[Bioperl-l] Mysql database connection from Gbrowse

Sean Davis sdavis2 at mail.nih.gov
Thu Feb 26 16:01:53 EST 2004

Lincoln and others,

With regard to my last e-mail, I simply used bp_load_gff.pl and was able to
load the human gff files from gmod.org within an hour or so.

In any case, I have a working mysql database called human that I can access
via mysql command line.  I also have a working version of gbrowse that
connects to the yeast_chr1 memory database.  (I also connected to the DAS
server at ucsc--WAY COOL.)

I am now trying to connect to my mysql human database and get the following
returned to the browser.


An internal error has occurred

Could not open database.
install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (@INC
contains: /System/Library/Perl/5.8.1/darwin-thread-multi-2level
/System/Library/Perl/5.8.1 /Library/Perl/5.8.1/darwin-thread-multi-2level
/Library/Perl/5.8.1 /Library/Perl
/Network/Library/Perl/5.8.1 /Network/Library/Perl .) at (eval 18) line 3.
Perhaps the DBD::mysql perl module hasn't been fully installed,
or perhaps the capitalisation of 'mysql' isn't right.
Available drivers: ExampleP, Multiplex, Proxy, Sponge.
 at /Library/Perl/5.8.1/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm line 139

 Please contact this site's maintainer ([no address given]) for assistance.

 For the source code for this browser, see the  Generic Model Organism
Database Project. For other questions, send mail to lstein at cshl.org.
$Id: yeast_chr1.conf,v 1.6 2004/02/04 15:03:43 marclogghe Exp $

 Note: This page uses cookie to save and restore preference information. No
information is shared.
Generic genome browser version Bio::Graphics::Browser=HASH(0x801294)

However, this works:
perl -e "use Bio::DB::GFF::Adaptor::dbi::mysql"
As does
perl -e "use DBD::mysql"

>From the human.conf file:
description   = human
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor dbi::mysql
                -dsn     human

Any ideas?  


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