[Bioperl-pipeline] runnable parameters

[Elia Stupka]

> Essentially, how does one submit a job with inputs to the node without
> having the inputs fetched. I can't think of many.  So this maybe
> silly.

Uh, thought we agreed on the cigar line, which sounds very sane to me.

> DataMonger runner.pl that takes in a file as a parameter. (this file
> path is stored in some table) This script then parses the file structure
> knowing how to  recreate the object from that minimal info.

You don't need that, you can use the Freeze-Thaw module to freeze objects
in files if we ever need that.

> it seems that a lot of performance hit is in method calls and a bit on
> object construction. (Think GFD/VirtualContig). 

of course Freezing-Thawing means recreating the objects anyway.... 

> of course the silly thing is we are moving the database in to flat
> files..a no no right?..maybe GFD is the way to go. comments?

cigar line is fine....

> oops sorry about that. you ready to enlighten them, 'Sid' ? ;)

Sure no problem.... have 40 slides, ready to rock :)

Elia

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