .zprofile

Resources

To get started.