Thursday, April 9, 2015

The ideal software tool is one that no end user can install

Did I write that I would not comment any more on fastStructure after my other two posts?

I just spent much of the evening trying to install it at home, and banging my head onto the desk for two hours would probably have been a more pleasant experience. After all that effort I got all the prerequisites - Numpy, Scipy, Cython and GSL installed, and even running the build seemed to have worked. At least when I try to do it over, it says, nope, I'm already done, no need.

But then when I try to run fastStructure, it says that it cannot find the libraries that are just sitting there in the same folder.

To all potential end users: Don't try this at home. Preferably ask your institution's IT people to put it onto some machine for you. Or use a different software.

To all bioinformaticians who hope that scientists will use their software: This is how not to do it. If you write a program that only another programmer can even so much as install, then hardly anybody will use it, and thus hardly anybody will cite your paper. Wasted effort. How about providing executables, like BEAST? Or at least something that can be installed by running a simple makefile, like r8s? Or an R package perhaps, like BioGeoBEARS? It's not as if there aren't people who get that right.

Update: It worked!

1 comment:

  1. Hi,
    i found that adding your libraries like "export LD_PRELOAD='location of libraries separated by spaces'" before running faststructure fixes the problem with missing libraries.