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

Dan Bolser dan.bolser at gmail.com
Mon Jul 12 08:42:58 EDT 2010


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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