Unix tutorial for scientists
You have heard it before : "I can write a script in Unix that will do in 5 seconds what you do in Excel in an hour", or if you haven't, you have thought: "There has to be a better way than clicking mindlessly for an hour". You would love to save time, but you don't know where to start. All tutorials on the web look like gibberish when you read them. This hopes to give you an overview of what it means "to write a Unix script" or "use Unix", what it can do and how to do it. At the end of this document, you will find a list of simple commands that you can cut and paste on your computer to do tasks that could be of general interest.
Note: Often, people will use these terms interchangeably: programming in Unix, or using Unix, shell programming, script writing, bash, sh, csh, perl, python, programming. You will learn below what it means to use a shell or write a script, and why these appear to be synonyms.
Introduction
Command-line tools can save you a lot of time because they can process large number of files very rapidly. They are called command-line tools because they require you to type a text command on a line instead of requiring you to point and click in a Graphical User Interface (or GUI). These tools are often called, or thought of as, Unix because the operating system Unix originally could only accept commands as text commands and includes a multitude of such tools. As an extension, Unix became a synonym (in people's minds) for command-line tools.
These tools are meant to operate on files or directories. Hence, they are accessed usually through a shell that places you into the file system, inside a given directory. Typically, you start a program called a Terminal, that will start a shell and place you in your main directory (or your home directory). Here is an example from Mac OS X Terminal.app application:
Here are examples of command-line tools (from now on, called simply tools or commands).
- The pwd command (print working directory) will tell you what directory you are in.
- The ls command (list), in its simplest form, will list all files in the current directory. In its most complex form, it can list files, order them by modification date and colour them depending on what type they are.
- The find command, in its simplest form, can find files with a certain name. In its most advanced form, it can find certain directories modified after a certain date and act on the group of directories or a group of files contained in them.
- The gzip command (gnu zip) will compress a file or multiple files
Starting
More to come.
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