[Biojava-dev] biojava SVN

[Andy Yates]

Well it's too bad a chicken & egg situation really. Looking at the Maven file the current BioJava has only 1 dependency on a non-Mavenized project which is bytecode.jar.

I can have a look at doing this for 1.7 if people don't mind.

Andy

On 4 May 2010, at 06:59, Michael Heuer wrote:

> 
> We recently went through the process of syncing a project to maven central
> repository using the OSS Repository Nexus installation at Sonatype.
> 
> http://code.google.com/p/piccolo2d/issues/detail?id=168
> 
> https://docs.sonatype.com/display/NX/OSS+Repository+Hosting
> 
> Using Nexus as a repository manager is quite nice (we use it at work too)
> but syncing to central carries some additional requirements (e.g. all
> releases must be signed with a PGP key hosted on the MIT keyserver) which
> take some time to work through.
> 
> All biojava dependencies (including maven plugins) must already be
> available on maven central or we won't be able to sync -- kind of a
> chicken and egg problem I know.
> 
>   michael
> 
> 
> On Fri, 30 Apr 2010, Richard Holland wrote:
> 
>> Could a small MVN repo be set up at OBF?
>> 
>> On 30 Apr 2010, at 16:48, Andy Yates wrote:
>> 
>>> Does anyone know how hard it would be to get these into the public maven repository? The EBI repo is all well & good but updating it relies on BioJava always having a committer at the EBI. Now I know that is a very likely statement but is it something we can rely on?
>>> 
>>> Andy
>>> 
>>> On 30 Apr 2010, at 16:44, Andreas Prlic wrote:
>>> 
>>>> Hi,
>>>> 
>>>> The BioJava SVN has not been fully compiling ever since the Hackathon. I
>>>> guess things were quite in flux the last months and it is now time to make
>>>> sure SVN fully compiles again.  There is a few things we need to figure out
>>>> in order for that:
>>>> 
>>>> * Jar files for libraries that are not in a public Maven repository. Jules :
>>>> at some point you indicated that we might be able to get such jar files
>>>> hosted by the EBI Maven repository. Do you think that is still an
>>>> possibility and could you get a few libraries into that? In particular that
>>>> would be Jmol, Astex, and probably one or two other Jar files. That would
>>>> make the BioJava checkout process much smoother and not require a developer
>>>> to manually install jars for full functionality.
>>>> 
>>>> * We have a couple of modules that are fragmented and broken. This is due to
>>>> historic leftovers from when we started the re-factoring process. If all the
>>>> functionality has been moved into the new biojava3-core module, I would vote
>>>> for removing the modules starting with sequence*
>>>> 
>>>> Andreas
>>>> 
>>>> 
>>>> --
>>>> -----------------------------------------------------------------------
>>>> Dr. Andreas Prlic
>>>> Senior Scientist, RCSB PDB Protein Data Bank
>>>> University of California, San Diego
>>>> (+1) 858.246.0526
>>>> -----------------------------------------------------------------------
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>> 
>>> --
>>> Andrew Yates                   Ensembl Genomes Engineer
>>> EMBL-EBI                       Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> 
>> --
>> Richard Holland, BSc MBCS
>> Operations and Delivery Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>> http://www.eaglegenomics.com/
>> 
>> 
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> 

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/