[Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql"
jason at bioperl.org
Tue Jul 13 18:48:20 EDT 2010
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
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.
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,
> On 12 July 2010 17:56, Chris Fields<cjfields at illinois.edu> wrote:
>> Is this maybe something for the GBrowse list? (cc'ing there JIC)
>> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote:
>>> Seems I still can't log bugs here:
>>> Artifact: Only Artifact Admins Can Modify Private ArtifactTypes
>>> Here I my bug report:
>>> I'm following the tutorial here:
>>> 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".
>>> 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 \
>>> 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
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