[Gmod-help] gmod tool db's and DBMS's

[Walk, Tom]

PostgreSQL is default for Chado

 

http://gmod.org/wiki/Databases_and_GMOD

 

 and MySQL is recommended for GBrowse

 

http://gmod.org/wiki/GBrowse_Install_HOWTO

 

That seems a bit complicated to me.  Does this mean that we should
populate and maintain our genome DB with PostgreSQL and use MySQL for
the browsing?

 

On the other hand, the Pg adaptor was supposed to be part of BioPerl
1.3.

 

http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk
/docs/pod/ORACLE_AND_POSTGRESQL.pod

 

Does BioPerl now have a Pg adaptor?

 

Can  we use Gbrowse with PostgreSQL without too much difficulty?  Has it
or is it being tested?  Is there any support if we want to use and/or
test it?

 

More basically, I see a list of adaptors

http://gmod.org/wiki/GBrowse#About_Databases

But at this point, I haven't seen a set of supported schema for GBrowse.
Has anybody compiled a list of supported schema?  Do I just need to get
them from the adaptor links above?

 

What about Jbrowse?  Does that do all of its queries with perl modules,
ie BioSQL or BioPerl?  Does it require or support any DBMS?

 

Additionally, what about Apollo?  Does it need a DBMS or does it rely
only on JAVA classes?

 

Finally, since I mentioned JAVA, do any of the tools have HQL
functionality.  Is there any HQL development in gmod?  Is there any
interest in HQL?

 

Thanks for the range of tools and any help you can provide with my
questions.

 

Tom Walk

tom.walk at ars.usda.gov

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20101020/9937ab12/attachment.html>