mkatari-bioinformatics-august-2013-introlinuxnotes
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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 [2015/06/11 11:31] – mkatari | ||
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* 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. | * 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 ====== | ====== Remote vs. Local ====== | ||
Line 38: | Line 34: | ||
====== Logging in with X Windows ====== | ====== 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 '' | ||
This opens a tunnel to your computer allowing all windows to open in your computer. | 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) | For this to work you need X11 installed on your computer (MobaXterm already has one) | ||
Line 46: | Line 45: | ||
< | < | ||
Last login: Wed Jun 3 15:49:01 on ttys000 | Last login: Wed Jun 3 15:49:01 on ttys000 | ||
- | Manpreets-MacBook-Pro: | + | Manpreets-MacBook-Pro: |
Unauthorized access is prohibited. | Unauthorized access is prohibited. | ||
mkatari@hpc.ilri.cgiar.org' | mkatari@hpc.ilri.cgiar.org' | ||
Last login: Wed Jun 3 16:33:26 2015 from 197.136.62.11 | Last login: Wed Jun 3 16:33:26 2015 from 197.136.62.11 | ||
- | [mkatari@hpc ~]$ | + | [mkatari@hpc ~]$ emacs |
</ | </ | ||
Line 57: | Line 57: | ||
{{: | {{: | ||
+ | Simply close the window to exit. | ||
+ | ====== Home Sweet Home ====== | ||
+ | When you first log in, you will be in a directory called “'' | ||
+ | < | ||
+ | / | ||
+ | </ | ||
+ | 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: '' | ||
+ | |||
+ | ===== 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, '' | ||
+ | |||
+ | < | ||
+ | [mkatari@hpc ~]$ date | ||
+ | Wed Jun 3 21:10:57 EAT 2015 | ||
+ | [mkatari@hpc ~]$ ls -l | ||
+ | total 19443152 | ||
+ | -rw-rw-r--. 1 mkatari mkatari | ||
+ | -rw-rw-r--. 1 mkatari mkatari | ||
+ | -rw-rw-r--. 1 mkatari mkatari | ||
+ | </ | ||
+ | |||
+ | |||
+ | ===== 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/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | ====== 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 | ||
+ | |||
+ | < | ||
+ | |||
+ | [mkatari@hpc ~]$ tail allusers.txt > bottomusers.txt | ||
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | -rw-rw-r--. 1 mkatari mkatari 772 Jun 11 13:54 bottomusers.txt | ||
+ | |||
+ | [mkatari@hpc ~]$ chmod u=+r-wx, | ||
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | -r--r-----. 1 mkatari mkatari 772 Jun 11 13:54 bottomusers.txt | ||
+ | |||
+ | [mkatari@hpc ~]$ rm bottomusers.txt | ||
+ | rm: remove write-protected regular file `bottomusers.txt'? | ||
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | ls: cannot access bottomusers.txt: | ||
+ | |||
+ | </ | ||
+ | Notice that since we have taken away our own write permission to the file we can not automatically delete it. The shell is asking to change the permission so it can delete. If we have write permissions that it would have delete right away. | ||
+ | |||
+ | ====== History ====== | ||
+ | |||
+ | Your shell saves all your commands and you can access them using the up and down keys. | ||
+ | |||
+ | Typing the command “history” returns all the commands you have entered and a number assigned to it. | ||
+ | |||
+ | You can run a specific one again by typing ! (also called “bang”) Followed by the job number. | ||
+ | |||
+ | !! Will perform the most recent command. | ||
+ | |||
+ | In the example code below, '' | ||
+ | |||
+ | < | ||
+ | [mkatari@hpc ~]$ history | grep bottom | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | [mkatari@hpc ~]$ !1000 | ||
+ | tail allusers.txt > bottomusers.txt | ||
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | -rw-rw-r--. 1 mkatari mkatari 772 Jun 11 14:01 bottomusers.txt | ||
+ | [mkatari@hpc ~]$ !1002 | ||
+ | chmod u=+r-wx, | ||
+ | [mkatari@hpc ~]$ ls -al bottomusers.txt | ||
+ | -r--r-----. 1 mkatari mkatari 772 Jun 11 14:01 bottomusers.txt | ||
+ | </ | ||
+ | |||
+ | ====== Transferring Files ====== | ||
+ | |||
+ | There are several ways to transfer files to a server. The most reliable and consistent way is to use '' | ||
+ | |||
+ | One major advantage of using mobaxterm on windows machines is that it comes with some basic linux commands, including scp. On a mac, scp comes with the operating system. So if you want to copy a file that is on your Desktop to hpc from your laptop you can use the following command: | ||
+ | |||
+ | < | ||
+ | [2015-06-11 07: | ||
+ | [Manpreet.WIN-OAOVO3NM02E] ➤ cp allusers.txt Desktop/ | ||
+ | ✔ | ||
+ | ──────────────────────────────────────────────────────────────────────────── | ||
+ | [2015-06-11 07: | ||
+ | [Manpreet.WIN-OAOVO3NM02E] ➤ scp Desktop/ | ||
+ | Unauthorized access is prohibited. | ||
+ | allusers_local.txt | ||
+ | |||
+ | </ | ||
+ | ====== Exercise ====== | ||
+ | |||
+ | - Download the file to your computer from the following url [[ftp:// | ||
+ | - Transfer it to your LinuxJune2015 directory on HPC. | ||
+ | - Gunzip the file and rename it to : Cassavagenes.txt | ||
+ | - Determine the number of different genes are present in the file. Hint – check the third column | ||
+ | - Save the rows that contain the word “gene” in the third column as a separate file. Call it “GeneTypes.txt” | ||
+ | - Create a directory called “Share” | ||
+ | - Move GeneTypes.txt into Share and change permissions on Share so others can read the file. | ||
====== 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