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

Dan Bolser dan.bolser at gmail.com
Tue Jul 13 03:49:44 EDT 2010


Cheers Chris,

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,
Dan.

On 12 July 2010 17:56, Chris Fields <cjfields at illinois.edu> wrote:
> 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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>
>



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