mkatari-bioinformatics-august-2013-introlinuxnotes
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mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/03 18:16] – mkatari | mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 09:11] – [File manipulation] 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 ''>'' | ||
+ | The following command gets details about all users' home directories and saves them into a file called '' | ||
+ | |||
+ | < | ||
+ | |||
+ | [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 | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | ===== 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 '' | ||
+ | |||
+ | < | ||
+ | [mkatari@hpc ~]$ ls /usr/bin/bz | ||
+ | bzcat | ||
+ | bzcmp | ||
+ | </ | ||
+ | |||
+ | ===== 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 / | ||
+ | / | ||
+ | </ | ||
+ | |||
+ | ===== 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. | ||
+ | |||
+ | < | ||
+ | [mkatari@hpc ~]$ whoami | ||
+ | mkatari | ||
+ | |||
+ | [mkatari@hpc ~]$ pwd | ||
+ | / | ||
+ | |||
+ | [mkatari@hpc ~]$ hostname | ||
+ | hpc.ilri.cgiar.org | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== File manipulation ===== | ||
+ | |||
+ | Useful commands for manipulating files and directories. To get details about how to use the commands type man < | ||
+ | |||
+ | ^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 | | ||
+ | |||
+ | < | ||
+ | [mkatari@hpc ~]$ mkdir temp | ||
+ | [mkatari@hpc ~]$ cd temp/ | ||
+ | [mkatari@hpc temp]$ ls | ||
+ | [mkatari@hpc temp]$ cp ../ | ||
+ | [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/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | wget ftp:// | ||
+ | |||
+ | [[ftp:// | ||
+ | ]] | ||
====== 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