Introduction to Compgenomics Part II. Lee Katz January 13, 2010

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1 Introduction to Compgenomics Part II Lee Katz January 13, 2010

2 All students and groups should be on the Wiki Wiki needs to be closed and secured by Friday How are we doing 2

3 Introduction to using the server You need to know how to Log into the server Make and run files on the server Maintain good behavior 3

4 Good Behavior Don t remove things that aren t yours. Don t change permissions on other peoples files. Don t edit other peoples files without their permission. Don t give more permissions than you need to. [gtg075i@genomics class ~]$ chmod a+rws veryimportantfile.fasta Make backup copies along the way. Remove old files that you are no longer using Or, at the least, move them to a "trash" folder. 4

5 Logging into compgenomics Open securecrt (windows) putty (Win) or terminal (Mac, Linux, Unix) is equally good You need to do a quick connect On terminal, instead use the following command ssh username@compgenomics.biology.gatech.edu hostname: compgenomics.biology.gatech.edu username: gt username 5

6 Logging into compgenomics Accept and Save host key Enter your gt password Now you are on the command line and can enter commands. Cheat sheets /unix.html udson/docs/unix_cheat_sheet.ht ml 6

7 WinSCP You can find this under the start menu or from software.oit.gatech.edu Fugu is a mac alternative Allows transfer of files between your local computer and the remote server (compgenomics) Due to time constraints I cannot show this, but you should try this on your own 7

8 Directories Directory = Folder pwd : Print Working Directory. Show where you are in the whole directory structure. [gtg075i@genomics class ~]$ pwd /home/gtg075i mkdir: Make Directory. Create a new directory [gtg075i@genomics class ~]$ mkdir anotherdirectory ls: List. Show the contents of the directory you re in. [gtg075i@genomics class ~]$ ls anotherdirectory browser 8

9 Changing Directories cd: Change directory. Move from one directory into another. class ~]$ cd anotherdirectory class anotherdirectory]$ pwd /home/gtg075i/anotherdirectory You can also move into sub directories this way. class ~]$ mkdir anotherdirectory/somesubdirectory class ~]$ cd anotherdirectory/somesubdirectory/ class somesubdirectory]$ pwd /home/gtg075i/anotherdirectory/somesubdirectory 9

10 Special Directories The directory you re currently in can be referenced with. class anotherdirectory]$ cd. class anotherdirectory]$ pwd /home/gtg075i/anotherdirectory This does nothing, but knowing that./ means this directory has it s uses, which you ll see later on. More useful, the directory above you re current one is.. [gtg075i@genomics class anotherdirectory]$ cd.. [gtg075i@genomics class gtg075i]$ pwd /home/gtg075i 10

11 Home Sweet Home Your home directory is another special directory. When you log in, you start in your home directory. You can move there any time by entering cd alone. class ~]$ cd /var/www/webhost/gbrowse/log/ class log]$ pwd /var/www/webhost/gbrowse/log class log]$ cd class ~]$ pwd /home/gtg075i It can be referenced with ~. class ~]$ cd ~/anotherdirectory/ class anotherdirectory]$ pwd /home/gtg075i/anotherdirectory 11

12 Looking Around: ls ls can also show you more about what s in the directory. Various flags are used for options. Use touch to create a file, then ls s to see how big it is. [gtg075i@genomics class ~]$ touch afile.txt [gtg075i@genomics class ~]$ ls s 0 afile.txt It s 0 bytes because it s just an empty file. ls l will give you lots of information. [gtg075i@genomics class ~]$ ls l afile.txt rw r r 1 gtg075i compgenomics Jan 6 11:37 afile.txt What does all that mean? 12

13 No! My file! File Permissions dictates who can read/write/use a file, and are shown as the rw r r from ls l. Type User(u) Group(g) Others(o) Read Write Exectute Read Write Exectute Read Write Exectute - r w - r - - r - - This means that the user, you, can read and write the file, but others can only read it. You can change this with the chmod command. [gtg075i@genomics class ~]$ chmod g+w afile.txt [gtg075i@genomics class ~]$ ls l afile.txt rw rw r 1 gtg075i compgenomics Jan 6 11:37 afile.txt The g+w argument would allow members of your group to write the file. A instead of + would remove the permission. Execute is used for when you have some script or program that you want to run. 13

14 More on Permissions ls l also shows who owns the file and what group the file belongs too. rw rw r 1 gtg075i compgenomics Jan 6 11:37 afile.txt In this case, it belongs to gtg075i and is in the compgenomics2008 group. Your s is probably different. chown and chgrp can be used to change the owner and group of a file. Then at the end you have the date the file was last modified, and the name of the file. Let s put some stuff in the file. 14

15 Messing with the File There are many text editors for linux, today we ll use emacs. class ~]$ emacs afile.txt Enter the numbers 1 12 on separate lines in the window. Then hit ctrl x, ctrl s to save it, and ctrl x, ctrl c to exit emacs. Check with ls s, and the file size should have changed: [gtg075i@genomics class ~]$ ls s afile.txt 4 afile.txt The head command will give you the first 10 lines of a file. [gtg075i@genomics class ~]$ head afile.txt head 12 will give you the first 12 lines [gtg075i@genomics class ~]$ head 12 afile.txt cat will print out the entire file. [gtg075i@genomics class ~]$ cat afile.txt 15

16 Moving and Copying the File mv: Move. Use the mv command to move a file from one directory to another. [gtg075i@genomics class ~]$ mv afile.txt anotherdirectory/ [gtg075i@genomics class ~]$ ls anotherdirectory/ afile.txt somesubdirectory cp: Copy. Try copying the file back into your home directory. [gtg075i@genomics class ~]$ cp anotherdirectory/afile.txt ~/ [gtg075i@genomics class ~]$ ls afile.txt mv and cp can also be used to rename files. [gtg075i@genomics class ~]$ mv afile.txt renamed.txt [gtg075i@genomics class ~]$ ls renamed.txt 16

17 Deleting the File rm: Remove. Delete a file. [gtg075i@genomics class ~]$ rm afile.txt Be very, very careful with this. You don t want to delete something by accident. rm r: Remove recursively. Remove a directory and it s contents. [gtg075i@genomics class ~]$ rm r anotherdirectory 17

18 Running Scripts Perl and Python scripts can be run from the Unix command line. Use emacs to edit script.pl and add this: use strict; print Compgenomics!\n ; Run the script from the command line [gtg075i@genomics class ~]$ perl script.pl Compgenomics! 18

19 More on Scripts You can say what program you want to run the script in the script itself. Add #!/usr/bin/perl as the first line of the script #!/usr/bin/perl use strict; print Compgenomics!\n ; Use chmod to make the script executable. [gtg075i@genomics class ~]$ chmod u+x script.pl Then run the script from the directory. [gtg075i@genomics class ~]$./script.pl Compgenomics! 19

20 Resources For help with a Unix command, use the man utility. This provides documentation for most utilities. [gtg075i@genomics class ~]$ man ls Google Unix cheat sheet. There are many good results. Some Cheat sheets For emacs, type the emacs command, then when it s open enter ctrl h, t for the tutorial. Or ask Andy 20

21 The Most Important Commands cat for creating and displaying short files cd change directory cp for copying files less for viewing files (q to quit) ls see what files you have mkdir create directory mv for moving and renaming files pwd find out what directory you are in rm remove a file rmdir remove directory commands.html 21