mkatari-bioinformatics-august-2013-introlinuxnotes
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mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:07] – mkatari | mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:40] – mkatari | ||
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- | ====== | + | ====== |
The standard user interface for personal computers is a GUI (Graphical User Interface). However for linux it is a command-line interpreter called 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. | 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 '' | ||
+ | This opens a tunnel to your computer allowing all windows to open in your computer. | ||
+ | For this to work you need X11 installed on your computer (MobaXterm already has one) | ||
+ | MAC – Xquartz (http:// | ||
+ | Windows – Xming (http:// | ||
+ | |||
+ | < | ||
+ | Last login: Wed Jun 3 15:49:01 on ttys000 | ||
+ | Manpreets-MacBook-Pro: | ||
+ | Unauthorized access is prohibited. | ||
+ | mkatari@hpc.ilri.cgiar.org' | ||
+ | Last login: Wed Jun 3 16:33:26 2015 from 197.136.62.11 | ||
+ | [mkatari@hpc ~]$ emacs | ||
+ | |||
+ | </ | ||
+ | |||
+ | You should have a window popup on your computer that looks something like this. | ||
+ | |||
+ | {{: | ||
+ | |||
+ | Simply close the window to exit. | ||
+ | |||
+ | ====== Home Sweet Home ====== | ||
+ | |||
+ | When you first log in, you will be in a directory called “'' | ||
+ | < | ||
+ | / | ||
+ | </ | ||
+ | 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: '' | ||
+ | |||
===== Command Line Editing ===== | ===== Command Line Editing ===== | ||
Line 54: | Line 85: | ||
Once you press enter the program will be executed. When your prompt returns, you know that the program has finished. If there is an output to the program it usually prints it on the screen (often referred to as the standard output) | Once you press enter the program will be executed. When your prompt returns, you know that the program has finished. If there is an output to the program it usually prints it on the screen (often referred to as the standard output) | ||
- | In the example below, '' | + | In the example below, '' |
+ | < | ||
+ | [mkatari@hpc ~]$ date | ||
+ | Wed Jun 3 21:10:57 EAT 2015 | ||
+ | [mkatari@hpc ~]$ ls -l | ||
+ | total 19443152 | ||
+ | -rw-rw-r--. 1 mkatari mkatari | ||
+ | -rw-rw-r--. 1 mkatari mkatari | ||
+ | -rw-rw-r--. 1 mkatari mkatari | ||
+ | </ | ||
- | ====== Logging in with X Windows ====== | ||
- | In cases where a program requires a GUI, you should log in using the –X option. | + | ===== Directing standard output ===== |
- | This opens a tunnel to your computer allowing all windows to open in your computer. | + | |
- | For this to work you need X11 installed on your computer (MobaXterm already has one) | + | Instead letting the output print to the screen we can save it to a file by using the ''>'' |
- | MAC – Xquartz (http:// | + | |
- | Windows – Xming (http:// | + | The following command gets details about all users' home directories and saves them into a file called '' |
< | < | ||
- | Last login: Wed Jun 3 15:49:01 on ttys000 | + | |
- | Manpreets-MacBook-Pro: | + | [mkatari@hpc |
- | Unauthorized access is prohibited. | + | [mkatari@hpc |
- | mkatari@hpc.ilri.cgiar.org' | + | -rw-rw-r--. 1 mkatari mkatari 18897 Jun 3 21:26 allusers.txt |
- | Last login: Wed Jun 3 16:33:26 2015 from 197.136.62.11 | + | |
- | [mkatari@hpc ~]$ | + | |
</ | </ | ||
- | You should have a window popup on your computer that looks something like this. | ||
- | {{: | + | ===== Command-line completion ===== |
- | ====== Home Sweet Home ====== | + | 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 '' | ||
- | When you first log in, you will be in a directory called “home directory” | ||
< | < | ||
- | /home/<your username> | + | [mkatari@hpc ~]$ ls /usr/bin/bz |
+ | bzcat | ||
+ | bzcmp | ||
</ | </ | ||
- | 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: “cd ~” at the prompt. Unless appropriate changes have been made you can can not enter anyone’s directory or even see what is in it. | ||
+ | ===== 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 | ||
====== Some useful information about linux ====== | ====== Some useful information about linux ====== |
mkatari-bioinformatics-august-2013-introlinuxnotes.txt · Last modified: 2015/06/11 11:50 by mkatari