mkatari-bioinformatics-august-2013-introlinuxnotes
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mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:15] – mkatari | mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/05 10:42] – mkatari | ||
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====== Logging in with X Windows ====== | ====== Logging in with X Windows ====== | ||
+ | |||
+ | The standard user interface for personal computers is a GUI (Graphical User Interface). However for linux it is a command-line interpreter called shell. | ||
+ | It is simply a prompt the awaits your command. There are several different shells, but the one used often is called “bash”, which is a mixture of a bunch of other shells. | ||
In cases where a program requires a GUI, you should log in using the '' | In cases where a program requires a GUI, you should log in using the '' | ||
Line 64: | Line 67: | ||
Generally in this directory you have complete control over creating, modifying, and executing files in this or any sub directory you create. In order to return to your home directory simply type the command: '' | Generally in this directory you have complete control over creating, modifying, and executing files in this or any sub directory you create. In order to return to your home directory simply type the command: '' | ||
- | ====== The Linux Shell ====== | ||
- | |||
- | The standard user interface for personal computers is a GUI (Graphical User Interface). However for linux it is a command-line interpreter called shell. | ||
- | It is simply a prompt the awaits your command. There are several different shells, but the one used often is called “bash”, which is a mixture of a bunch of other shells. | ||
===== Command Line Editing ===== | ===== Command Line Editing ===== | ||
Line 99: | Line 98: | ||
+ | ===== Directing standard output ===== | ||
+ | Instead letting the output print to the screen we can save it to a file by using the ''>'' | ||
+ | The following command gets details about all users' home directories and saves them into a file called '' | ||
+ | |||
+ | < | ||
+ | |||
+ | [mkatari@hpc ~]$ ls -l /home/ > allusers.txt | ||
+ | [mkatari@hpc ~]$ ls -l allusers.txt | ||
+ | -rw-rw-r--. 1 mkatari mkatari 18897 Jun 3 21:26 allusers.txt | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | ===== Command-line completion ===== | ||
+ | |||
+ | In some cases the commands or the file names that you need as arguments can be very long which increases the chance of spelling mistakes. | ||
+ | |||
+ | To prevent such mistakes simply type the enough letters to unambiguously identify the command or file and then pressing tab will complete it for you. | ||
+ | |||
+ | In the case you don’t know how many letters you need, simply press tab twice to see all your options. | ||
+ | |||
+ | In the example below, after typing the command and its options, the tab key was pressed twice to get this. The command will not be executed until the '' | ||
+ | |||
+ | < | ||
+ | [mkatari@hpc ~]$ ls /usr/bin/bz | ||
+ | bzcat | ||
+ | bzcmp | ||
+ | </ | ||
+ | |||
+ | ===== Wildcards ===== | ||
+ | |||
+ | In cases where you want to refer to multiple files you can use '' | ||
+ | |||
+ | In the example below, the first line gives all files/ | ||
+ | |||
+ | < | ||
+ | [mkatari@hpc ~]$ ls / | ||
+ | / | ||
+ | / | ||
+ | [mkatari@hpc ~]$ ls / | ||
+ | / | ||
+ | </ | ||
+ | |||
+ | SLIDE16 | ||
+ | |||
+ | wget ftp:// | ||
+ | |||
+ | [[ftp:// | ||
+ | ]] | ||
====== Some useful information about linux ====== | ====== Some useful information about linux ====== | ||
+ | |||
+ | |||
=== Environment variables and PATH === | === Environment variables and PATH === |
mkatari-bioinformatics-august-2013-introlinuxnotes.txt · Last modified: 2015/06/11 11:50 by mkatari