Basic commands

Below is a list of commands that are very commonly used. Of these, cd and ls are essential to using the command line, and you should be familiar with them.

Each command described below has a syntax line, which gives a brief description of how it should be used. The first item on the line is always the name of the command, followed by a number of arguments. Arguments given in square brackets are optional and can be omitted. If an argument is followed by three dots (‘…’), it means that any number of that type of argument can be provided, and each will be processed in turn. In addition, any options that are of particular interest are listed in the corresponding section for each command.

pwd: print working directory

$ pwd

Print the current working directory onto the screen.

cd: change working directory

$ cd [folder]

Change the current working directory. If no folder is specified, the current working directory will be set to the home folder. Otherwise, it will be set to folder, assuming that it is a valid path.

Note that in this command, the token - has special meaning when passed instead of folder: it refers to the previous working directory. This can be useful to rapidly change back and forth between folders, e.g.:

# our current working directory is /home/donald/Documents

$ cd ../data/project/patient2
...         # current working directory is now /home/donald/data/project/patient2
...         # do something useful

$ cd -      # switch back to /home/donald/Documents when you're done

ls: list files

$ ls [option]... [target]...

List files. If no target is specified, the contents of the current working directory are listed. Otherwise, the files specified are listed in the order provided, assuming that they are valid paths. If a target is a folder, its contents will be listed.

Options:

  • -a

    list all files, including hidden files (hidden files are those that start with a full stop ‘.’).

  • -l

    provide a long listing, including file size, ownership, permissions, and modification date.

cp: copy files or folders

$ cp [option]... source target
$ cp [option]... source... folder

In its first form, copy the file source to create the file target, assuming both are valid paths. You should be aware that in general, if the file target already exists, it will be overwritten (although this behaviour can be modified through an alias).

The second form is used to copy one or more source files into the target folder. In this case, target must be a pre-exising folder. Each newly created file will have the same base name as the original.

Options:

  • -i

    ask for confirmation before overwriting any files.

  • -r

    recursive copy: use this option to copy an entire folder and its contents.

mv: move/rename files or folders

$ mv [option]... source target
$ mv [option]... source... folder

In its first form, move or rename the file (or folder) source to target, assuming both are valid paths. Note that renaming is essentially equivalent to moving the file to a different location, if source and target reside in different folders.

The second form is used to move one or more source files into the target folder. In this case, target must be a pre-existing folder.

Options:

  • -i

    ask for confirmation before overwriting any files.

echo: output strings to the terminal

$ echo [option]... [string]...

The echo command writes any specified arguments, separated by single space characters and followed by a newline (\n) character to the standard output.

Examples of typical command use

Below are some examples of commands in typical use, illustrating some of the concepts explained in this document. To fully understand the examples, you may need to refer back to the sections on Specifying filenames: paths, using special filenames, or using wildcards.

  • To change your current working directory to its parent folder (move one branch down the directory tree):

    $ cd ..

  • To change your current working directory from whatever it was to the data folder in your home directory:

    $ cd ~/data

  • To list all images (with the .png suffix) whose filename start with ns from the controls folder:

    $ ls controls/ns*.png

  • To move the file data.mat, residing in the current working directory, into the parent folder of that directory:

    $ mv data.mat ..

  • To copy the file info.txt from the folder important into the current working directory:

    $ cp important/info.txt .

  • To copy all shell script files from the data folder in your home directory into the scripts folder in the current working directory:

    $ cp ~/data/*.sh scripts/

  • To copy all images for study 3 of patient Joe Bloggs from the /data folder into the current working directory (assuming the images are named according to the convention ID-study-slice.ima):

    $ cp /data/bloggsj_010203_123/*-3-*.ima .