[Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"
dan.bolser at gmail.com
Mon Jul 12 08:42:58 EDT 2010
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
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
1) I loaded the GFF:
bp_seqfeature_load.pl -v -v -f -c -z \
--dsn dbi:mysql:mydb:myhost \
--namespace volvox \
-u me -p secret \
2) I changed the volvox.conf file:
#db_args = -adaptor memory
# -dir '$HTDOCS/databases/volvox'
db_args = -adaptor DBI::mysql
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