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--- mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 17:10] – mkatari
+++ mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:16] – mkatari
@@ Line 27: / Line 27: @@
       * 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.
-====== The Linux Shell ======
+====== Remote vs. Local ======
+{{:servercomputerrelation.png?600|}}
+====== 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.
-====== Remote vs. Local ======
+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://xquartz.macosforge.org/landing/)
+Windows – Xming (http://sourceforge.net/projects/xming/)
+<code>
+Last login: Wed Jun  3 15:49:01 on ttys000
+Manpreets-MacBook-Pro:~ manpreetkatari$ ssh -X mkatari@hpc.ilri.cgiar.org
+Unauthorized access is prohibited.
+mkatari@hpc.ilri.cgiar.org's password:
+Last login: Wed Jun  3 16:33:26 2015 from 197.136.62.11
+[mkatari@hpc ~]$ emacs
+</code>
+You should have a window popup on your computer that looks something like this.
+{{:emacswindow.png?300|}}
+Simply close the window to exit.
+====== Home Sweet Home ======
+When you first log in, you will be in a directory called “''home directory''”
+<code>
+/home/<your username>
+</code>
+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.
+===== 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|
+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, ''date'' is a command that is being executed with no arguments. Many commands/programs have options that are provided immediately following the command. In the ''ls -l'' example, ls is the command and everything else are options that are provided.
+<code>
+[mkatari@hpc ~]$ date
+Wed Jun  3 21:10:57 EAT 2015
+[mkatari@hpc ~]$ ls -l
+total 19443152
+-rw-rw-r--. 1 mkatari mkatari      16263 Jun  3 16:29 03-06-2015.pdf
+-rw-rw-r--. 1 mkatari mkatari     990646 Jun 12  2014 _1.fastq
+-rw-rw-r--. 1 mkatari mkatari     381856 Jun 12  2014 _2.fastq
+</code>
-{{:servercomputerrelation.png?600|}}