.. _basic_unix: .. role:: var ================================== 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 .. parsed-literal:: :class: codebg pwd Make a new directory ​called ``dir​`` inside the working directory .. parsed-literal:: :class: codebg mkdir ​./dir Change working directory to a directory named to ​dir​ that is inside the working directory .. parsed-literal:: :class: codebg cd ​./dir Change working directory to the parent of the working directory .. parsed-literal:: :class: codebg cd ../ Show the contents of the working directory .. parsed-literal:: :class: codebg ls Show the contents in an ordered list with file sizes .. parsed-literal:: :class: codebg ls -lh Create a blank file called ``fileA`` .. parsed-literal:: :class: codebg touch fileA Move ``fileA`` ​to the parent of the working directory .. parsed-literal:: :class: codebg mv fileA ../ Copy ``fileA`` from the parent of the working directory to the working directory .. parsed-literal:: :class: codebg cp ../fileA ./ Rename ``fileA`` to ``fileB`` .. parsed-literal:: :class: codebg mv fileA fileB Delete ``fileA`` (be careful!) .. parsed-literal:: :class: codebg rm fileA Delete an empty directory called ``dirA`` .. parsed-literal:: :class: codebg rm -d dirA Move all files starting with ``file`` in the current directory to directory ``dir`` .. parsed-literal:: :class: codebg mv file\* ./dir Delete all files ending with ``.fasta`` (be really careful!) .. parsed-literal:: :class: codebg rm \*.fasta Delete the directory called ``dirA`` and its contents (be extremely careful!) .. parsed-literal:: :class: codebg rm -rf dirA Display first 10 lines of ``fileB`` .. parsed-literal:: :class: codebg head ​fileB Display first 20 lines of ``fileB`` .. parsed-literal:: :class: codebg head -n 20 ​fileB Display ``fileB`` in a scrollable format (press :menuselection:`q` to quit) .. parsed-literal:: :class: codebg 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. .. parsed-literal:: :class: codebg cd :var:`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. .. parsed-literal:: :class: codebg mkdir :var:`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. .. parsed-literal:: :class: codebg touch :var:`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: .. parsed-literal:: :class: codebg 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. .. parsed-literal:: :class: codebg 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: .. parsed-literal:: :class: codebg 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: .. parsed-literal:: :class: codebg 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``: .. parsed-literal:: :class: codebg mv fileA.txt fileD.txt It's that simple!