[Bioperl-l] new cvs module bioperl-runnable

[Elia Stupka]

> There are LOTS of files now in Bio::Tools::Run.  For people who aren't
> running analysis this is a bit of a bite for the building and downloading
> and I think it is appropriate for the core of bioperl to be a little
> lighter.  If the opportunity and (lack of) hassle were there, I would want
> bioperl-live to become bioperl-core.

The whole extra effort of writing stuff in Bio::Tools::Run from our side
was because we wanted to make sure people could use our work for
standalone analyses, so I wouldn't like to see them move to
bioperl-pipeline. I like the bioperl-run CVS module idea, that is a nice
split. Basically it's important for people to realise that the pipeline is
workflow management code, and not much else, and it wraps whatever
databases and run modules one wants to wrap.

Another side comment is about the Pise run modules. This is in no way a
criticism, there is lots of useful code, but I wonder if we have just
"overlapped it" with bioperl run, and whether some reationalisation should
be done (i.e. what is covered by Pise, what is covered by
Bio::Tools::Run) or perhaps again whether they should go in a module. In
other words we are not very clear about the rational of Pise's integration
with bioperl at the moment I think.

Elia

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