Re: [Gmod-gbrowse] gbrowse2

[Scott C. <sc...@sc...>]

Are there any error messages in the apache error log?

The connection bit I use in my (very old but still mostly functional)
GBrowse instance looks like this:

[this_database:database]
db_args = -adaptor DBI::mysql -dsn
dbi:mysql:database=c_elegans_PRJNA13758_WS284;host=rdbms.wormbase.org -user
********* -pass *********
search options = default, +wildcard, -stem, +fulltext, +autocomplete
db_adaptor = Bio::DB::SeqFeature::Store

On Fri, Apr 29, 2022 at 4:34 PM Rajaya, Kiran <ra...@bc...> wrote:

> Hi Scott,
>
> Thanks for your prompt response.  The MySQL is on a different server from
> where gbrowse is installed and we are able to connect to MySQL fine..   the
> modules are also installed.
>
> Thanks
> Kiran
>
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> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Friday, April 29, 2022, 6:10 PM
> *To:* Rajaya, Kiran <ra...@bc...>; Gbrowse (E-mail) <
> gmo...@li...>
> *Cc:* he...@gm... <he...@gm...>
> *Subject:* Re: gbrowse2
>
> ****CAUTION:*** This email is not from a BCM Source. Only click links or
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> ------------------------------
> Hi Kiran,
>
> Oh, that could be difficult to debug. I'll start with suggesting that you
> move to JBrowse 1 (quite stable) or JBrowse 2 (active development with new
> features getting added often).  http://jbrowse.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__jbrowse.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=XIIakvN9-mX88hFwKeTtLHUhV8huao67UvIqVIjAhFw&e=>
>
> I'll start with this: is the mysql database on the same machine as the
> GBrowse 2 install, and are there any useful error messages in the apache
> error log? Are the DBI and DBD::mysql perl modules installed?
>
> Scott
>
>
> On Fri, Apr 29, 2022 at 3:33 PM Rajaya, Kiran <ra...@bc...> wrote:
>
>> Hi,
>>
>>
>>
>> I have question about gbrowse2 that we have setup on a new server since
>> we migrated.  We have setup everything however the gbrowse is not able to
>> call the MySQL database.  How can I check what is missing to make the
>> connection successfully?
>>
>>
>>
>> Thanks!
>>
>> Kiran
>>
>>
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
> GMOD Project Manager (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=hmi0kfFk5a_xIUXLEhr_Ig&m=ZrqfUL5Wc7zcI-cWuUp8As2kv--PheEQTN5B8ieXJvL1DK-vfVzJUZGnNym2IScA&s=Fd7Ky6SNhoDPhG4W0EMV0GiQqIxTaqUUWyAPj3KKnWc&e=>)
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)