[Bioperl-l] Another small bump

[Hilmar Lapp]

Correct. It comes with biosql, not bioperl-db. The reason is that  
although it's in perl it doesn't use bioperl - so as long as you have  
perl installed and your DBD driver you can use it regardless of whether  
you're home in biojava, biophython, bioruby, or bioperl.

	-hilmar

On Friday, February 11, 2005, at 12:28  PM, Brian Osborne wrote:

> Mike,
>
> It's in the biosql package, not the bioperl-db package. Go to:
>
> http://obda.open-bio.org/
>
> or
>
> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/ 
> ?cvsro
> ot=biosql
>
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Mike Muratet
> Sent: Friday, February 11, 2005 1:59 PM
> To: Brian Osborne
> Cc: Hilmar Lapp; bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Another small bump
>
>
>
>
> On Fri, 11 Feb 2005, Brian Osborne wrote:
>
>> Mike,
>>
>> Ah. Error in the bioperl-db document, that should be
>> "scripts/load_ncbi_taxonomy.pl".
>>
>> Brian O.
>>
>>
>
> Brian
>
> I just checked the directory (again) where I unpacked the tarball--I  
> don't
> see it. What was in the tarball:
>
> In /usr/local/lib/perl5/site_perl/5.8.0/bioperl-db/scripts/biosql
>
> bioentry2flat.pl
> cgi-bin
> clean_ontology.pl
> del-assocs-sql.pl
> drop_mysql_biosql_test_dbs
> freshen-annot.pl
> load_interpro.pl
> load_ontology.pl
> load_seqdatabase.pl
> merge-unique-ann.pl
> terms
> update-on-new-date.pl
> update-on-new-version.pl
>
> It's not in the subdirectories.
>
> I recall seeing it last time I built a database on another machine  
> (which
> has been awhile).
>
> I haven't had any problems loading sequences, but it would be a handy
> table to have.
>
> Thanks
>
> Mike
>
>> -----Original Message-----
>> From: bioperl-l-bounces at portal.open-bio.org
>> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Mike  
>> Muratet
>> Sent: Friday, February 11, 2005 10:21 AM
>> To: Hilmar Lapp
>> Cc: bioperl-l at bioperl.org
>> Subject: [Bioperl-l] Another small bump
>>
>>
>> Hilmar
>>
>> The bioperl-db installation notes speaks of load_taxonomy.pl in the  
>> biosql
>> distribution. I got the CVS tarball and there doesn't appear to be any
>> perl in it at all. I see in the archives that there was some  
>> discussion
>> about where it should live. Where does it live?
>>
>> Maybe there should be a 'beers for the developers' session in Detroit  
>> this
>> summer....
>>
>> Thanks
>>
>> Mike
>>
>>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------