[BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb

[Nick Matzke]

Hi all,

(sorry that I cross-posted this to the biopython lis, I only just 
realized I should get on the bioSQL list)



I'm following the BioSQL tutorial at the biopython website 
(http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy ).  I can get 
bioseqdb to work, and the biosql python scripts etc.

However I can't get these directions to work in loading the taxonomy 
database into bioseqdb.  I get: "Can't locate object method "connect" 
via package "DBI" "

I double-checked to make sure I've got DBI in perl (see error message 
below) but that doesn't seem to help.

Any help appreciated!
Nick



commands/returns:
===========================
mws2:/bioinformatics/eg nick$ perl -v

This is perl, v5.10.0 built for darwin-thread-multi-2level
(with 3 registered patches, see perl -V for more detail)

Copyright 1987-2007, Larry Wall

Binary build 1002 [283697] provided by ActiveState 
http://www.ActiveState.com
Built Jan 10 2008 11:08:33

Perl may be copied only under the terms of either the Artistic License 
or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.






mws2:/bioinformatics/eg nick$ sudo cpan DBI
Password:

CPAN: Storable loaded ok (v2.18)
Going to read /usr/local/Metadata
   Database was generated on Wed, 23 Jul 2008 10:02:50 GMT
CPAN: LWP::UserAgent loaded ok (v5.810)
CPAN: Time::HiRes loaded ok (v1.9711)
Fetching with LWP:
   http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz
CPAN: YAML loaded ok (v0.66)
Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz
............................................................................DONE
Fetching with LWP:
   http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz
Going to read /Users/nick/.cpan/sources/modules/02packages.details.txt.gz
   Database was generated on Mon, 01 Sep 2008 10:02:51 GMT
............................................................................DONE
Fetching with LWP:
   http://ppm.activestate.com/CPAN/modules/03modlist.data.gz
Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz
............................................................................DONE
Going to write /usr/local/Metadata
DBI is up to date (1.607).






mws2:/bioinformatics/eg nick$ 
/bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl 
--dbname bioseqdb --driver mysql --dbuser root --download true


Can't locate object method "connect" via package "DBI" at 
/bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl 
line 323.

mws2:/bioinformatics/eg nick$
===========================



Additional sleuthing:
===========================
Based on some web advice on this general error I also did this:

sudo cpan DBD::mysql

...which did install something that wasn't installed.  But the same 
error resulted when the load_ncbi_taxonomy.pl script was run.
===========================


Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not 
finding them in @INC or something doesn't seem to be the problem...

(these commands return '1' if the module is successfully found)
============
perl -MDBD::mysql -e 'print 1'
1

perl -MDBI -e 'print 1'
1
============