Introduction to Bio-Linux

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.
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