The important thing here is to allow people to recognize that each is a spectrum: chaining command line tools together is far easier than writing a program in a programming language. At the same time a GUI based program may require the user to make use of programming concept. For example entering formulas into an Excel worksheet - that is programming. So the divide is far less sharp than many might think.

My 2 cents to the matter is that graphical user interfaces are akin to speaking by using only a limited number predetermined sentences. You are given a limited amount of choices and and as long as what you want to say can be expressed with them it "seems" easier. But soon one runs into not being able to express what they really wanted to say.

Command line programming is like free speech, you can express far more detailed thoughts but at the same time you can say complete nonsense with ease.

For our teaching courses, and from your question I think we are targeting the same audience, we try to take the fear from our students. For this we train them in Galaxy and demonstrate how easy reproducible science and HPC computing can be. If you can make the point that everyone can reproduce (or not ;)) a Nature/Cell paper with Galaxy, you can motivate your students a lot without scaring them away with complicated installations and command line hacking.

Galaxy is very much like a shell pipe and to understand the concept of chaining together simple, already existing commands to complex workflows is a key message I guess.

If you are afraid of restricting your users and taking away freedom, don't worry any more. We have integrated IPython and RStudio in Galaxy.

So you now can combine both worlds. Shiny workflows and free speech. Isn't this what we are aiming for? Enable every researcher the take advantage of his/her skills without restricting them?

P.S. We using Galaxy/IPython to train programming lessons with real life-science data. If you are interested in teaching material let me know or have a look at: https://github.com/bgruening/

Coding gives you flexibility. With GUIs you're limited to the options offered. When GUIs become very flexible then they can reach a level of complexity close to that of programming, with an equally steep learning curve. In the end, even for using GUI tools, one ends up coding if only just to assemble data or convert data to a format acceptable by the GUI tool. Also, GUIs take time to develop so they are only available for established and/or well-funded tools. When you're in a lab exploring new avenues, you often need to develop your own tools (or adapt existing ones). If you can't code, then you're limiting your options. Given the importance of computational and statistical tools in modern biology or science in general, I don't see how one could be a scientist (or at least have a lasting career in science) and not have some basic skill/understanding in these areas. In my view if someone is not willing to learn the tools of the trade, then they should reconsider their career choices.

I often try in some intro courses to stress the importance of learning a little bit of UNIX/Linux and the command-line, or push all wet-lab people towards OS X and learning a little command-line so they can have the bets of both worlds. Because really, if you are scripting or programming with a fairly standard language (Python, Perl, C, C++, Java) you won't really be able to much that is terribly effective in Windows and even there they would need to learn the Windows command-line to do anything remotely interesting. And Windows is terrible for bioinformatics analyses in general.

Learning just a little bit of the command-line opens up all of the command-line tools that exist. Even if they are running their workflow manually they are one step ahead. I think it is a shorter jump from there to programming (at least light scripting).

IMO the most important message is that putting a few months into learning the command-line will enable them to do stuff that would be simply impossible to achieve through a GUI during a human lifespan. A simple example would be blasting 1 million protein sequences against nr. Imagine how long it would take if you did it one by one through the NCBI web service GUI (OK, maybe they allow more than one sequence, but certainly not 1 million).

A strong point in favour of scripting is that a job accomplished with a script is reproducible and self-documented (it's called script for a reason...!). This makes it easier in the future to understand what you have done. Sure you can write very obfuscated code, but still better then GUIs where you have no track left^*. In this perspective, the task at hand doesn't have to be very sophisticated or "high throughput" to justify scripting over GUI, it can be as simple as renaming a column in a data file.

On the other hand, as pointing out before, GUIs are great for data exploration and to generate hypothesis. Think IGV, but also a quick look at a table in Excel can tell something interesting for further analyses. So there shouldn't be a competition between the two, really.

My 2p...

^* As far as I know Galaxy is pretty good in recording the executed commands, so it's a notable exception.

CLI and GUI are redundant terms.

Is samtools CLI or GUI?

I guess you can execute it with parameters. What about htop which is rarely run with parameters and almost configured in the "GUCLI"?

What about this garbage RESTful interface which drove me to learn how to program 10 years ago:

There is good algorithm design, and there is good user interface design (or UX), and the two are totally separate things.

If the question is "why learn to program?" or "why learn linux/shell tools", I think that's a very different question and the interface differences are only going to confuse the situation.

For an audience of non-experts, absolutely focus on basic concepts and the GUI. I come from a different background (protein crystallography) but I spent several years going to workshops and training scientists in the use of the software I helped develop. At the beginning we just taught command-line tools and it was torture - at least half of any given audience had almost no command-line experience and we would waste time going over the basics. And we weren't even trying to teach them programming, just basic use of Unix commands. Once we had a GUI available, the difference in what material we could cover and what the students could absorb in the relatively short time allotted was enormous.

Of course this depends on the availability of a decent GUI; I have no experience with Galaxy so I can't comment on that. But I do not think that the average biologist will become a better scientist by learning Linux command-line use; they would be far better off learning math and statistics instead.