[Biojava-dev] biojava SVN

Tue May 4 20:12:12 UTC 2010

The answer how to get non-mavenized Jars out is probably a simple one:

here how to set up our own repository. I will look at setting one up
at one of the OBF servers. This can then be pointed to from our pom
files...

http://steve-on-sakai.blogspot.com/2009/12/setting-up-your-own-maven-repository.html

Andreas

On Tue, May 4, 2010 at 9:14 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> 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/
>
>
>
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------