Mark Morgan wrote:
I have to disagree. My implementation is not correct in so much as my job is to run jobs for scientists here at UVa. Those scientist use BLAST. Blast currently cannot run on my implementation because my implementation can have spaces in the path to where the BES jobs run. Therefor I have failed my scientists. We all know that BLAST is crapping out on spaces because it is poorly written and in a perfect world we would be able to justify the failure based off of that, but unfortunately, we are in the business of supporting poorly written applications. An application that cannot handle spaces in the paths is a fact of life and we need to be able to describe that unfortunately circumstance.
I agree that there's a system failure. I just disagree that this is JSDL's fault; it is correctly describing what people want to run. It's just a shame that the application isn't as capable as that. Guessing from what you say that we're talking about running stuff on Windows with its odd ideas about user-specific temp directory names, the immediate fix is probably to add an OS constraint because changing the temporary directory is plain awkward and the default in most languages has a space in it. And complain to the BLAST maintainers, of course. If I'm guessing wrong and the issue is users' files with spaces in the names (as opposed to in the path) I'd just call that PEBKAC and stop worrying about it. ;-) Donal.