Introduction to Bio-Linux

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File naming conventions a.) Certain characters should not be used in filenames in Linux/Unix. If you stick with letters, numbers, hyphens, underscores and full stops, you will be fine. b.) Linux/Unix cannot deal with spaces in filenames! Make sure your filenames do not contain them. Filenames with spaces in them are a common problem when transferring files to Linux/Unix from a computer running Windows, or Mac operating systems. If you end up with filenames with spaces in them, you will need to enclose the entire filename in quotation marks so that Linux/Unix understands that the space is part of the name. Alternatively, you can “escape” the space using a backslash. For example, if I have a file called my document Linux/Unix will see this as two filenames, “my” and “document”. But you could write either of the following to make it understand you mean a single file: “my document” my\ document We advise that you change the name of such files to remove the space. A common practice is to replace the space with an underscore. E.g. mv “my document” my_document Keeping points a and b in mind, the files in your account can be named whatever you like. If you have a lot of files with names including spaces in your account on your Bio-Linux machine (or which you will be moving into your account), then please get in touch with us – we may be able to help you automate the renaming of these files. Having said this, please note that there are common naming conventions in place that you should try to follow. More is said on this in the bioinformatics practical. 4
Basic commands It is possible for users to achieve a great deal with only a small number of commands. Anatomy of a Command Linux/Unix commands usually take the form: command parameters arguments what I want to do how I want to do it on what do I want to do it You have already seen a command with this structure when you used ls with the parameter l and the argument of a file or directory name. ls -l intro_pract Some commands may not need parameters or arguments, or will use defaults if nothing is specified, but most will have options available to you if you choose to use them. For example, just typing ls will list the contents of the current directory. If a command is executed without any problems, it will usually not report anything back to you, (unless reporting to you was the purpose of the command!). If the command does not execute properly, you will often see an error message returned. Whether or not the error is meaningful to you depends on what your level of experience with Linux/Unix is and how user-friendly the errors generated by that command were designed to be. Linux/Unix shorthand and shortcuts At first understanding example Linux/Unix commands can seem daunting. This is often due to shorthand that can be employed when using commands. However, the common shorthand characters are very useful. The following incomplete list covers the symbols you will see most often today and describes their meanings as you will most likely encounter them in this course. Warning: some symbols have different meanings depending where they are used, A short incomplete list includes: * matches any character appearing 0 or more times, also known as a wildcard ls mydir/* list all the files under the directory mydir ls cat* list all files starting with the letters cat 5
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Introduction to Bio-Linux

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