[Bioperl-l] Bptutorial.pl

[Jason Stajich]

On Fri, 20 Dec 2002, Peter Schattner wrote:

>
> I dunno, Jason. The bptuorial script was working before the change to
> StandAloneBlast.pm was made. I would suppose that any other
> previously-working script which uses any of the exists_blast,
> exists_clustalw  etc methods will also crash after upgrading bioperl-run.

> Moreover the crash will be accompanied by a cryptic message such as the
> one Paul initially received (the messages are coming from the module’s
> AUTOLOADER trying unsuccessfully to interpret the method call).  Anyway
> I think if no clear warning is added for people uisng the exists_blast
> etc methods, there will be a bunch of qustions coming onto the bioperl
> bug and/or query lists.
>

I'm sorry that is the case but we need to build a general extensible
framework for runnable wrappers which includes a single method one can
call to test for the existance of the executable.  This permits a much
more extensible pipeline system and a unified interface to application
wrappers.  If you have feedback or comments on how to structure these the
base class is Bio::Tools::Run::WrapperBase and we would welcome
contributions.  The Fugu team has been quite actively developing new
wrapper tools in this manner.

I think in fact that no one is helping maintain the scripts and examples
files after Brian O needed to take a hiatus so I'm quite sure there are
things that don't work.  Scripts which run things probably should be
reorganized into the bioperl-run directory as well.

If you would like the old exists_XX functions to be there we can add them
back in for backwards compatability.

> > Peter - I think it makes sense perhaps to split the parts which run
> > applications out of bptutorial into something in
> > bioperl-run/bpruntutorial.pl or core/bpruntutorial.pl to avoid throwing
> > people for too much of a loop.  What do you think?
>
> Well I agree with you here.  Actually there are only three bptutorial demos
> that use the run-library programs, so, unless there is loud complaint, I
> intend to simply remove the 3 demos from bptutorial.pl (and _not_ create a
> new script "bpruntutorial.").
>
> My first thought here was to simply point the bptutorial reader to the
> standaloneblast.pl script in the script/tools directory as an example.
> However the interface has changed sufficiently that this script now gives
> multiple errors with no clear indication of what is causing them. I don’t
> have the time to track these down myself right now,  so I am separately
> submitting a bug report on them.
>
> All of this does bring up another issue: Is anyone checking that the sample
> scripts in the "examples" and "scripts" directories still work?  Having lots
> of examples is nice but only if they work.  Otherwise better to remove them.
> Unfortunately I do not have the time to pursue this myself.  Any interest
> Brian or anyone else?
>
> Peter
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu