[Biojava-l] error: Program ncbi-blastn Version 2.2.17 is not supported

[Andy Yates]

I think Groovy have adopted a similar system recently & have guidelines 
for how each module should behave (dependencies, build system etc). This 
enforces the idea that a module whilst not part of the core project must 
behave in the same manner the core does. I do like the idea that we can 
have a core biojava & things get added around it & it might encourage 
other users to start developing their own modules for any 
formats/purpose they want.

Richard Holland wrote:
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>> What format options are there from blast? Just thinking if it supports
>> CIGAR or something like that are we better providing a parser for that
>> format & saying that we do not support the traditional blast output?
>> That said it doesn't help is when that format changes so maybe what is
>> needed is a way to push out parser changes without requiring a full
>> biojava release (v3 discussion) ...
> 
> Exactly! So the modular idea would work nicely here - we could have a
> blast module and only update that single module (which would be its own
> JAR) whenever the format changes. In a way, BioJava releases as such
> would no longer happen, except maybe for some kind of core BioJava
> module. Everything would be done in terms of individual module+JAR
> releases instead - one for Genbank, one for BioSQL, one for NEXUS, one
> for Phylogenetic tools, one for translation/transcription, etc. etc.
> 
> cheers,
> Richard