LogoMat-M and its uses
I have recently struggled to install a bioinformatics program called LogoMat-M. LogoMat-M is a command line based program that creates visual representations of HMM-profiles. An excellent example of the program in action can be viewed at Sanger’s LogoMat-M website. It creates images that looks a bit like this:
The problem is that the web service was not designed to work with large amounts of sequences, and thus returns nada when such sequence alignments are used. To solve this problem, I thought I would try to install the program locally, on my own computer, at least to receive a proper error message. This was a big mistake.
The “install” process
I started by downloading the LogoMat-M package (i.e. the source code – this is open source software, which often means that there are no pre-compiled binaries). However, the build files for the program complained that my computer missed certain libraries and programs required for the LogoMat software to compile. Well, alright, I went out to find the pieces of missing software. Quite fast I could track down the two missing components and download these. Once again, these were open source programs – meaning no pre-compiled binaries. I tried to compile the first of those and rapidly got the answer that a component called PDL was required and could be obtained via a service called cpan.
I started to get a bit frustrated, since I didn’t want to spend the whole day installing software – I wanted to construct images like the one above. However, I did as the instructions said and text started flashing down my screen. Suddenly, cpan exited and said “Could not compile. Compiler returned bad status.” Wow. How informative! How do you expect me to know what caused that?! So, now I was stuck. I could not compile LogoMat because I was missing another program that was required, and I couldn’t install that program because I lacked a component that wasn’t, for some unknown reason, able to compile.
Now, the big problem here is that there is no way for me to get around this, because the documentation does not mention this kind of situation. I could, of course, contact the developers, but I was on a tight time schedule, and needed this to work. It was possible, if not likely, that it would take days for the developers (who do not get paid for this software, i.e. there is no official support channel) to sort out my problem.
Again, a mentality problem
Many times, open source software is praised for being open, but what people tend to forget is that a lot of this software is not at all easy to use. Or, in this case, even install. On Windows or Mac OS X, I would have fired up an installer, which would have installed a working pre-compiled binary on my system, with all its required libraries. It would work out-of-the-box. And if it didn’t, there would be someone to call.
Now, I don’t want to call for open source developers to set up call centres for supporting their programs, that would just be ridiculous. But I beg you to please make pre-compiled, working versions, including required libraries, and supply these for at least the most common platforms. Depending on the kind of software, that could be Windows, Mac OS X, Ubuntu and Red Hat Linux, for example. Don’t bother with pre-compiled software for strange and uncommon architecture, people running these things probably know how to compile their software anyway. But please, supply some easy to use, pre-compiled program for the rest of us. Because otherwise we will never be able to get our work done using open source alternatives, and that does not benefit either our work or the open source community in general. The situation described above only benefit big corporations selling overpriced software. And that is really, really sad.