[Biojava-dev] Missing licence on BlastLikeDataSetCollection.dtd

[Andreas Prlic]

Hi Steffen,

> I was just going through last year's work on the packaging and found
> that you are happily using libjgraphT now and (as it just had to be) I
> ran into problem. Could you just indicate to me what version of that
> library you are using?

not exactly sure which version is being used, therefore CCing the dev 
list, where Richard might be able to help.  As far as I know, this is an 
optional dependency, which is only required for the new nexus parser.


> I am trying to use the Debian package of
> libjgraphT, which is of version 0.6.0 (0.7.x are incompatible with
> another program and was hence not yet update). Please also state this
> dependency somehere on your wiki pages.

That's true, it was missing from the docu there. I added it to the 
list of support libraries at the Download page in the wiki.

>
> On a sidenote, I know it to be common practice to ship the external jar
> files together with the local source. For the packagers however this is
> then always a bit difficult since one needs to amend everything to the
> versions that area already available locally.If would be preferable, in
> my view, to have the jar files distributed separatedly for those who
> want them, and with explicit instructions on how to retrieve them from
> external sources or even how to rebuild them from source.


We try to make life as easy as possible for the users. As such we provide 
a biojava-all jar file that contains the complete source code, javadocs 
and all jar files that biojava is dependent on as well as the biojava.jar.
It should be easy to extract whatever you need from that download. Let me 
know if anything is missing for you.  Additionally, if you only want the 
biojava.jar you can get that from the download site as well. We have not 
discussed bundling the dependencies separately, but my feeling is 
that this would add another step in the installation process, and just 
getting it all in one download might be the easiest.

Would a Maven setup be useful for you?

Andreas



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.