[Gmod-help] Re: Gbrowse

[Brenton Graveley]

Hi Dave,

Thanks!  This is great.

I'll post to the mailing list once I subscribe, but in the case I  
catch you before you leave.....

I tried this and got the following.

sh-3.2# mysql -uroot -e 'create database smed'
ERROR 1007 (HY000) at line 1: Can't create database 'smed'; database  
exists

I also tried to load some data in using 'smed' instead of 'Smed' and  
it said the database didn't exist.

Hmmmmm.....puzzling

Any ideas?

Thanks,

Brent



On Nov 6, 2008, at 3:18 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Brent,
>
> It's always nice to meet a new GMOD user.  I recommend posting any
> GBrowse queries directly to the the GBrowse mailing list. If you
> haven't done so already, I recommend subscribing to that list (see
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse).  Everyone
> at the help desk plus over 100 other people will see it that way.  I
> have edited out some text below just in case this conversation
> continues and ends up on that list (a likely event).
>
> I am not positive, but what I think is going on here is the Perl is
> tripping up on the case of the database name.  (Database names are
> case sensitive in MySQL.)  You are consistently capitalizing it
> "Smed", but the error messages imply that the code is shifting the
> name to lower case.  Try repeating the earlier steps, but this time
> use "smed" instead.  I *think* this will get you farther.
>
> Starting in about 30 minutes, I'm either away from my e-mail, or darn
> busy, for the next 3 days.  I'll try to followup, but it may take me a
> while.
>
> Thanks,
>
> Dave C
> GMOD Help Desk
> --
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
> On Thu, Nov 6, 2008 at 11:49 AM, Dave Clements  
> <clements at nescent.org> wrote:
>> ---------- Forwarded message ----------
>> From: Brian Osborne <briano at bioteam.net>
>> Date: Thu, Nov 6, 2008 at 10:57 AM
>> Subject: Re: Gbrowse
>> To: Brenton Graveley <graveley at neuron.uchc.edu>
>> Cc: Dave Clements <clements at nescent.org>
>>
>>
>> Brent,
>> I'm writing Dave Clements here, he is a bioinformatics person and
>> GMOD/Gbrowse expert at NESCent, part of his job is to help out
>> scientists who are using these tools.
>> Dave, I'd like to introduce you to Brent Graveley, he's a PI at U.
>> Conn. and a new Illumina user, he's generating enormous amounts of
>> sequence and would like to set up GBrowse as a viewer.
>> Brian O.
>> --
>> Brian Osborne, PhD
>> BioTeam: http://bioteam.net
>> email: briano at bioteam.net
>> mobile: 978-317-3101
>>
>> On Nov 6, 2008, at 1:40 PM, Brenton Graveley wrote:
>>
>> Hi Brian,
>> Ok, so I did:
>> export PERL5LIB=/sw/lib/perl5/5.8.6/darwin-thread-multi-2level
> [[snip]]
>> prior to doing this, I did tried to create a mysql database by doing
>> the following:
>>
>> mysql -uroot -e 'create database Smed'
>>
>> mysql -uroot -e 'grant all privileges on Smed.* to  
>> graveley at localhost'
>>
>> mysql -uroot -e 'grant file on *.* to graveley at localhost'
>>
>> mysql -uroot -e 'grant select on Smed.* to www at localhost'
>>
>> I then tried to load a .gff file into the database using:
>>
>> bp_bulk_load_gff.pl -d Smed 454_REGEN_miRNAs.gff3
>>
>> It returned the following:
>>
>> sh-3.2# bp_bulk_load_gff.pl -d Smed 454_REGEN_miRNAs.gff3
>>
>> This operation will delete all existing data in database Smed.   
>> Continue? y
>>
>> DBI connect('Smed','',...) failed: Unknown database 'smed' at
>> /Library/Perl/5.8.8/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm line 134
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>
>> MSG: Can't connect to database: Unknown database 'smed'
>>
>> STACK: Error::throw
>>
>> STACK: Bio::Root::Root::throw /Library/Perl/5.8.8/Bio/Root/Root.pm: 
>> 357
>>
>> STACK: Bio::DB::GFF::Adaptor::dbi::caching_handle::new
>> /Library/Perl/5.8.8/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:88
>>
>> STACK: Bio::DB::GFF::Adaptor::dbi::new
>> /Library/Perl/5.8.8/Bio/DB/GFF/Adaptor/dbi.pm:95
>>
>> STACK: Bio::DB::GFF::Adaptor::dbi::mysql::new
>> /Library/Perl/5.8.8/Bio/DB/GFF/Adaptor/dbi/mysql.pm:269
>>
>> STACK: Bio::DB::GFF::new /Library/Perl/5.8.8/Bio/DB/GFF.pm:704
>>
>> STACK: /usr/local/bin/bp_bulk_load_gff.pl:317
>>
>> -----------------------------------------------------------
>>
>> It seems like it can't find it, but if I do the following:
>> sh-3.2# mysql -uroot -e 'create database Smed'
>> It returns the following:
>> ERROR 1007 (HY000) at line 1: Can't create database 'Smed';  
>> database exists
>> So, it's there, but can't see it.
>>
>>
>> Also, I modified the config file for the browser so that the top  
>> lines read as:
>> description   = Schmidtea mediterranea Genome Database
>> db_adaptor    = Bio::DB::SeqFeature::Store
>> db_args       = -adaptor DBI::mysql
>>               -dsn    dbi:mysql:database=Smed
>>               -user   www
>>