There are two caveats for the user of SyQADA:

1. This is a used car, not a Formula One racer.

2. SyQADA does not solve problems of complexity.

Used Car

Please, look under the hood at SyQADA’s Model-A engine with single-bore, manual choke carburetor. The tires have a lot of tread on them — kick them to see that the ball-joints are sound. Then test-drive the manual clutch, which slips going from second to third gear. Don’t expect the car to win at Indy, Daytona, or Le Mans, but it just might get you from St. Louis to Seattle as fast as driving a Lotus without a radar detector, and probably consuming less fuel. Unfortunately, our shop is not on that route, so we may not be able to tinker under the hood of your particular problem.

Let me rephrase that a little lighter on the metaphor: We are well enough pleased with this system that we think it might be useful to others, but we are analysts first, and software developers second. Consequently, many features and misfeatures that a major software house might provide in a shrink-wrapped SyQADA are not to be found here, among them a web interface, support for “the cloud,” and an animated marketing presentation that promises the best product since sliced Italian-roast quinoa capuccino. Features are missing for one or more of several main reasons:

We have never had a use-case for the "feature."

Adding the "feature" would unduly sacrifice simplicity.

Adding the "feature" would cause an analysis deadline to slip.

Adding the "feature" did not seem like a good expenditure of public funds.

SyQADA is pretty versatile and is very effective in simple applications. SyQADA’s console output strives to be clear and informative and even does a pretty good job of identifying problems, because it’s useful to us, too. That console output is about all the help we can promise to give you, though, because our mandate is to cure cancer, not to write software.

Bioinformatics is Complex

SyQADA DOES NOT SOLVE PROBLEMS OF COMPLEXITY, and it cannot teach you Unix. SyQADA tries to create as few additional complexities as possible, but please remember that managing big data and performing bioinformatics computations are inherently complex tasks, and that being comfortable with Unix is a modern scientist’s life skill.

It is my goal that any time SyQADA can recognize a problem with its inputs, it will give a reasonably informative message. However, once SyQADA submits jobs to the system to run, it does a little, but not much, to help understand errors that may result. It can and does put those errors in a standard place so that you can find them easily.

The more you know about the Unix file system and the standard Unix tools for file and directory manipulation, the easier you will find it to use SyQADA. SyQADA makes no attempt to hide any of the complexity of data management from you. Its purpose is to provide tools that simplify the task of creating and running jobs, not to figure out what is wrong with a program or script. SyQADA’s competence has grown since this caveat was first written, and so some of the reason to know these things has been superseded by the syqada error command. However, one is almost certain to encounter issues that warrant comfort with Unix. I encourage you to be familiar with the following Unix commands (see Useful Shell Stuff Primer for a very shallow primer):

  • ls
  • find
  • grep
  • head
  • tail
  • cut
  • wc
  • shell globbing
  • shell pipelines
  • shell looping operators
  • shell event designators, word designators, and word modifiers