[Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"
dan.bolser at gmail.com
Tue Jul 13 03:49:44 EDT 2010
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
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