[Bioperl-l] Revising the bioperl tutorial for release 1.2

[Peter Schattner]

Hello all

I am working on updating the "bptutorial.pl" bioperl tutorial in so that it
accurately reflects changes and additions in release 1.2.

To that end I have just committed a new (draft) version to bioperl-live CVS.
The main changes include:
1  Reorganization of the tutorial so descriptions of all modules which
require bioperl "auxiliiry" packages (eg bioperl-run, bioperl-ext) in a
separate section with a brief description of how to obtain them (which as far
as I can tell means using anonymous CVS)
2. more emphasis on SearchIO rather than other parsers
3. brief descriptions of Cluster / ClusterIO, GFF parsing and the PAML result
parser

At this point I need some help.  Bioperl has gotten too big for me to be able
to be facile with all of it.  I have done my best to describe its features,
but I am pretty sure there are mistakes and/or omissions.  So I’d be grateful
if some of you who use (or revised or wrote) some of the modules that are
being added or substantially revised for release 1.2 would check the tutorial
and make sure it is as error free as possible.

The runnable bptutorial.pl script has also been updated a bit and it would be
worth confirming that it runs on other environments.  Also if there are
significant new features that will be included in 1.2 that I have missed,
please let me know and I’ll include them.

For any corrections or additions, either email me with the text and I’ll
insert it or do it yourself in the CVS (in that case I’d appreciate if you’d
just let me know).

Needless to say, keeping the tutorial accurate and up-to-date for the 1.2
release will make everyone’s life a lot easier.

Thanks.

Peter