[Bioperl-l] Mysql database connection from Gbrowse

[Lincoln Stein]

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Hi Sean,

I can think of two explanations for this:

	1) you have two versions of perl and the one that you call when you
		are on the command line is different from the one that the
		CGI script calls

	2) you have two installations of the Perl library files, and the
		PERL5LIB environment variable is different under the CGI
		script than when you are logged in yourself.

Does this ring any bells?

Lincoln

On Thursday 26 February 2004 11:01 pm, Sean Davis wrote:
> 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.
>
> http://localhost/cgi-bin/gbrowse/human
>
> -----------------
> 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/darwin-thread-multi-2level
> /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:
> [GENERAL]
> description   = human
> db_adaptor    = Bio::DB::GFF
> db_args       = -adaptor dbi::mysql
>                 -dsn     human
>
> Any ideas?
>
> Thanks,
> Sean
>
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> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

- -- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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