Basic UNIX commands

Some commonly used commands

The following are some basic commands you might use to navigate around and manipulate files on a linux computer using the command line interface. You can read more about some of these commands below.

Print the current working directory

pwd

Make a new directory ​called dir​ inside the working directory

mkdir ​./dir

Change working directory to a directory named to ​dir​ that is inside the working directory

cd ​./dir

Change working directory to the parent of the working directory

cd ../

Show the contents of the working directory

ls

Show the contents in an ordered list with file sizes

ls -lh

Create a blank file called fileA

touch fileA

Move fileA ​to the parent of the working directory

mv fileA ../

Copy fileA from the parent of the working directory to the working directory

cp ../fileA ./

Rename fileA to fileB

mv fileA fileB

Delete fileA (be careful!)

rm fileA

Delete an empty directory called dirA

rm -d dirA

Move all files starting with file in the current directory to directory dir

mv file* ./dir

Delete all files ending with .fasta (be really careful!)

rm *.fasta

Delete the directory called dirA and its contents (be extremely careful!)

rm -rf dirA

Display first 10 lines of fileB

head ​fileB

Display first 20 lines of fileB

head -n 20 ​fileB

Display fileB in a scrollable format (press q to quit)

more ​fileB

More detailed examples for beginners

Navigating a linux system

To check where you are in a system you type in pwd and press Enter (Return). This will show you your current working directory. If you need to change directory you can type cd followed by the path of the directory you want.

cd path/to/directory

If you need to create a new directory you can use the mkdir command followed by what name you want to give the new directory.

mkdir new_directory

Creating a file

To create a file you can either use commands echo or touch, or the nano text editor (described in a later section). To create an empty file you can use the touch command followed by the name you want to save the empty file under.

touch filename

To create a file that has certain contents you can use echo or nano. Lets say you want a file that contains the text “this is a file” and you wanted to name that file fileA.txt. You would do this as shown below:

echo "this is a file" > fileA.txt

If you want to create a text file with multiple lines of text from the terminal it will be easier to use nano (see later section).

Copying files

You might want to copy a file under a different name so you can edit it but still keep the original. To do this we can us the cp command. Type cp followed by the name of the file you want to copy then the name you want to give the copy. Lets say we wanted to make a copy of fileA.txt named fileB.txt. The block below shows us how we would do this.

cp fileA.txt fileB.txt

You can also copy a file into a different directory by putting the target directory path as the second argument followed by a / and the name you want the copy to be saved under. For example, if we wanted to copy fileA.txt to a directory named dirB that was in our current parent directory and name the copy fileB.txt, we would run the below command:

cp fileA.txt ../dirB/fileB.txt

Moving files

If you want to move a file into a different directory without copying it you can use the mv command. You type mv followed by the name of the file you would like to move then the target directory path. Lets say we want to move a file named fileC.txt into a directory named dirB which is contained within our current parent directory:

mv fileC.txt ../dirB/

Renaming files

The simplest way to rename files is to use the mv command. This might seem strange, but think of the path of a file as being simply a longer version of the file name. Thus moving files between directories is essentially just a matter of changing their name. So you can rename a file by “moving” it to another file name. So say you wanted to change the name of fileA.txt to fileD.txt:

mv fileA.txt fileD.txt

It’s that simple!