[Pipet Devel] ideas for a smaller piper core

[J.W. Bizzaro]

Jean-Marc Valin wrote:
> 
> No. This will make matters even more complicated, since we'd have to
> support Piper without Overflow and Piper with Overflow.

I don't think that it would mean supporting two code bases, as you're saying. 
If Overflow is a plugin to Piper, then, like all plugins, there should be no
major modification required for Piper.

> Besides that, I
> managed to get rid of most of Overflow dependencies. The only required
> library is now libxml, which is used by the DL anyway.

Great!

> It would also be
> easy to put the Overflow tree into the Piper tree for releases, so
> there's no big deal...

Hmmm.  I suppose we could pop Overflow in there for major releases.  I guess
we were thinking that people would have to go fetch it as a separate package. 
But it would require some changes to the build scripts.  Would you like to
help us change the build scripts to support Overflow options?

> Last thing I was not sure I understood from your previous mail: were you
> thinking of allowing another PL than Overflow or releasing Piper without
> a PL at all. Either way, I don't think I see the point...

I was thinking about a very small PL that would simply allow command-line
options to be strung together as nodes in a network, like Overflow does, but
that would be the only thing that this PL would do.  The point?  To let users
use Piper for just command-line wrapping without the overhead of a dataflow
system, also to make it more obvious how command-line wrapping is done.

In any case, I want to emphasize that we don't want to drop support for
Overflow or make it more difficult to run Piper with Overflow.  Talking to
some people about Piper over the past year, I've been frequently asked if
Piper could support a certain existing system (e.g., some collaboratory),
which would work in place of Overflow.  And the question that I have to ask
(of us) is "can Piper even work without Overflow?"  Again, Jean-Marc, I'm not
trying to ditch Overflow, so please don't take it the wrong way.  Overflow can
work without Piper, and I simply think that Piper users may want the same
flexibility.

Perhaps I'm just a raving lunatic.

Cheers.
Jeff
-- 
J.W. Bizzaro                                jeff at bioinformatics.org
Director, Bioinformatics.org        http://bioinformatics.org/~jeff
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