Problem of Gbrowse with Chado

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Problem of Gbrowse with Chado

Jieyu Wang-2
Dear colleague,
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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Fwd: Problem of Gbrowse with Chado

Jieyu Wang
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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Re: Fwd: Problem of Gbrowse with Chado

randalls
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" <[hidden email]>
To: [hidden email]
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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Re: Fwd: Problem of Gbrowse with Chado

Jieyu Wang
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  <[hidden email]>:

> 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" <[hidden email]>
> To: [hidden email]
> 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.
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________ Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

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Re: Fwd: Problem of Gbrowse with Chado

randalls
Could it be a problem with runtime linking then?



Randall Svancara
Systems Administrator/DBA/Developer
Main Bioinformatics Laboratory



----- Original Message -----
From: "Jieyu Wang" <[hidden email]>
To: [hidden email]
Sent: Tuesday, August 10, 2010 10:00:44 AM
Subject: Re: [Gmod-schema] Fwd: Problem of Gbrowse with Chado

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 <[hidden email]>:

> 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" <[hidden email]>
> To: [hidden email]
> 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.
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________ Gmod-schema mailing
> list [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

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Re: Fwd: Problem of Gbrowse with Chado

Scott Cain
In reply to this post by Jieyu Wang
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 <[hidden email]> 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  <[hidden email]>:
>> 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" <[hidden email]>
>> To: [hidden email]
>> 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.
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev
>> _______________________________________________ Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
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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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Re: Fwd: Problem of Gbrowse with Chado

Jieyu Wang
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 <[hidden email]>:

> 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 <[hidden email]> 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  <[hidden email]>:
>>> 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" <[hidden email]>
>>> To: [hidden email]
>>> 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.
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by
>>>
>>> Make an app they can't live without
>>> Enter the BlackBerry Developer Challenge
>>> http://p.sf.net/sfu/RIM-dev2dev
>>> _______________________________________________ Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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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Re: Fwd: Problem of Gbrowse with Chado

Jieyu Wang
I think I should try to specify the port imformation in tchado.conf
file. Thank you all.



2010/8/10 Jieyu Wang <[hidden email]>:

> 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 <[hidden email]>:
>> 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 <[hidden email]> 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  <[hidden email]>:
>>>> 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" <[hidden email]>
>>>> To: [hidden email]
>>>> 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.
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by
>>>>
>>>> Make an app they can't live without
>>>> Enter the BlackBerry Developer Challenge
>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>> _______________________________________________ Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by
>>>
>>> Make an app they can't live without
>>> Enter the BlackBerry Developer Challenge
>>> http://p.sf.net/sfu/RIM-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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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Re: Fwd: Problem of Gbrowse with Chado

Scott Cain
In reply to this post by Jieyu Wang
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 <[hidden email]> 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 <[hidden email]>:
>> 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 <[hidden email]> 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  <[hidden email]>:
>>>> 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" <[hidden email]>
>>>> To: [hidden email]
>>>> 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.
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by
>>>>
>>>> Make an app they can't live without
>>>> Enter the BlackBerry Developer Challenge
>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>> _______________________________________________ Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by
>>>
>>> Make an app they can't live without
>>> Enter the BlackBerry Developer Challenge
>>> http://p.sf.net/sfu/RIM-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
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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Re: Fwd: Problem of Gbrowse with Chado

Jieyu Wang
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 <[hidden email]>:

> 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 <[hidden email]> 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 <[hidden email]>:
>>> 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 <[hidden email]> 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  <[hidden email]>:
>>>>> 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" <[hidden email]>
>>>>> To: [hidden email]
>>>>> 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.
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net email is sponsored by
>>>>>
>>>>> Make an app they can't live without
>>>>> Enter the BlackBerry Developer Challenge
>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>> _______________________________________________ Gmod-schema mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by
>>>>
>>>> Make an app they can't live without
>>>> Enter the BlackBerry Developer Challenge
>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>> _______________________________________________
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>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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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Re: Fwd: Problem of Gbrowse with Chado

Scott Cain
Hi Jieyu,

The Chado install doesn't ask for a http port to listen on, only a
postgres port, and the default for that is 5432.  There isn't a web
interface for Chado per se.  If you want to use the apache that got
installed from the EnterpriseDB package, you'll have to find where
it's conf files are and change the "Listen" setting and restart
apache.  You'll also want to reinstall GBrowse and use the appropriate
paths for all of the file locations (I can't tell you what those are
because I don't know anything about the apache that EnterpriseDB
installs).  It would be a lot easier if you used the apache that came
with the OS.

About DBD::Pg, if those are the only files you found, you have
problems, as none of them are DBD::Pg.  However, the command you used
to locate them (I used locate) is case sensative, and it looks like
you looked for pg.pm, not Pg.pm.

Scott


On Thu, Aug 12, 2010 at 6:56 PM, Jieyu Wang <[hidden email]> wrote:

> 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 <[hidden email]>:
>> 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 <[hidden email]> 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 <[hidden email]>:
>>>> 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 <[hidden email]> 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  <[hidden email]>:
>>>>>> 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" <[hidden email]>
>>>>>> To: [hidden email]
>>>>>> 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.
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net email is sponsored by
>>>>>>
>>>>>> Make an app they can't live without
>>>>>> Enter the BlackBerry Developer Challenge
>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>> _______________________________________________ Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net email is sponsored by
>>>>>
>>>>> Make an app they can't live without
>>>>> Enter the BlackBerry Developer Challenge
>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>> _______________________________________________
>>>>> Gmod-schema mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by
>>>
>>> Make an app they can't live without
>>> Enter the BlackBerry Developer Challenge
>>> http://p.sf.net/sfu/RIM-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>



--
------------------------------------------------------------------------
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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Re: Fwd: Problem of Gbrowse with Chado

Jieyu Wang
Thank you.
The two paths have Pg.pm. Just clarify. Sorry for the confusion.

>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bundle/DBD
>> /Library/Perl/5.10.0/DBIx/DBSchema/DBD

Have a good one.



2010/8/12 Scott Cain <[hidden email]>:

> Hi Jieyu,
>
> The Chado install doesn't ask for a http port to listen on, only a
> postgres port, and the default for that is 5432.  There isn't a web
> interface for Chado per se.  If you want to use the apache that got
> installed from the EnterpriseDB package, you'll have to find where
> it's conf files are and change the "Listen" setting and restart
> apache.  You'll also want to reinstall GBrowse and use the appropriate
> paths for all of the file locations (I can't tell you what those are
> because I don't know anything about the apache that EnterpriseDB
> installs).  It would be a lot easier if you used the apache that came
> with the OS.
>
> About DBD::Pg, if those are the only files you found, you have
> problems, as none of them are DBD::Pg.  However, the command you used
> to locate them (I used locate) is case sensative, and it looks like
> you looked for pg.pm, not Pg.pm.
>
> Scott
>
>
> On Thu, Aug 12, 2010 at 6:56 PM, Jieyu Wang <[hidden email]> wrote:
>> 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 <[hidden email]>:
>>> 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 <[hidden email]> 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 <[hidden email]>:
>>>>> 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 <[hidden email]> 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  <[hidden email]>:
>>>>>>> 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" <[hidden email]>
>>>>>>> To: [hidden email]
>>>>>>> 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.
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> This SF.net email is sponsored by
>>>>>>>
>>>>>>> Make an app they can't live without
>>>>>>> Enter the BlackBerry Developer Challenge
>>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>>> _______________________________________________ Gmod-schema mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net email is sponsored by
>>>>>>
>>>>>> Make an app they can't live without
>>>>>> Enter the BlackBerry Developer Challenge
>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by
>>>>
>>>> Make an app they can't live without
>>>> Enter the BlackBerry Developer Challenge
>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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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Re: Fwd: Problem of Gbrowse with Chado

Scott Cain
Jieyu,

If that's the case, you don't have DBD::Pg installed.  I don't
understand how that is possible if loading GFF worked before, but
there you have it.  Could it be installed somewhere local in your
account that isn't visible to your web browser?

Scott


On Fri, Aug 13, 2010 at 11:58 AM, Jieyu Wang <[hidden email]> wrote:

> Thank you.
> The two paths have Pg.pm. Just clarify. Sorry for the confusion.
>
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bundle/DBD
>>> /Library/Perl/5.10.0/DBIx/DBSchema/DBD
>
> Have a good one.
>
>
>
> 2010/8/12 Scott Cain <[hidden email]>:
>> Hi Jieyu,
>>
>> The Chado install doesn't ask for a http port to listen on, only a
>> postgres port, and the default for that is 5432.  There isn't a web
>> interface for Chado per se.  If you want to use the apache that got
>> installed from the EnterpriseDB package, you'll have to find where
>> it's conf files are and change the "Listen" setting and restart
>> apache.  You'll also want to reinstall GBrowse and use the appropriate
>> paths for all of the file locations (I can't tell you what those are
>> because I don't know anything about the apache that EnterpriseDB
>> installs).  It would be a lot easier if you used the apache that came
>> with the OS.
>>
>> About DBD::Pg, if those are the only files you found, you have
>> problems, as none of them are DBD::Pg.  However, the command you used
>> to locate them (I used locate) is case sensative, and it looks like
>> you looked for pg.pm, not Pg.pm.
>>
>> Scott
>>
>>
>> On Thu, Aug 12, 2010 at 6:56 PM, Jieyu Wang <[hidden email]> wrote:
>>> 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 <[hidden email]>:
>>>> 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 <[hidden email]> 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 <[hidden email]>:
>>>>>> 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 <[hidden email]> 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  <[hidden email]>:
>>>>>>>> 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" <[hidden email]>
>>>>>>>> To: [hidden email]
>>>>>>>> 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.
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> This SF.net email is sponsored by
>>>>>>>>
>>>>>>>> Make an app they can't live without
>>>>>>>> Enter the BlackBerry Developer Challenge
>>>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>>>> _______________________________________________ Gmod-schema mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> This SF.net email is sponsored by
>>>>>>>
>>>>>>> Make an app they can't live without
>>>>>>> Enter the BlackBerry Developer Challenge
>>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>>> _______________________________________________
>>>>>>> Gmod-schema mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>> Ontario Institute for Cancer Research
>>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net email is sponsored by
>>>>>
>>>>> Make an app they can't live without
>>>>> Enter the BlackBerry Developer Challenge
>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>> _______________________________________________
>>>>> Gmod-schema mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
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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Re: Fwd: Problem of Gbrowse with Chado

Jieyu Wang
I think I installed DBD::Pg, as I said, I found Pg.pm
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bundle/DBD
>>>> /Library/Perl/5.10.0/DBIx/DBSchema/DBD
And I think Perl can search the subroutine in the two paths
(environment path setting).

Sorry I don't quite understand your questions about the web browser.
But I will take some time to check, and thank you for your help.

2010/8/13 Scott Cain <[hidden email]>:

> Jieyu,
>
> If that's the case, you don't have DBD::Pg installed.  I don't
> understand how that is possible if loading GFF worked before, but
> there you have it.  Could it be installed somewhere local in your
> account that isn't visible to your web browser?
>
> Scott
>
>
> On Fri, Aug 13, 2010 at 11:58 AM, Jieyu Wang <[hidden email]> wrote:
>> Thank you.
>> The two paths have Pg.pm. Just clarify. Sorry for the confusion.
>>
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bundle/DBD
>>>> /Library/Perl/5.10.0/DBIx/DBSchema/DBD
>>
>> Have a good one.
>>
>>
>>
>> 2010/8/12 Scott Cain <[hidden email]>:
>>> Hi Jieyu,
>>>
>>> The Chado install doesn't ask for a http port to listen on, only a
>>> postgres port, and the default for that is 5432.  There isn't a web
>>> interface for Chado per se.  If you want to use the apache that got
>>> installed from the EnterpriseDB package, you'll have to find where
>>> it's conf files are and change the "Listen" setting and restart
>>> apache.  You'll also want to reinstall GBrowse and use the appropriate
>>> paths for all of the file locations (I can't tell you what those are
>>> because I don't know anything about the apache that EnterpriseDB
>>> installs).  It would be a lot easier if you used the apache that came
>>> with the OS.
>>>
>>> About DBD::Pg, if those are the only files you found, you have
>>> problems, as none of them are DBD::Pg.  However, the command you used
>>> to locate them (I used locate) is case sensative, and it looks like
>>> you looked for pg.pm, not Pg.pm.
>>>
>>> Scott
>>>
>>>
>>> On Thu, Aug 12, 2010 at 6:56 PM, Jieyu Wang <[hidden email]> wrote:
>>>> 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 <[hidden email]>:
>>>>> 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 <[hidden email]> 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 <[hidden email]>:
>>>>>>> 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 <[hidden email]> 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  <[hidden email]>:
>>>>>>>>> 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" <[hidden email]>
>>>>>>>>> To: [hidden email]
>>>>>>>>> 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.
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> This SF.net email is sponsored by
>>>>>>>>>
>>>>>>>>> Make an app they can't live without
>>>>>>>>> Enter the BlackBerry Developer Challenge
>>>>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>>>>> _______________________________________________ Gmod-schema mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> This SF.net email is sponsored by
>>>>>>>>
>>>>>>>> Make an app they can't live without
>>>>>>>> Enter the BlackBerry Developer Challenge
>>>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-schema mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>>> Ontario Institute for Cancer Research
>>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net email is sponsored by
>>>>>>
>>>>>> Make an app they can't live without
>>>>>> Enter the BlackBerry Developer Challenge
>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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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Re: Fwd: Problem of Gbrowse with Chado

Scott Cain
Hi Jieyu,

Two paths you pointed out were for Bundle::DBD::Pg and
DBIx::DBSchema::DBD::Pg, neither of which is DBD::Pg.  I believe you
did install it, as I said, I don't know how loading Chado would have
worked before.  I'm just telling you that you didn't find it here, and
if you didn't find it, I'm not sure that your web server can either.

Scott


On Fri, Aug 13, 2010 at 1:41 PM, Jieyu Wang <[hidden email]> wrote:

> I think I installed DBD::Pg, as I said, I found Pg.pm
>>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bundle/DBD
>>>>> /Library/Perl/5.10.0/DBIx/DBSchema/DBD
> And I think Perl can search the subroutine in the two paths
> (environment path setting).
>
> Sorry I don't quite understand your questions about the web browser.
> But I will take some time to check, and thank you for your help.
>
> 2010/8/13 Scott Cain <[hidden email]>:
>> Jieyu,
>>
>> If that's the case, you don't have DBD::Pg installed.  I don't
>> understand how that is possible if loading GFF worked before, but
>> there you have it.  Could it be installed somewhere local in your
>> account that isn't visible to your web browser?
>>
>> Scott
>>
>>
>> On Fri, Aug 13, 2010 at 11:58 AM, Jieyu Wang <[hidden email]> wrote:
>>> Thank you.
>>> The two paths have Pg.pm. Just clarify. Sorry for the confusion.
>>>
>>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bundle/DBD
>>>>> /Library/Perl/5.10.0/DBIx/DBSchema/DBD
>>>
>>> Have a good one.
>>>
>>>
>>>
>>> 2010/8/12 Scott Cain <[hidden email]>:
>>>> Hi Jieyu,
>>>>
>>>> The Chado install doesn't ask for a http port to listen on, only a
>>>> postgres port, and the default for that is 5432.  There isn't a web
>>>> interface for Chado per se.  If you want to use the apache that got
>>>> installed from the EnterpriseDB package, you'll have to find where
>>>> it's conf files are and change the "Listen" setting and restart
>>>> apache.  You'll also want to reinstall GBrowse and use the appropriate
>>>> paths for all of the file locations (I can't tell you what those are
>>>> because I don't know anything about the apache that EnterpriseDB
>>>> installs).  It would be a lot easier if you used the apache that came
>>>> with the OS.
>>>>
>>>> About DBD::Pg, if those are the only files you found, you have
>>>> problems, as none of them are DBD::Pg.  However, the command you used
>>>> to locate them (I used locate) is case sensative, and it looks like
>>>> you looked for pg.pm, not Pg.pm.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Thu, Aug 12, 2010 at 6:56 PM, Jieyu Wang <[hidden email]> wrote:
>>>>> 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 <[hidden email]>:
>>>>>> 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 <[hidden email]> 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 <[hidden email]>:
>>>>>>>> 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 <[hidden email]> 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  <[hidden email]>:
>>>>>>>>>> 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" <[hidden email]>
>>>>>>>>>> To: [hidden email]
>>>>>>>>>> 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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>>>>>>>>>
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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
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> 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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--
------------------------------------------------------------------------
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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Re: Fwd: Problem of Gbrowse with Chado

Jieyu Wang
In reply to this post by Scott Cain
Dear Colleagues,
About the problem with "dyld: lazy symbol binding failed: Symbol not
found: _PQconnectdb", I think it is the problem of setting
VERSIONER_PERL_PREFER_32_BIT="yes", perl 5.10 can be 32 bit or 64 bit.
Without the setting, when I used gmod_bulk_load_gff3.pl, the same
error. After I export VERSIONER_PERL_PREFER_32_BIT="yes", it loads
data to CHADO.

So I think the problem with Gbrowse with CHADO is similar. I probably
fail to let the environment know that I want to use perl 32 bit. The
question is how can I do that?

Hope it is useful information for MAC users and I can get solutions finally.

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