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--- mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 17:37] – [Logging in with X Windows] mkatari
+++ mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:40] – 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 ======
-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 ======
@@ Line 38: / Line 34: @@
 ====== Logging in with X Windows ======
-In cases where a program requires a GUI, you should log in using the –X option.
+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 ''–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)
@@ Line 46: / Line 45: @@
 <code>
 Last login: Wed Jun  3 15:49:01 on ttys000
-Manpreets-MacBook-Pro:~ manpreetkatari$ ssh mkatari@hpc.ilri.cgiar.org
+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 ~]$
+[mkatari@hpc ~]$ emacs
 </code>
@@ Line 57: / Line 57: @@
 {{: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>
+===== Directing standard output =====
+Instead letting the output print to the screen we can save it to a file by using the ''>'' sign and then giving the file name.  This will replace a file if it already exists without a warning. To append use an existing file use ''>>''. It is important to mention here that once you overwrite a file, it is deleted. It is gone. There is no recycling bin to restore from trash.
+The following command gets details about all users' home directories and saves them into a file called ''allusers.txt''
+<code>
+[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
+</code>
+===== 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 ''enter'' key is pressed.
+<code>
+[mkatari@hpc ~]$ ls /usr/bin/bz
+bzcat         bzdiff        bzip2         bzless
+bzcmp         bzgrep        bzip2recover  bzmore
+</code>
+===== Wildcards =====
+In cases where you want to refer to multiple files you can use ''*'' to represent any characters of any length. You can also use ''?'' To represent any character of one length.
+In the example below, the first line gives all files/programs that start with bz. The second only gives which begin with bz and three letters afterwards, represented by ?
+<code>
+[mkatari@hpc ~]$ ls /usr/bin/bz*
+/usr/bin/bzcat  /usr/bin/bzdiff  /usr/bin/bzip2         /usr/bin/bzless
+/usr/bin/bzcmp  /usr/bin/bzgrep  /usr/bin/bzip2recover  /usr/bin/bzmore
+[mkatari@hpc ~]$ ls /usr/bin/bz???
+/usr/bin/bzcat  /usr/bin/bzcmp  /usr/bin/bzip2
+</code>
+SLIDE16
 ====== Some useful information about linux ======