[Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"
cjfields at illinois.edu
Mon Jul 12 12:56:12 EDT 2010
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
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