[Bioperl-l] Bptutorial.pl

[Peter Schattner]

Jason Stajich wrote:

> >
> > I think that exists_blast, exists_clustal and exists_tcoffee should at
> > least be reinstated with the message that they are now "deprecated" and
> > will be removed in the future and the user is advised to use
> > Bio::Root::IO::exists_exe instead. Otherwise lots of scripts will crash
> > when people install/update bioperl-run.
> >
> actually not quite true - see below.

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.

> 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