Re: [Gmod-schema] Fwd: Problem of Gbrowse with Chado

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Thank you very much.
When I installed Chado, I think it automatically takes the Localhost
(http://localhost:8081/, LISTEN 8081) as default. And When I installed
Gbrowse, it take the MAC localhost (http://localhost LISTEN 80).
But it seemed I can't use localhost:8081 to find the localhost I want,
can I, in chado.conf? How can I specify which port to listen?

THere is no DBD::Pg with EnterpriseDB since it is not written in Perl.
All the locations I found DBD::pg (pg.pm) are
/Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBD
/Library/Perl/5.10.0/darwin-thread-multi-2level/Bundle/DBD
/Library/Perl/5.10.0/DBIx/DBSchema/DBD

2010/8/11 Scott Cain <sc...@sc...>:
> Hi Jieyu,
>
> While there shouldn't be a GBrowse2 directory in
> /Library/Perl/5.10.0/darwin-thread-multi-2level/, having a GBrowse
> directory is perfectly fine.  Having two apaches might be leading to
> some confusion, since they can't both be listening on port 80.  If
> they are both trying to, I'm not sure which one would win; probably
> the system one.
>
> About the location of perl modules: what really matters in this case
> is where DBD::Pg is, and if there is more than one of them on the
> system.  It wouldn't surprise me if EnterpriseDB installed its own
> DBD::Pg, and that could be a problem as well.
>
> Scott
>
>
> On Tue, Aug 10, 2010 at 3:10 PM, Jieyu Wang <joy...@gm...> wrote:
>> I installed another Apache on the Mac which is a plug-in together with
>> PostgreSQL (/Library/PostgreSQL/EnterpriseDB-ApachePhp/apache), while
>> I installed Gbrowse under the original Apache (/etc/apache2).  I think
>> this may be the problem. But I don't know why?
>> Because PostgreSQL is relative independent, which should be called
>> from whichever Apache if the parameters are correct. And all the perl
>> modules are in the  /Library/Perl/5.10.0/darwin-thread-multi-2level/
>> and  /Library/Perl/5.10.0/ (eg.
>> /Library/Perl/5.10.0/Bio/DB/Das/Chado.pm) .
>> If it is the Apache problem, how can I specify which Apache I want to
>> install Gbrowse?
>>
>> Is that also possible that Growse2 was installed /etc/gbrowse2/ but
>> not successful or completely installed , makes some connection
>> problem?
>> For example, there is "GBrowse folder (for GBrowse2)" installed at
>> /Library/Perl/5.10.0/darwin-thread-multi-2level/.
>>
>> Thank you.
>>
>>
>> 2010/8/10 Scott Cain <sc...@sc...>:
>>> Hi Jieyu,
>>>
>>> Is it possible that there is more than one copy of DBD::Pg (or for
>>> that matter, perl) on your system, and that you are using a different
>>> version than apache is?
>>>
>>> Scott
>>>
>>>
>>> On Tue, Aug 10, 2010 at 1:00 PM, Jieyu Wang <joy...@gm...> wrote:
>>>> Thank you.
>>>> But perl 5.10.0 can work as 32 bit by setting VERSIONER_PERL_PREFER_32_BIT=yes.
>>>> I installed postgreSQL 8.3.11 which I think the lib
>>>> postgresql-libs-32bit-8.3.11.
>>>> The thing is that, when I use "gmod_bulk_load_gff3.pl  --organism
>>>> yeast -gfffile saccharomyces_cerevisiae.gff ",
>>>> there is no problem. So I think the connection between perl and
>>>> postgresql is good.
>>>>
>>>>
>>>>
>>>> 2010/8/10  <ran...@bi...>:
>>>>> Hi,
>>>>>
>>>>> Looks like you installed the incorrect version of the Postgresql libraries.
>>>>>
>>>>> I am not an Apple user, nor will I pretend to know anything, but you can not mix 64 bit and 32 bit.
>>>>>
>>>>> I would look into obtaining the correct version of of the postgresql libraries to match against the version of perl you have installed.
>>>>>
>>>>> That may solve your issue.
>>>>>
>>>>> Thanks,
>>>>>
>>>>>
>>>>>
>>>>> Randall Svancara
>>>>> Systems Administrator/DBA/Developer
>>>>> Main Bioinformatics Laboratory
>>>>>
>>>>>
>>>>>
>>>>> ----- Original Message -----
>>>>> From: "Jieyu Wang" <joy...@gm...>
>>>>> To: gmo...@li...
>>>>> Sent: Tuesday, August 10, 2010 8:55:00 AM
>>>>> Subject: [Gmod-schema] Fwd: Problem of Gbrowse with Chado
>>>>>
>>>>> Dear colleagues,
>>>>> I try to make Gbrowse work with Chado. So I followed the instruction ,
>>>>> install Bio::DB::Das::Chado
>>>>> and modify the /contrib/conf_files 07.chado.conf
>>>>> *********************** [GENERAL]
>>>>> description = test implementation of chado
>>>>> db_adaptor = Bio::DB::Das::Chado
>>>>> db_args = -dsn dbi:Pg:dbname=mychadodb
>>>>> -user mychado
>>>>> -srcfeatureslice 1
>>>>> -organism yeast
>>>>> -version 1
>>>>> #-inferCDS ***********************
>>>>> rename it to chado.conf and move it to gbrowse.conf.
>>>>> Try to load http://localhost/cgi-bin/gbrowse/chado/
>>>>> error: The server encountered an internal error or misconfiguration
>>>>> and was unable to complete your request.
>>>>>
>>>>>
>>>>> error_log
>>>>> **********
>>>>>
>>>>> [Tue Aug 10 10:23:50 2010] [error] [client ::1] dyld: lazy symbol
>>>>> binding failed: Symbol not found: _PQconnectdb
>>>>> [Tue Aug 10 10:23:50 2010] [error] [client ::1] Referenced from:
>>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBD/Pg/Pg.bundle
>>>>> [Tue Aug 10 10:23:50 2010] [error] [client ::1] Expected in: flat
>>>>> namespace [Tue Aug 10 10:23:50 2010] [error] [client ::1]
>>>>> [Tue Aug 10 10:23:50 2010] [error] [client ::1] dyld: Symbol not
>>>>> found: _PQconnectdb
>>>>> [Tue Aug 10 10:23:50 2010] [error] [client ::1] Referenced from:
>>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBD/Pg/Pg.bundle
>>>>> [Tue Aug 10 10:23:50 2010] [error] [client ::1] Expected in: flat
>>>>> namespace [Tue Aug 10 10:23:50 2010] [error] [client ::1]
>>>>> [Tue Aug 10 10:23:50 2010] [error] [client ::1] Premature end of
>>>>> script headers: gbrowse
>>>>> *********
>>>>>
>>>>> I don't think it is the DBD::pg problem, since I think when I load gff
>>>>> file to Chado, I have to use DBD::pg, and it works.
>>>>> Maybe connection problem with Bio::DB::Das::Chado. I am trying to read
>>>>> Bio::DB::Das::Chado and I hope you know the answer or can direct me to
>>>>> the right place.
>>>>> The problem is the same as the last part of
>>>>> http://www.perlmonks.org/?node_id=801645, but no solution provided
>>>>> there.
>>>>>
>>>>> Thank you.
>>>>>
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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
>