Daily Life in an Ivory Basement

If you're like me, we pretend to care about the science in bioinformatics software. But what we really do is try to find reasons not to outright loathe the software -- because, lud knows, there are usually plenty of reasons to hate it.

In no particular order, here are the top 10 things I hate about your bioinformatics software. You know who I'm talking about.

1. You posted it on SourceForge (and so I can't download the damn thing using a simple URL).
2. You're not using version control (and hence are not a scientist).
3. You put _ in the damned file name unnecessarily (that requires a shift key on my keyboard).
4. fizbam-0.9.3.tar.gz either untars into the current directory, OR a directory named 'fizbam'. Alternatively, you named it fizbam-0.9.3-2011010101010101010101010101020.tar.gz and it untars into THAT monster of a name (and my ls goes off the screen).
5. You have no README, or, if you do, it's a one-liner that refers to a URL (didn't I already download your damned software?) OR 5a. Your README file is in HTML (less is better than lynx, dontcha know?)
6. Running 'make' rebuilds everything from scratch every time you run it (seriously?)
7. There are neither tests nor examples; or, if there are, I can't run 'em, and even if they do run, I have no idea if the results are correct.
8. The output is in some weird format and/or location (wait, I have to do a find to find the last file written, and then guess as to its format?)
9. The command line options are poorly labeled and described, use random abbreviations, and/or are sensitive to order (unlike every good command-line parsing library written).
10. You CaMEl-CaSED your software name so that not even tab completion can figure it out (program names should be all lower-case, as Darwin intended).

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Post your top ten and send me the URLs... :)

--titus