[BioPython] problem loading NCBI_taxonomy database into bioseqdb

[Nick Matzke]

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 found)
============
perl -MDBD::mysql -e 'print 1'
1

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



Nick Matzke wrote:
> 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.
> 
> Nick
> 
> 
> Nick Matzke wrote:
>> Hi all,
>>
>> 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$
>> ===========================
>> ===========================
>> ===========================
>>
>>
>>
>>
>>
>>
>>
>>
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab websites:
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Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================