[Pipet Devel] yum, canned locus (was: from Justin)

J.W. Bizzaro bizzaro at bc.edu
Tue Jun 15 18:14:04 EDT 1999

Humberto Ortiz Zuazaga wrote:
> Boulderio is a much simpler solution to the same problem we're looking at, how
> to pipeline biological data through a set of command line programs. It was
> designed for cgi based apps, and is written in perl.

I have to take a look at it, but what do you mean by "much simpler"?  Do you
mean simpler in design but less functional, or simpler in design with the same
function?  If it's the latter, why not take the same approach?

> But you can't put together a locus that depends on the availability of a
> network resource (the net may not be up).

I agree, we have to consider that all of a canned (run-time) locus's resources
may not always be available.  This could be because (1) a server is down, (2)
some remote component was removed, or (3) the canned locus came from elsewhere,
and the user doesn't have permission to access the same resources.

I think that we need BOTH design-time AND run-time checks.  Are you saying that
there should be no design-time check or that nearly all of the design should be
a run-time decision by the locus?

The user/developer should have control over the details of a locus canning, if
he/she would like to can a locus.  And the locus should first try to follow its
canned path, deviating from the path only if resources are no longer available. 
Do you agree?

> But that's the point, everyone is going to be constructing a command line,
> every time they run an analysis. In many cases, it will be the trivial command
> line input -> canned locus -> output, but often it won't be so simple. The
> people who really need help running the tools aren't the developers, it's the
> bench scientitsts.

IMHO, we have to expect that bench scientists are no more computer-savvy than
the general public.  They will expect Loci to operate, on the surface, like any
other GUI application.  They'll want to choose File->Open, then select a
sequence or whatever, and then push a button and get pretty pictures (well,
something useful anyway :-)  So, we must have lots of pre-canned command-lines
too.  I'd like the "learning curve" to be low.  Later on, the user can peel away
the layers of Loci to find an incredibly powerful and flexible system.

J.W. Bizzaro                  mailto:bizzaro at bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/

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