Bioperl: Module collections...

[Ewan Birney]

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?)

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?)

c) My Align module - renamed Bio::SimpleAlign


The proposal at the moment is to have a CVS with the following directory
structure....

Bioperl/
	README (?)
	Docs/
		html/(?)
	Examples/ 
	Bio/
		bioperl.pod (so perldoc bioperl gives you info) 
		Seq.pm
		Parse.pm
		SimpleAlign.pm
		Tools/
			Blast.pm
			Fasta.pm
			Blast/
                            <the rest of stevec's stuff>

At the moment I'm not going to put UnivAlign.pm or a holder for
Entry.pm (the shopping bag from Ian korf...) or other things, but
the aim is that when Georg or Ian want to do it they can just do
a cvs add xxxx


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).


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

For people not in the core, it will take us a couple of months probably
before we are working cleanly from the CVS system. Following the
cathederal and the bazaar mode, I want bioperl to be a bazaar (with a
strong core) and so release as soon as we have a working version of the
modules in the CVS system.


For additions outside of the 'core' (eg, Jongs function library, Ian's GSC
stuff, some of the Sanger stuff) we will have to figure out a way of
keeping the packages/links on the machine which works well with the core.



Any comments on this?



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


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