mysql backend problem

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mysql backend problem

by Tatamil Tatamil :: Rate this Message:

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Hello gbrowse people,

I need to construct a relatively complex representations of contigs with features, glyphs, and so on. Currently contigs data is stored in Mysql databse, but not in the formats used by gbrowse. I just installed it successfully ( on Ubuntu 8.04) and was able to build and view the Volvox contig according to the tutorial (http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml). I can also the view the S. cerevisiae genome (if I spell him correctly).
The problems start when I attempt to use the Mysql Backend for Volvox, instead of the standard memory option:

This is what I did
1) loaded successfully the Volvox .fa and .gff3 files into Mysql using bp_seqfeature_load.pl
(here I changed the script to accept Mysql user password, and changed user name)

2) I changed the volvox.conf to be:

description   = Volvox Example Database 1
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
            -dsn     volvox
                -user    nobody

3) I typed http://localhost/cgi-bin/gbrowse/volvox , and then I still see the databse I installed with the -adaptor memory option, though I previously deleted all files from the /var/www/gbrowse/databases/volvox folder.

What is wrong?

thanks

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Re: mysql backend problem

by Scott Cain-4 :: Rate this Message:

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Hi,

It is hard to say what is going on from your description. Server or client side caching, perhaps? Do you have things installed in more than one location? Are you sure that GBrowse is reading the configuration file you edited and not another one in a different location? Is there anything in the apache error_log that might shed light on what is happening?

Scott

On Mon, Oct 5, 2009 at 3:52 PM, Tatamil Tatamil <taltamil@...> wrote:

Hello gbrowse people,

I need to construct a relatively complex representations of contigs with features, glyphs, and so on. Currently contigs data is stored in Mysql databse, but not in the formats used by gbrowse. I just installed it successfully ( on Ubuntu 8.04) and was able to build and view the Volvox contig according to the tutorial (http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml). I can also the view the S. cerevisiae genome (if I spell him correctly).
The problems start when I attempt to use the Mysql Backend for Volvox, instead of the standard memory option:

This is what I did
1) loaded successfully the Volvox .fa and .gff3 files into Mysql using bp_seqfeature_load.pl
(here I changed the script to accept Mysql user password, and changed user name)

2) I changed the volvox.conf to be:

description   = Volvox Example Database 1
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
            -dsn     volvox
                -user    nobody

3) I typed http://localhost/cgi-bin/gbrowse/volvox , and then I still see the databse I installed with the -adaptor memory option, though I previously deleted all files from the /var/www/gbrowse/databases/volvox folder.

What is wrong?

thanks
------------------------------------------------------------------------------
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9-12, 2009. Register now!
http://p.sf.net/sfu/devconf
_______________________________________________
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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

------------------------------------------------------------------------------
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9-12, 2009. Register now!
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Re: mysql backend problem

by Tatamil Tatamil :: Rate this Message:

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Some parts of this message have been removed. Learn more about Nabble's security policy.

Hi Scott,

I simply try to see if everything works with the tutorial example of Volvox according in the tutorial. When the Volvox.conf file is set with the "-adaptor memory" option, and the file volvox1.gff3 is placed in gbrowse/databases/volvox, everything works perfectly. I can change the parameters in the .gff3 and .conf files, and see how they effects the picture created in browser.

I added the relevant portion of the appache log file ---->

Tahnks,
Tal tamil

[Mon Oct 05 19:20:10 2009] [error] [client 127.0.0.1] Premature end of script headers: gbrowse

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Couldn't execute query SELECT fref,fstart,fstop,fsource,fmethod,fscore,fstrand,fphase,gclass,gname,ftarget_start,ftarget_stop,fdata.fid,fdata.gid
FROM fdata USE INDEX(gid),ftype,fgroup
WHERE fgroup.gclass=? AND fgroup.gname=? AND fgroup.gid = fdata.gid
AND ftype.ftypeid = fdata.ftypeid
:
Table 'volvox.fdata' doesn't exist

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.8.8/Bio/Root/Root.pm:357
STACK: Bio::DB::GFF::Adaptor::dbi::caching_handle::do_query /usr/local/share/perl/5.8.8/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:123
STACK: Bio::DB::GFF::Adaptor::dbi::_feature_by_name /usr/local/share/perl/5.8.8/Bio/DB/GFF/Adaptor/dbi.pm:400
STACK: Bio::DB::GFF::get_feature_by_name /usr/local/share/perl/5.8.8/Bio/DB/GFF.pm:1162
STACK: Bio::Graphics::Browser::_feature_get /usr/local/lib/perl/5.8.8/Bio/Graphics/Browser.pm:2236
STACK: Bio::Graphics::Browser::name2segments /usr/local/lib/perl/5.8.8/Bio/Graphics/Browser.pm:2169
STACK: main::lookup_features_from_db /usr/lib/cgi-bin/gbrowse:2307
STACK: main::get_features /usr/lib/cgi-bin/gbrowse:2200
STACK: /usr/lib/cgi-bin/gbrowse:199
-----------------------------------------------------------
[Mon Oct 05 19:27:57 2009] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
[Mon Oct 05 21:07:34 2009] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico
[Mon Oct 05 21:07:37 2009] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico

From: Scott Cain <scott@...>
To: Tatamil Tatamil <taltamil@...>
Cc: gmod-gbrowse@...
Sent: Mon, October 5, 2009 9:57:47 PM
Subject: Re: [Gmod-gbrowse] mysql backend problem

Hi,

It is hard to say what is going on from your description. Server or client side caching, perhaps? Do you have things installed in more than one location? Are you sure that GBrowse is reading the configuration file you edited and not another one in a different location? Is there anything in the apache error_log that might shed light on what is happening?

Scott

On Mon, Oct 5, 2009 at 3:52 PM, Tatamil Tatamil <taltamil@...> wrote:

Hello gbrowse people,

I need to construct a relatively complex representations of contigs with features, glyphs, and so on. Currently contigs data is stored in Mysql databse, but not in the formats used by gbrowse. I just installed it successfully ( on Ubuntu 8.04) and was able to build and view the Volvox contig according to the tutorial (http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml). I can also the view the S. cerevisiae genome (if I spell him correctly).
The problems start when I attempt to use the Mysql Backend for Volvox, instead of the standard memory option:

This is what I did
1) loaded successfully the Volvox .fa and .gff3 files into Mysql using bp_seqfeature_load.pl
(here I changed the script to accept Mysql user password, and changed user name)

2) I changed the volvox.conf to be:

description   = Volvox Example Database 1
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
            -dsn     volvox
                -user    nobody

3) I typed http://localhost/cgi-bin/gbrowse/volvox , and then I still see the databse I installed with the -adaptor memory option, though I previously deleted all files from the /var/www/gbrowse/databases/volvox folder.

What is wrong?

thanks
------------------------------------------------------------------------------
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9-12, 2009. Register now!
http://p.sf.net/sfu/devconf
_______________________________________________
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Re: mysql backend problem

by Scott Cain-4 :: Rate this Message:

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Hello Tal tamil,

It appears that you are mixing two different database backends:
Bio::DB::GFF (which is loaded with bp_bulk_load_gff.pl and
bp_load_gff.pl) and Bio::DB::SeqFeature::Store (which is loaded with
bp_seqfeature_load.pl). You have to pick one and stick to it. The
error message indicates that your configuration file is trying to use
a Bio::DB::GFF database, but you indicated that you loaded your
database with bp_seqfeature_load.pl.

Scott

On Oct 5, 2009, at 4:29 PM, Tatamil Tatamil wrote:

> Hi Scott,
>
> I simply try to see if everything works with the tutorial example of
> Volvox according in the tutorial. When the Volvox.conf file is set
> with the "-adaptor memory" option, and the file volvox1.gff3 is
> placed in gbrowse/databases/volvox, everything works perfectly. I
> can change the parameters in the .gff3 and .conf files, and see how
> they effects the picture created in browser.
>
> I added the relevant portion of the appache log file ---->
>
>
> Tahnks,
> Tal tamil
>
> [Mon Oct 05 19:20:10 2009] [error] [client 127.0.0.1] Premature end
> of script headers: gbrowse
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Couldn't execute query SELECT
> fref
> ,fstart
> ,fstop
> ,fsource
> ,fmethod
> ,fscore
> ,fstrand
> ,fphase,gclass,gname,ftarget_start,ftarget_stop,fdata.fid,fdata.gid
> FROM fdata USE INDEX(gid),ftype,fgroup
> WHERE fgroup.gclass=? AND fgroup.gname=? AND fgroup.gid = fdata.gid
> AND ftype.ftypeid = fdata.ftypeid
> :
> Table 'volvox.fdata' doesn't exist
>
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.8.8/Bio/Root/
> Root.pm:357
> STACK: Bio::DB::GFF::Adaptor::dbi::caching_handle::do_query /usr/
> local/share/perl/5.8.8/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:123
> STACK: Bio::DB::GFF::Adaptor::dbi::_feature_by_name /usr/local/share/
> perl/5.8.8/Bio/DB/GFF/Adaptor/dbi.pm:400
> STACK: Bio::DB::GFF::get_feature_by_name /usr/local/share/perl/5.8.8/
> Bio/DB/GFF.pm:1162
> STACK: Bio::Graphics::Browser::_feature_get /usr/local/lib/perl/
> 5.8.8/Bio/Graphics/Browser.pm:2236
> STACK: Bio::Graphics::Browser::name2segments /usr/local/lib/perl/
> 5.8.8/Bio/Graphics/Browser.pm:2169
> STACK: main::lookup_features_from_db /usr/lib/cgi-bin/gbrowse:2307
> STACK: main::get_features /usr/lib/cgi-bin/gbrowse:2200
> STACK: /usr/lib/cgi-bin/gbrowse:199
> -----------------------------------------------------------
> [Mon Oct 05 19:27:57 2009] [error] [client 127.0.0.1] Premature end
> of script headers: gbrowse
> [Mon Oct 05 21:07:34 2009] [error] [client 127.0.0.1] File does not
> exist: /var/www/favicon.ico
> [Mon Oct 05 21:07:37 2009] [error] [client 127.0.0.1] File does not
> exist: /var/www/favicon.ico
>
> From: Scott Cain <scott@...>
> To: Tatamil Tatamil <taltamil@...>
> Cc: gmod-gbrowse@...
> Sent: Mon, October 5, 2009 9:57:47 PM
> Subject: Re: [Gmod-gbrowse] mysql backend problem
>
> Hi,
>
> It is hard to say what is going on from your description. Server or
> client side caching, perhaps? Do you have things installed in more
> than one location? Are you sure that GBrowse is reading the
> configuration file you edited and not another one in a different
> location? Is there anything in the apache error_log that might shed
> light on what is happening?
>
> Scott
>
>
> On Mon, Oct 5, 2009 at 3:52 PM, Tatamil Tatamil <taltamil@...>
> wrote:
>
>
> Hello gbrowse people,
>
> I need to construct a relatively complex representations of contigs
> with features, glyphs, and so on. Currently contigs data is stored
> in Mysql databse, but not in the formats used by gbrowse. I just
> installed it successfully ( on Ubuntu 8.04) and was able to build
> and view the Volvox contig according to the tutorial (http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml
> ). I can also the view the S. cerevisiae genome (if I spell him
> correctly).
> The problems start when I attempt to use the Mysql Backend for
> Volvox, instead of the standard memory option:
>
> This is what I did
> 1) loaded successfully the Volvox .fa and .gff3 files into Mysql
> usingbp_seqfeature_load.pl
> (here I changed the script to accept Mysql user password, and
> changed user name)
>
> 2) I changed the volvox.conf to be:
>
> description = Volvox Example Database 1
> db_adaptor = Bio::DB::SeqFeature::Store
> db_args = -adaptor DBI::mysql
> -dsn volvox
> -user nobody
>
> 3) I typed http://localhost/cgi-bin/gbrowse/volvox , and then I
> still see the databse I installed with the -adaptor memory option,
> though I previously deleted all files from the /var/www/gbrowse/
> databases/volvox folder.
>
> What is wrong?
>
> thanks
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry® Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart
> your
> developing skills, take BlackBerry mobile applications to market and
> stay
> ahead of the curve. Join us from November 9-12, 2009. Register now!
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> 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

------------------------------------------------------------------------------
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9-12, 2009. Register now!
http://p.sf.net/sfu/devconf
_______________________________________________
Gmod-gbrowse mailing list
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