[Gmod-help] Re: Gbrowse

[Scott Cain]

Hi Dave and Brent,

I think this is really the fault of the operating system.  Here is a
comment from the documentation for DBD::mysql about table names:

-------------------
Table names are limited by the fact that tables are stored in files
and the table names are really file names. In particular, the case
sensitivity of table names depends on the underlying file system.
-------------------

Since database names are also stored in the file system, they have to
behave as the operating system does.  Since Macs have a case
insensitive file system(! shocking, I know), you have to be case
insensitive too.  Unfortunately, what that really means is that
everything gets folded to lower case.

Scott


On Thu, Nov 6, 2008 at 3:18 PM, Dave Clements, GMOD Help Desk
<gmodhelp at googlemail.com> 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
>>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research