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.
- You posted it on SourceForge (and so I can't download the damn thing using a simple URL).
- You're not using version control (and hence are not a scientist).
- You put _ in the damned file name unnecessarily (that requires a shift key on my keyboard).
- 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).
- 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?)
- Running 'make' rebuilds everything from scratch every time you run it (seriously?)
- 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.
- 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?)
- 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).
- 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).
Post your top ten and send me the URLs... :)
Posted by Paul Agapow on 2012-01-05 at 04:26.
My complaints are more about the pragmatic issues of using software: <<a href="http://biocoders.net/groups/bioinformatics-and- computational-biology/forum/topic/what-im-really-thinking-about-when-i -use-your-bioinformatics-software/">http://biocoders.net/groups /bioinformatics-and-computational-biology/forum/topic/what-im-really- thinking-about-when-i-use-your-bioinformatics-software/</a>>
Posted by Ian Holmes on 2012-01-05 at 05:20.
Re point #8, see also <a href="http://biowiki.org/FileFormatDesign">ht tp://biowiki.org/FileFormatDesign</a>
Posted by Egon Willighagen on 2012-01-05 at 07:02.
Maybe talk to Cameron Neylon to write up a 'user perspective' for Open Research Computation? BTW, SourceForge perfectly well allows deeplinking to downloadables with a single URL. I make use of that myself.
Posted by Preecha Patumcharoenpol on 2012-01-05 at 07:40.
I thing I hate most is ad-hoc fetch-and-build.sh
Posted by Ian Holmes on 2012-01-05 at 08:32.
That "file format design" list was actually a response to a less facetious (and far less amusing) post that is more relevant here <a href="http://biowiki.org/BioinformaticsToolDesign">http://biowiki.org/ BioinformaticsToolDesign</a>
Posted by Aaron Quinlan on 2012-01-05 at 10:51.
Thanks for the chuckle. Unfortunately, I think my software suffers from a few of these - a resolution for the new year, I suppose.
Posted by Arend Hintze on 2012-01-06 at 08:03.
Don't forget: linking to libraries that are not included and can't be found anymore Cheers Arend