[Bioperl-l] Accessing database settings

[Scott Cain]

Generally, the load script will get the user name from the shell, but in
your case it seems to not be picking it up.  From `perldoc
bp_load_gff.pl`, you can supply a --user argument to supply a MySQL
username.  This, of course, assumes that you have already granted your
MySQL user permission to operate on the database as the directions in
the INSTALL doc and the tutorial indicate.

Scott


On Mon, 2005-07-25 at 17:28 -0400, Wacki wrote:
> When I run:  bp_load_gff.pl -c -d volvox volvox_all.fa volvox_all.gff
> 
> 
> I get:
> ------------------------------------------------------------------------------------------------------------------------------------------------
> 
> DBI connect('volvox','',...) failed: Access denied for user
> ''@'localhost' to database 'volvox'
> at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm line 139
> 
> ------------- EXCEPTION  -------------
> MSG: Can't connect to database: Access denied for user ''@'localhost'
> to database 'volvox'
> STACK
> Bio::DB::GFF::Adaptor::dbi::caching_handle::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:89
> STACK
> Bio::DB::GFF::Adaptor::dbi::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/GFF/Adaptor/dbi.pm:93
> STACK
> Bio::DB::GFF::Adaptor::dbi::mysql::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/GFF/Adaptor/dbi/mysql.pm:270
> STACK
> Bio::DB::GFF::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/GFF.pm:599
> STACK toplevel /usr/bin/bp_load_gff.pl:103
> 
> --------------------------------------
> 
> 
> --------------------------------------
> 
> 
> On 7/25/05, Scott Cain <cain at cshl.edu> wrote:
>         Hello,
>         
>         I am guessing you are writing about accessing a GFF database,
>         since you
>         are also posting questions to the gbrowse mailing list.  Also,
>         from your
>         posts there, I'm guessing that you have figured it out.  If I
>         am not 
>         guessing correctly, please re-ask the question and make it a
>         little more
>         clear what you mean.
>         
>         Scott
>         
>         
>         On Sat, 2005-07-23 at 22:53 -0500, Wacki wrote:
>         > I installed bioperl but didn't use the right
>         password/username combo. How do 
>         > I change it? Thanks for the help.
>         >
>         > _______________________________________________
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>         > Bioperl-l at portal.open-bio.org
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>         --
>         ------------------------------------------------------------------------
>         Scott Cain, Ph. D.
>         cain at cshl.edu
>         GMOD Coordinator (http://www.gmod.org/)
>         216-392-3087
>         Cold Spring Harbor Laboratory
>         
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory