Introduction to Bio-Linux

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Note: While grep is a very useful utility, if you want to search biological sequences for patterns, there are sophisticated programs designed especially for this, and we advise against using grep in all but the most trivial cases. Clearing your terminal of text Your terminal windows can fill up with lots of text, and it can become difficult to see the information you want because of all the clutter. You can clear the terminal window of all previous text by typing clear The result is a prompt in a nice clean window. Copying files To copy files, the basic command is cp. At minimum, you must also specify the name of the file(s) to be copied, and the destination location. cp firstfile dest_location cp file1 file2 file3 location cp directory/* location copies all files in the directory to location To move whole directories, with all the subfiles and subdirectories, use the –R option, (meaning recursive). cp –R mydir location The Linux/Unix shorthand for “this directory right here” (a dot . )comes in very handy when copying: cp –R mydir . Copy all files/directories under mydir to this directory here Make sure you leave a space between the directory name and the shorthand dot. Also useful is the shorthand for someone’s home account. e.g. instead of having to know and type the location of their account, you can use ~username In the case of your own account, you need only use ~ cp ~user2/somefile . copy the file somefile from user2’s home directory here. Note that user2 would have to have given you permission to do this! cp ~/somedir/somefile . copy the file somefile from within my account/somedir to here. Exercise Copy all the files that start with the letters tes and end in .embl into the directory testdir that you made earlier. 12
There are many different ways to accomplish the above. If you have problems, or would like to know if you have done it in the most efficient way, then please ask a demonstrator. Removing files and directories To remove a file or files, use the rm command followed by the name of the file(s) you wish to delete. rm file1 rm file2 file3 file4 rm cat* remove all files starting with the letters cat Note On Bio-Linux the command rm has been aliased to rm –i. This means the system will ask you if you really mean to delete the file you have just asked to delete, and you must answer yes if you do. Other Linux/Unix systems may not be so polite, and unlike Windows systems, the files you delete are not stored in a trash can for you to retrieve – they’re gone! (Unless the file has been there for some time and you are making proper backups….which you should be!) If you have a lot of files to delete, confirming each one can be tedious. You can escape this safety feature by using a backslash in front of the rm command. \rm files To remove an empty directory, you can use the rmdir command: rmdir thisdir If that directory contains any files, you will not able to delete the directory using rmdir until you have deleted all the files within it. To delete a directory and all the files in it, use the rm command with the options -rf rm –rf fulldir You may be prompted to confirm that you wish to delete each file. If this is too tedious, and you are certain that you want to delete all the files in that directory as well as the directory itself, remember that you can “escape” this safety feature using the backslash: Exercise \rm –rf fulldir Delete one of the files you created earlier with pico or nedit. Delete the entire testdir directory. 13
Page 1 and 2: Introduction to Bio-Linux Logging i
Page 3 and 4: You can also use regular expression
Page 5 and 6: Basic commands It is possible for u
Page 7 and 8: Making a directory To make a new fi
Page 9 and 10: With less (but not more), you can u
Page 11: Piping commands - how to make the o

Introduction to Bio-Linux

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