[Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql"

Jason Stajich jason at bioperl.org
Tue Jul 13 18:48:20 EDT 2010


Dan -
I'm not convinced that contig:example is proper type/source for the 
landmarks & scaffold - i use 'scaffold:chromosome' in my data:

What happens if you change the GFF3 file line from
ctgA example contig 1 50000 . . . Name=ctgA
to
ctgA chromosome scaffold 1 50000 . . . Name=ctgA


I think this can be tweaked in the config but there may be different 
defaults for the in memory and DBI::mysql implementation.

-jason
Dan Bolser wrote, On 7/13/10 12:49 AM:
> Cheers Chris,
>
> Is there a known good version of
> "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to?
> I believe that this is one of the more common databases, so I'm
> surprised to find it broken.
>
> What would be the git command to roll back to a stable BioPerl / GBrowse?
>
>
> Sorry for the basic questions,
> Dan.
>
> On 12 July 2010 17:56, Chris Fields<cjfields at illinois.edu>  wrote:
>    
>> Dan.
>>
>> Is this maybe something for the GBrowse list? (cc'ing there JIC)
>>
>> chris
>>
>> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote:
>>
>>      
>>> Seems I still can't log bugs here:
>>> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474
>>>
>>> Error:
>>>         Artifact: Only Artifact Admins Can Modify Private ArtifactTypes
>>>
>>>
>>> Here I my bug report:
>>>
>>> I'm following the tutorial here:
>>>
>>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html
>>>
>>>
>>> I successfully set up and browsed the first database (going no further
>>> than #data_file). I decided to try switching from an in memory
>>> (file-based) database to a DBI::mysql database. After taking the
>>> appropriate steps (see below), I get the following error when viewing
>>> the database in GB:
>>>
>>>         The landmark named ctgA is not recognized. See the help pages
>>> for suggestions.
>>>
>>>
>>> I'm not sure why the landmark is found using a memory (file-based)
>>> database, but not found when using the same GFF loaded into mysql.
>>>
>>> This is the latest bioperl-live (although I'm still struggling with git).
>>>
>>> Any hints on what might be going wrong? I've a feeling I should
>>> perhaps roll back a few versions, as I noticed some SQL errors coming
>>> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm".
>>>
>>>
>>> Cheers,
>>> Dan.
>>>
>>>
>>>
>>> 1) I loaded the GFF:
>>>
>>> bp_seqfeature_load.pl -v -v -f -c -z \
>>>   --dsn dbi:mysql:mydb:myhost \
>>>   --namespace volvox \
>>> --summary \
>>>   -u me -p secret \
>>> databases/volvox/volvox_remarks.gff3
>>>
>>>
>>> 2) I changed the volvox.conf file:
>>>
>>> #db_args       = -adaptor memory
>>> #               -dir '$HTDOCS/databases/volvox'
>>>
>>> db_args       = -adaptor DBI::mysql
>>>                 -dsn mydb:myhost
>>>                 -namespace volvox
>>>                 -user me
>>>                 -pass secret
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>        
>>      
>
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