[Bioperl-l] Reliable working version of Biosql

[Hilmar Lapp]

I should add that a release of biosql and bioperl-db is imminent. The
missing piece in the picture is catching up the Oracle part. While at
CSHL last week I got a fair step further: the Singapore version of
biosql-ora works, and I checked in fixes to bioperl-db on that Oracle
version, which passes all tests. I hope I get the PL/SQL API migrated
this week, and then both are basically ready for release.

MySQL and Postgres should be supported already without problems.

	-hilmar

> -----Original Message-----
> From: Hilmar Lapp 
> Sent: Monday, May 12, 2003 1:10 PM
> To: Zayed Albertyn; bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Reliable working version of Biosql
> 
> 
> You'll need at least bioperl-1.2.1 (released), or the bioperl 
> main trunk from CVS, biosql main trunk from CVS, and 
> bioperl-db main trunk from CVS.
> 
> If you decide to go with bioperl-1.2.1, you'll need a patch. 
> Let me know and I'll send it you. (I've posted it before but 
> yes, I need to commit this patch ...) Don't let the patch 
> discourage you; it's a very simple one and 1.2.1 is a very 
> good and stable version if you're not comfortable living on the edge.
> 
> With the above version combination you should be OK. If you 
> do get errors from the bioperl-db test suite, post the output 
> and I'll try and help you until you're set. So far I've got 
> everybody going who wanted to.
> 
> 	-hilmar
> 
> > -----Original Message-----
> > From: Zayed Albertyn [mailto:zayed at sanbi.ac.za]
> > Sent: Monday, May 12, 2003 3:21 AM
> > To: bioperl-l at bioperl.org
> > Subject: [Bioperl-l] Reliable working version of Biosql
> > 
> > 
> > HI there
> > 
> > I am trying to get the Biosql schema running on my local
> > mysql database but I have run into an incredible amount of 
> > problems. I did recieve some help previously regarding what 
> > versions of bioperl-live, bioperl-db and biosql to use but it 
> > didnt help that my mysql installation didnt talk 'innodb'.
> > 
> > So, I have heard that a relatively stable version of biosql
> > will be/or has been released on linux that will work with 
> > bioperl and its accessory modules. Could you please direct me 
> > which versions of these to download (with which flags in CVS) 
> > so that I can have some success in loading all my sequences 
> > in a database and working with them without recieving a 
> > multitude of perl error messages?
> > 
> > 
> > 
> > Many thanks in advance.
> > 
> > Zayed
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://pw600a.bioperl.org/mailman/listinfo/> bioperl-l
> > 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://pw600a.bioperl.org/mailman/listinfo/bioperl-l
>