Last week I installed a relatively new read aligner with the humorous name of ARYANA:
The journal article describing the tool was published on September 10th 2014, and the associated code repository on GitHub first appeared earlier in the same year. So we're not talking about an old program here.
If I have time I'm planning to investigate the use of ARYANA alongside other established mapping tools like BWA and Bowtie 2. Installing ARYANA was straightforward, so then I proceeded to try the first thing that I attempt with all new bioinformatics software (and most Unix command-line software):
Run the program without any parameters to see what happens
I don't think I'm alone in this approach. In the absence of any necessary command-line options, a good Unix program will return helpful information about how it should be used. At the very least it might prompt you with the minimal use scenario and/or point out how you can find out more information by invoking the help mode. So here is what happened with ARYANA:
% aryana
Need more inputs
Not very helpful. So I tried the next obvious thing, let's see if there is a help mode:
% aryana -h
Need more inputs
% aryana --help
Need more inputs
Hmm. This is really not helpful. Out of curiosity, I tried to see if ARYANA would tell me what version it is (a fairly common behavior for a lot of command-line software):
% aryana -v
Need more inputs
% aryana --version
Need more inputs
At this point I sighed. Not figuratively. I literally sighed, because this type of feedback from a program — especially a bioinformatics program developed in the year 2014 — is maddening. I tweeted about this issue and judging by the feedback, I am not alone with my views on this.
It may have been less frustrating to return no output at all rather than return just those three words. I feel like the program is taunting me. It may as well have returned any of the following output:
% aryana
Not gonna work
% aryana
No can do
% aryana
Please go away
I could use this blog post to tell you about some of the basic requirements of a bioinformatics command-line program, but I don't need to do this because others have already done so. Specifically, people should look at this great paper by Torsten Seemann (@torstenseemann), published in GigaScience last year:
Ten recommendations for creating usable bioinformatics command line software
This is a fantastic set of recommendations, and coincidentally the first three things on the list relate to the first three things that I tried doing when running the ARYANA program:
- Print something if no parameters are supplied
- Always have a “-h” or “--help” switch
- Have a “-v” or “--version” switch
This is good advice of developers of bioinformatics software, but equally it is good advice for reviewers of bioinformatics software. If I was a reviewer of the ARYANA paper, I would have made comments regarding the lack of useful output from the program.
