One aspect of Gnuastro that might be a little troubling to new GNU/Linux users is that (at least for the time being) it only has a command-line user interface (CLI). This might be contrary to the mostly graphical user interface (GUI) experience with proprietary operating systems. Since the various actions available are not always on the screen, the command-line interface can be complicated, intimidating, and frustrating for a first-time user. This is understandable and also experienced by anyone who started using the computer (from childhood) in a graphical user interface (this includes most of Gnuastro’s authors). Here we hope to convince you of the unique benefits of this interface which can greatly enhance your productivity while complementing your GUI experience.
Through GNOME 315, most GNU/Linux based operating systems now have an advanced and useful GUI. Since the GUI was created long after the command-line, some wrongly consider the command-line to be obsolete. Both interfaces are useful for different tasks. For example, you cannot view an image, video, PDF document or web page on the command-line. On the other hand you cannot reproduce your results easily in the GUI. Therefore they should not be regarded as rivals but as complementary user interfaces, here we will outline how the CLI can be useful in scientific programs.
You can think of the GUI as a veneer over the CLI to facilitate a small subset of all the possible CLI operations. Each click you do on the GUI, can be thought of as internally running a different CLI command. So asymptotically (if a good designer can design a GUI which is able to show you all the possibilities to click on) the GUI is only as powerful as the command-line. In practice, such graphical designers are very hard to find for every program, so the GUI operations are always a subset of the internal CLI commands. For programs that are only made for the GUI, this results in not including lots of potentially useful operations. It also results in ‘interface design’ to be a crucially important part of any GUI program. Scientists do not usually have enough resources to hire a graphical designer, also the complexity of the GUI code is far more than CLI code, which is harmful for a scientific software, see Gnuastro manifesto: Science and its tools.
For programs that have a GUI, one action on the GUI (moving and clicking a mouse, or tapping a touchscreen) might be more efficient and easier than its CLI counterpart (typing the program name and your desired configuration). However, if you have to repeat that same action more than once, the GUI will soon become frustrating and prone to errors. Unless the designers of a particular program decided to design such a system for a particular GUI action, there is no general way to run any possible series of actions automatically on the GUI.
On the command-line, you can run any series of actions which can come from various CLI capable programs you have decided yourself in any possible permutation with one command16. This allows for much more creativity and exact reproducibility that is not possible to a GUI user. For technical and scientific operations, where the same operation (using various programs) has to be done on a large set of data files, this is crucially important. It also allows exact reproducibility which is a foundation principle for scientific results. The most common CLI (which is also known as a shell) in GNU/Linux is GNU Bash, we strongly encourage you to put aside several hours and go through this beautifully explained web page: https://flossmanuals.net/command-line/. You do not need to read or even fully understand the whole thing, only a general knowledge of the first few chapters are enough to get you going.
Since the operations in the GUI are limited and they are visible, reading a manual is not that important in the GUI (most programs do not even have any!). However, to give you the creative power explained above, with a CLI program, it is best if you first read the manual of any program you are using. You do not need to memorize any details, only an understanding of the generalities is needed. Once you start working, there are more easier ways to remember a particular option or operation detail, see Getting help.
To experience the command-line in its full glory and not in the GUI terminal emulator, press the following keys together: CTRL+ALT+F417 to access the virtual console. To return back to your GUI, press the same keys above replacing F4 with F7 (or F1, or F2, depending on your GNU/Linux distribution). In the virtual console, the GUI, with all its distracting colors and information, is gone. Enabling you to focus entirely on your actual work.
For operations that use a lot of your system’s resources (processing a large number of large astronomical images for example), the virtual console is the place to run them. This is because the GUI is not competing with your research work for your system’s RAM and CPU. Since the virtual consoles are completely independent, you can even log out of your GUI environment to give even more of your hardware resources to the programs you are running and thus reduce the operating time.
Since it uses far less system resources, the CLI is also convenient for remote access to your computer. Using secure shell (SSH) you can log in securely to your system (similar to the virtual console) from anywhere even if the connection speeds are low. There are apps for smart phones and tablets which allow you to do this.
By writing a shell script and running it, for example, see the tutorials in Tutorials.
Instead of F4, you can use any of the keys from F1 to F6 for different virtual consoles depending on your GNU/Linux distribution, try them all out. You can also run a separate GUI from within this console if you want to.