[Bioperl-l] bioperl-run; size/complexity of bioperl for 1.2

[Hilmar Lapp]

If you can get c) to work with an affordable amount of pain on our 
(maintainers') end, that'd be cool and my clear favorite.

What would people have to do if they wanted to expand on top of 
their 'starter pack'? Complementary tars? Anonymous checkouts?

	-hilmar

On Friday, November 22, 2002, at 02:15 PM, Ewan Birney wrote:

>
>
> We are starting to run into a problem due to the sheer size of Bioperl;
> we have 500 odd modules in bioperl-live (perhaps better thought of as
> bioperl-core) - but some of the first "use case" problems - like 
> running
> BLAST we have quite sensibly separated out into bioperl-run - which 
> itself
> has some 306 modules. In bioperl-run we hope to put lots of generic run
> functionality, not least it is the bridge between biopipe and the core
> (or, in Ensembl speak, it is the runnables) and we'd probably like 
> to put
> generic job control, primitive queue mangement and stuff in there.
>
> So... separate cvs modules - good. But... for new users... not having
> "BLAST a sequence" in the first thing they download - Bad.
>
>
> What we are struggling with is that our logical description is cutting
> across our "starting functionality" set. This I am sure is 
> something many
> projects have faced before - does anyone know how they square this 
> circle?
> Does anyone square this circle?
>
>
> More practically/importantly, for bioperl-1.2, do we:
>
>
>   (a) distributed bioperl-1.2, bioperl-run-1.2 and say "if you want 
> to get
> remote BLAST parsing, you have to download and install both" (I 
> don't like
> this - new users are getting freaked out enough just by installing 
> one of
> these beasts)
>
>   (b) Have a bioperl-all-1.2.tar.gz, which is everything in which case:
>     - how is it structured internally?
>     - do we do this with cvs aliases or scripts
>     - does bioperl-db come in? bioperl-ext? Oh... vey...
>
>   (c) Have bioperl-1.2 being actually "starter-pack bioperl" which is a
> merge-and-prune of bioperl-core and bioperl-run (and perhaps 
> others) and
> then distribute bioperl-live as bioperl-core-1.2.tar.gz,
> bioperl-run-1.2.tar.gz etc.
>
>
>
> Any ideas? I sort of favour (c) and am happy to write the necessary
> scripts for this and/or learn deep cvs aliasing magic for this.
>
>
>
> Basically the aim is to keep the learning curve as-flat-as-possible for
> newbies without having
> everything-in-one-cvs-module-and-everything-a-function-in-one-file for
> developers.
>
>
>
> The eternal problem for software engineers I am sure. Any thoughts out
> there?
>
>
> e.
>
>
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--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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