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mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:16] mkatarimkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 09:22] – [Permissions] mkatari
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 +===== 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>
 +
 +===== Finding Your Way =====
 +
 +Often you will get lost on the hpc and you will need to know where you are, which computer did you log into, or even which account have you logged into. Below are some simple commands that help you find your way.
 +
 +<code>
 +[mkatari@hpc ~]$ whoami
 +mkatari
 +
 +[mkatari@hpc ~]$ pwd
 +/home/mkatari
 +
 +[mkatari@hpc ~]$ hostname
 +hpc.ilri.cgiar.org
 +
 +</code>
 +
 +===== File manipulation =====
 +
 +Useful commands for manipulating files and directories. To get details about how to use the commands type man <command>.
 +
 +^Command ^Action ^
 +|mkdir | make a directory |
 +|rmdir | remove a directory (only works if the directory is empty ) |
 +|cd    | change directory |
 +|pwd   | present working directory |
 +|ls    | list of files and directories in the directory. You can use wild card to look for specific files. You can also use -l to see details such as permission for files and directories |
 +|cp    | copy a file and/or directories. Use -r to recursively copy.  |
 +|mv    | move a file. It will copy and then delete the source. This can be used to rename files as well. |
 +|rm    | remove a file |
 +
 +<code>
 +[mkatari@hpc ~]$ mkdir temp
 +[mkatari@hpc ~]$ cd temp/
 +[mkatari@hpc temp]$ ls
 +[mkatari@hpc temp]$ cp ../allusers.txt ./
 +[mkatari@hpc temp]$ ls
 +allusers.txt
 +[mkatari@hpc temp]$ mv allusers.txt allusers.backup
 +[mkatari@hpc temp]$ ls
 +allusers.backup
 +[mkatari@hpc temp]$ rm allusers.backup
 +[mkatari@hpc temp]$ ls
 +[mkatari@hpc temp]$ cd ../
 +[mkatari@hpc ~]$ rmdir temp/
 +
 +</code>
 +
 +====== Permissions ======
 +
 +There are three levels of permissions that can be assigned to all files, programs, and directories
 +  * Read: open the file and copy it
 +  * Write: edit the file and delete it
 +  * Execute: Run the commands in the file or change into the directory if it is a directory
 +
 +There are also three different levels of users:
 +  * User – you
 +  * Group – A collection of users that are in a group
 +  * Everyone - Not just the people who have accounts on the machine but if the directory is open to the public and any one.
 +
 +The commands used to change owner, group, and specific permissions are:
 +  * chown – changes the owner
 +  * chgrp – changes the group
 +  * chmod – change read, write, and execute permissions
 +    * +/- r = read
 +    * +/- w = write
 +    * +/- x = execute
 +    * u = user level
 +    * g = group level
 +    * o = others
 +    * a = all
 +  * chmod can also use three numbers to set permissions where the value of the number represents a specific combination of rwx and their order assigns it to the different levels (u,g,o)
 +    * 0 = none
 +    * 1 = execute only
 +    * 2 = write only
 +    * 3 = write and execute only
 +    * 4 = read only
 +    * 5 = read and execute only
 +    * 6 = read and write only
 +    * 7 = read, write and execute
 +
 +
 +
 +        wget ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/v5.0assembly/cassavaV5_0.chromsomesRomanNumerals.fa.gz
 +
 +[[ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/annotation/Mesculenta_147_gene.gff3.gz
 +]]
  
  
 ====== 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