On Fri, Jul 27, 2012 at 4:01 PM, Jeang, David - ARS
<
David.Jeang-yPPU2dwoW2ufRvmTrFJqzg@public.gmane.org> wrote:
>
> Scott, I said before it WAS a permission problem and it was solved...
>
> David Jeang
> -----Original Message-----
> From: Scott Cain [mailto:
scott <at> scottcain.net]
> Sent: Friday, July 27, 2012 2:28 PM
> To: Raymond Wan
> Cc: Jeang, David - ARS;
gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> Subject: Re: [Gmod-gbrowse] establishing chado connections
>
> Hi Ray,
>
> Thanks, though in this case I don't think that is the problem. The error message was that it couldn't find cv, not that it had a permission problem.
>
> Scott
>
>
> On Fri, Jul 27, 2012 at 1:32 PM, Raymond Wan <
rwan-0/wyVZ4TESw+M+u0nzDfMQ@public.gmane.org> wrote:
>>
>> Hi Scott/David,
>>
>> It's been a while ago, but for what it's worth, when I set up GBrowse
>> + Chado, cv was one of the tables (perhaps the only table) which
>> didn't have permissions granted to it. I had to grant the permissions
>> manually. I never investigated what the reason was, though.
>>
>> Ray
>>
>>
>> On Thursday, July 26, 2012 11:49 PM, Scott Cain wrote:> Hi David,
>>>
>>> I agree that using ALTER USER should do the trick. What happens when
>>> you use the psql shell on the command line as that user? You could
>>> try a simple query like SELECT
>>> count(*) FROM cv; to see if it finds the cv table. If that appears
>>> to work, we should ask on the tripal mailing list, since they more
>>> experience with this sort of thing.
>>>
>>> Scott
>>
>>
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>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (
http://gmod.org/)
216-392-3087
> Ontario Institute for Cancer Research
>
>
>
>
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (
http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research
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> i have upload the seq into mysql but it doesnt appear when i click the
> gene....
That sounds like a problem with something else such as how GBrowse is connected
to your database. If you can load sequences fine but are unable to click on
genes, it is possible you haven't loaded the gene annotations yet?
Ray
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