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

Chris Fields cjfields at illinois.edu
Mon Jul 12 12:56:12 EDT 2010


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
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