Bioperl: Module collections...

[Steve A. Chervitz]

Ewan,

> Looking ahead to next week when chris and I are going to 
> get together to make the CVS system I'm downloading modules
> to put in....
> 
> a) Bio::PreSeq.pm (can we start calling this Seq.pm now?)

The name change should coincide with a functionality change, namely, 
adding a feature description mechanism. We'll have to hear from ChrisD 
and Ian about their progress along these lines.
 
> b) Stevec's Blast module 
> 
> 	This use's Steves Bio::Root::Global (at least) and ??
> Bio::Root::Object 
> 
> 	Steve - can we get rid of these things? (Do you want to?)
> 

Well, my modules rely on these so they are a necessary part of my Blast 
distribution as it currently stands. You could put my Bio::Root directory 
under CVS as well (it's bundled with my Blast distribution). Removing 
them from my design would take a fair bit of non-trivial de-engineering 
that I would hesitate to do (but would consider if people complained loud 
enough :). 

Note that I'm planning a new release of my Blast distribution (0.058) 
that should be ready next week. It will have some significant changes.


> [ snip ]
> 
> Once we have a CVS system up the core group can start maintaining
> things from the CVS system. I *hope* that a clean dump of the CVS
> system will be a clean build with a
> 
> 	perl Makefile.PL
> 	make, make install
> 
> but who is our Makefile.PL guru  ( its not me!) to get this thing to
> recurse into directories (or does it anyway. I'm slightly in awe of
> Makefile.PL).

The make process will recurse automatically. Let me know if you run into 
specific problems. (I'm no guru but I have some experience with it).

 
> Stevec - do you want to write bioperl.pod and the README (you seem the
> natural person for it as leader etc...)?

I can come up with a draft. Do you have some ideas in mind for what these 
documents should say? 

SteveC

-------------------------------------------------------------------
Steve A. Chervitz                          Department of Genetics
sac@genome.stanford.edu                    Stanford University
http://www-genome.stanford.edu/~sac        Stanford, CA 94305-5120
-------------------------------------------------------------------

> Ewan Birney
> <birney@sanger.ac.uk>
> http://www.sanger.ac.uk/Users/birney/

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