mkatari-bioinformatics-august-2013-introlinuxnotes
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mkatari-bioinformatics-august-2013-introlinuxnotes [2013/08/13 15:58] – mkatari | mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 17:57] – [Command Line Editing] mkatari | ||
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- | ====== | + | [[mkatari-bioinformatics-august-2013|Back to Manny' |
+ | |||
+ | ====== | ||
+ | |||
+ | It is a free and open source operating system released in 1991 under the GNU GPL license.GPL allows anyone | ||
+ | |||
+ | It is the leading operating system of choice for servers such as supercomputers. | ||
+ | More than 90% of the top 500 fastest computers are based on Linux. | ||
+ | |||
+ | MAC computers are related to Linux because they are also based on UNIX | ||
+ | |||
+ | Depending on the purpose of the Linux machine, it may or may not have a Desktop environment that we are familiar with on our personal computers. Linux uses X Window System to provide the Desktop environment. | ||
+ | |||
+ | A popular distribution of Linux operating system is called Ubuntu. | ||
+ | |||
+ | REF: [[http:// | ||
+ | |||
+ | ====== Why do bioinformaticians use Linux? ====== | ||
+ | |||
+ | * Many bioinformatics core tools are written in Linux. | ||
+ | * BLAST, CLUSTALW, PHRAP, etc | ||
+ | * Many web applications are also supported on web servers hosted on linux machines | ||
+ | * Linux supports development of software for many different programming languages. | ||
+ | * Developers are lazy so creating a software that does not require a window is much faster and easier | ||
+ | |||
+ | * Multiple users can log in at the same time. | ||
+ | * A user logging in over the network can do just about anything a user sitting in front of the computer can do. Which also means linux handles multitasking very well. | ||
+ | |||
+ | |||
+ | ====== Remote vs. Local ====== | ||
+ | |||
+ | {{: | ||
+ | |||
+ | ====== 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 ===== | ||
+ | |||
+ | The command is only executed once you press enter. Till then you can edit the line by using the following key strokes: | ||
+ | |||
+ | ^Action ^Result ^ | ||
+ | |Backspace (delete on MACs) |delete previous character| | ||
+ | |Left Arrow, Right Arrow| move left and right on lines | | ||
+ | |Up Arrow, down Arrow| previous and following command| | ||
+ | |Ctrl-A| go to front of line| | ||
+ | |Ctrl-E| go to end of line| | ||
+ | |Ctrl-D| delete next character| | ||
+ | |Ctrl-K| delete everything to the right of the character| | ||
+ | |Ctrl-Y| paste| | ||
+ | |Ctrl-C| stop a running job| | ||
+ | |||
+ | ====== Logging in with X Windows ====== | ||
+ | |||
+ | In cases where a program requires a GUI, you should log in using the –X option. | ||
+ | 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 ~]$ | ||
+ | </ | ||
+ | |||
+ | You should have a window popup on your computer that looks something like this. | ||
+ | |||
+ | {{: | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | ====== 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