DAS client Problems

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

DAS client Problems

Matthias Gierth
Hi all

I have a problem with gbrowse as a das client.

Installation (via netinstall) went fine, also the make_das_client.pl

it cretaed a valid conf file. make_das_conf.pl
http://genome.cse.ucsc.edu/cgi-bin/das/mm9 >
/etc/apache2/gbrowse.conf/mouse_ucsc.conf

my problem is the browser shows no tracks and in the apache log I get
the following Error:

Use of uninitialized value in hash element at
/usr/local/share/perl/5.10.0/Bio/Das/Request/Features.pm line 127.

the yeast sample is running fine for me.

any Ideas on this?

many Thanks
Matthias

--
Matthias Gierth
System Administrator
Bioinformatics Service
TU Dresden, Biotec
Tatzberg 47-51
01307 Dresden
Phone:   +49 (0)351 463 40020
Fax:     +49 (0)351 463 40087
Email:   [hidden email]



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: DAS client Problems

Wes Barris
On 10/06/2010 10:59 PM, Matthias Gierth wrote:
> Hi all
>
> I have a problem with gbrowse as a das client.

I do as well.

> Installation (via netinstall) went fine, also the make_das_client.pl
>
> it cretaed a valid conf file. make_das_conf.pl
> http://genome.cse.ucsc.edu/cgi-bin/das/mm9>
> /etc/apache2/gbrowse.conf/mouse_ucsc.conf

I tried the same thing and successfully created a mm9.conf file.

> my problem is the browser shows no tracks and in the apache log I get
> the following Error:

For me, this error is shown in Gbrowse2 where the track would normally
be displayed:

Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
not implemented by package Bio::Das.

> Use of uninitialized value in hash element at
> /usr/local/share/perl/5.10.0/Bio/Das/Request/Features.pm line 127.

I get a boatload of errors in my apache error log:

[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ------------- EXCEPTION Bio::Root::NotImplemented -------------, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] MSG: Abstract method "Bio::DasI::get_seq_stream" is not implemented by package Bio::Das., referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] This is not your fault - author of Bio::Das should be blamed!, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Root::RootI::throw_not_implemented /usr/lib/perl5/site_perl/5.8.5/Bio/Root/RootI.pm:739, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::DasI::get_seq_stream /usr/lib/perl5/site_perl/5.8.5/Bio/DasI.pm:429, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::get_iterator
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1785, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1596, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK (eval) /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1371, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1336, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::request_panels
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:160, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::render_deferred
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:3186, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::background_track_render
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:390, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Action::ACTION_navigate
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Action.pm:66, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::asynchronous_event
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:330, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::run_asynchronous_event
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:262, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::run /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:199,
referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK toplevel /htdocs/gbrowse2/cgi-bin/gbrowse:43, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ---------------------------------------------------------------, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10


> the yeast sample is running fine for me.

The rest of gbrowse2 is working fine for me too.

> any Ideas on this?
>
> many Thanks
> Matthias
>


--
Wes Barris

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: DAS client Problems

Lincoln Stein
It's puzzling. A lot of people are reporting this, but I did fix the problem several weeks ago and reported it to the mailing list. You need version 2.09.

Under GBrowse version 2.09, Bio::Das version 1.12, I can connect to UCSC and show various mouse tracks. My test configuration track looks like this:

[ENSGENE]
glyph        = transcript
bgcolor      = orange
fgcolor          = gray
das category = transcription
key          = ensGene
citation     = These are UCSC ensGene features.

No server error log messages, and the screenshot looks like this.

Lincoln



On Thu, Jun 10, 2010 at 9:18 PM, Wes Barris <[hidden email]> wrote:
On 10/06/2010 10:59 PM, Matthias Gierth wrote:
> Hi all
>
> I have a problem with gbrowse as a das client.

I do as well.

> Installation (via netinstall) went fine, also the make_das_client.pl
>
> it cretaed a valid conf file. make_das_conf.pl
> http://genome.cse.ucsc.edu/cgi-bin/das/mm9>
> /etc/apache2/gbrowse.conf/mouse_ucsc.conf

I tried the same thing and successfully created a mm9.conf file.

> my problem is the browser shows no tracks and in the apache log I get
> the following Error:

For me, this error is shown in Gbrowse2 where the track would normally
be displayed:

Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
not implemented by package Bio::Das.

> Use of uninitialized value in hash element at
> /usr/local/share/perl/5.10.0/Bio/Das/Request/Features.pm line 127.

I get a boatload of errors in my apache error log:

[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ------------- EXCEPTION Bio::Root::NotImplemented -------------, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] MSG: Abstract method "Bio::DasI::get_seq_stream" is not implemented by package Bio::Das., referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] This is not your fault - author of Bio::Das should be blamed!, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Root::RootI::throw_not_implemented /usr/lib/perl5/site_perl/5.8.5/Bio/Root/RootI.pm:739, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::DasI::get_seq_stream /usr/lib/perl5/site_perl/5.8.5/Bio/DasI.pm:429, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::get_iterator
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1785, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1596, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK (eval) /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1371, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1336, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::request_panels
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:160, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::render_deferred
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:3186, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::background_track_render
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:390, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Action::ACTION_navigate
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Action.pm:66, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::asynchronous_event
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:330, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::run_asynchronous_event
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:262, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::run /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:199,
referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK toplevel /htdocs/gbrowse2/cgi-bin/gbrowse:43, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ---------------------------------------------------------------, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10


> the yeast sample is running fine for me.

The rest of gbrowse2 is working fine for me too.

> any Ideas on this?
>
> many Thanks
> Matthias
>


--
Wes Barris

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Screenshot-13.png (59K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: DAS client Problems

Wes Barris
On 11/06/2010 11:43 PM, Lincoln Stein wrote:
> It's puzzling. A lot of people are reporting this, but I did fix the
> problem several weeks ago and reported it to the mailing list. You need
> version 2.09.
>
> Under GBrowse version 2.09, Bio::Das version 1.12, I can connect to UCSC
> and show various mouse tracks. My test configuration track looks like this:

I just upgraded to GBrowse 2.10 (revision 23376) and Bio::Das 1.15.
I am still getting the same errors listed below when trying to use
the .conf file created from ./share/bin/make_das_conf.pl .  However,
if I place the "remote feature" line shown below into the proper
stanza, I can get that track to display.  So it would appear that
DAS/remote features work but defining a DAS database as is done in
the make_das_conf.pl script may not work.

>     [ENSGENE]
>     remote feature = http://genome.cse.ucsc.edu/cgi-bin/das/mm9?type=ensGene
>     glyph        = transcript
>     bgcolor      = orange
>     fgcolor          = gray
>     das category = transcription
>     key          = ensGene
>     citation     = These are UCSC ensGene features.
>
>
> No server error log messages, and the screenshot looks like this.
>
> Lincoln
>
>
>
> On Thu, Jun 10, 2010 at 9:18 PM, Wes Barris <[hidden email]> wrote:
>
>     On 10/06/2010 10:59 PM, Matthias Gierth wrote:
>      > Hi all
>      >
>      > I have a problem with gbrowse as a das client.
>
>     I do as well.
>
>      > Installation (via netinstall) went fine, also the
>     make_das_client.pl <http://make_das_client.pl>
>      >
>      > it cretaed a valid conf file. make_das_conf.pl
>     <http://make_das_conf.pl>
>      > http://genome.cse.ucsc.edu/cgi-bin/das/mm9>
>      > /etc/apache2/gbrowse.conf/mouse_ucsc.conf
>
>     I tried the same thing and successfully created a mm9.conf file.
>
>      > my problem is the browser shows no tracks and in the apache log I get
>      > the following Error:
>
>     For me, this error is shown in Gbrowse2 where the track would normally
>     be displayed:
>
>     Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
>     not implemented by package Bio::Das.
>
>      > Use of uninitialized value in hash element at
>      > /usr/local/share/perl/5.10.0/Bio/Das/Request/Features.pm line 127.
>
>     I get a boatload of errors in my apache error log:
>
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217]
>     ------------- EXCEPTION Bio::Root::NotImplemented -------------,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] MSG:
>     Abstract method "Bio::DasI::get_seq_stream" is not implemented by
>     package Bio::Das., referer:
>     https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] This is
>     not your fault - author of Bio::Das should be blamed!, referer:
>     https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Root::RootI::throw_not_implemented
>     /usr/lib/perl5/site_perl/5.8.5/Bio/Root/RootI.pm:739, referer:
>     https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::DasI::get_seq_stream
>     /usr/lib/perl5/site_perl/5.8.5/Bio/DasI.pm:429, referer:
>     https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::RenderPanels::get_iterator
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1785,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::RenderPanels::add_features_to_track
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1596,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     (eval)
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1371,
>     referer:
>     https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::RenderPanels::run_local_requests
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1336,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::RenderPanels::request_panels
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:160,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::Render::render_deferred
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:3186,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::Render::background_track_render
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:390,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::Action::ACTION_navigate
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Action.pm:66,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::Render::asynchronous_event
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:330,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::Render::run_asynchronous_event
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:262,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     Bio::Graphics::Browser2::Render::run
>     /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:199,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
>     toplevel /htdocs/gbrowse2/cgi-bin/gbrowse:43, referer:
>     https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217]
>     ---------------------------------------------------------------,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>     [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ,
>     referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
>
>
>      > the yeast sample is running fine for me.
>
>     The rest of gbrowse2 is working fine for me too.
>
>      > any Ideas on this?
>      >
>      > many Thanks
>      > Matthias
>      >
>
>
>     --
>     Wes Barris
>
>     ------------------------------------------------------------------------------
>     ThinkGeek and WIRED's GeekDad team up for the Ultimate
>     GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>     lucky parental unit.  See the prize list and enter to win:
>     http://p.sf.net/sfu/thinkgeek-promo
>     _______________________________________________
>     Gmod-gbrowse mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]
> <mailto:[hidden email]>>


--
Wes Barris

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: DAS client Problems

Lincoln Stein
Ok, this explains it. I will have to do some work on the Bio::Das adaptor.

Lincoln

On Mon, Jun 14, 2010 at 10:17 PM, Wes Barris <[hidden email]> wrote:
On 11/06/2010 11:43 PM, Lincoln Stein wrote:
It's puzzling. A lot of people are reporting this, but I did fix the
problem several weeks ago and reported it to the mailing list. You need
version 2.09.

Under GBrowse version 2.09, Bio::Das version 1.12, I can connect to UCSC
and show various mouse tracks. My test configuration track looks like this:

I just upgraded to GBrowse 2.10 (revision 23376) and Bio::Das 1.15.
I am still getting the same errors listed below when trying to use
the .conf file created from ./share/bin/make_das_conf.pl .  However,
if I place the "remote feature" line shown below into the proper
stanza, I can get that track to display.  So it would appear that
DAS/remote features work but defining a DAS database as is done in
the make_das_conf.pl script may not work.

   [ENSGENE]
   remote feature = http://genome.cse.ucsc.edu/cgi-bin/das/mm9?type=ensGene
   glyph        = transcript
   bgcolor      = orange
   fgcolor          = gray
   das category = transcription
   key          = ensGene
   citation     = These are UCSC ensGene features.


No server error log messages, and the screenshot looks like this.

Lincoln



On Thu, Jun 10, 2010 at 9:18 PM, Wes Barris <[hidden email]> wrote:

   On 10/06/2010 10:59 PM, Matthias Gierth wrote:
    > Hi all
    >
    > I have a problem with gbrowse as a das client.

   I do as well.

    > Installation (via netinstall) went fine, also the
   make_das_client.pl <http://make_das_client.pl>

    >
    > it cretaed a valid conf file. make_das_conf.pl
   <http://make_das_conf.pl>

    > http://genome.cse.ucsc.edu/cgi-bin/das/mm9>
    > /etc/apache2/gbrowse.conf/mouse_ucsc.conf

   I tried the same thing and successfully created a mm9.conf file.

    > my problem is the browser shows no tracks and in the apache log I get
    > the following Error:

   For me, this error is shown in Gbrowse2 where the track would normally
   be displayed:

   Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
   not implemented by package Bio::Das.

    > Use of uninitialized value in hash element at
    > /usr/local/share/perl/5.10.0/Bio/Das/Request/Features.pm line 127.

   I get a boatload of errors in my apache error log:

   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217]
   ------------- EXCEPTION Bio::Root::NotImplemented -------------,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] MSG:
   Abstract method "Bio::DasI::get_seq_stream" is not implemented by
   package Bio::Das., referer:
   https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] This is
   not your fault - author of Bio::Das should be blamed!, referer:
   https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Root::RootI::throw_not_implemented
   /usr/lib/perl5/site_perl/5.8.5/Bio/Root/RootI.pm:739, referer:
   https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::DasI::get_seq_stream
   /usr/lib/perl5/site_perl/5.8.5/Bio/DasI.pm:429, referer:
   https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::RenderPanels::get_iterator
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1785,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::RenderPanels::add_features_to_track
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1596,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   (eval)
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1371,
   referer:
   https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::RenderPanels::run_local_requests
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1336,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::RenderPanels::request_panels
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:160,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::Render::render_deferred
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:3186,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::Render::background_track_render
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:390,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::Action::ACTION_navigate
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Action.pm:66,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::Render::asynchronous_event
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:330,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::Render::run_asynchronous_event
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:262,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   Bio::Graphics::Browser2::Render::run
   /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:199,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK
   toplevel /htdocs/gbrowse2/cgi-bin/gbrowse:43, referer:
   https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217]
   ---------------------------------------------------------------,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
   [Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ,
   referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10


    > the yeast sample is running fine for me.

   The rest of gbrowse2 is working fine for me too.

    > any Ideas on this?
    >
    > many Thanks
    > Matthias
    >


   --
   Wes Barris

   ------------------------------------------------------------------------------
   ThinkGeek and WIRED's GeekDad team up for the Ultimate
   GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
   lucky parental unit.  See the prize list and enter to win:
   http://p.sf.net/sfu/thinkgeek-promo
   _______________________________________________
   Gmod-gbrowse mailing list
   [hidden email]
   <mailto:[hidden email]>

   https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]
<mailto:[hidden email]>>


--
Wes Barris



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: DAS client Problems

Lincoln Stein
In reply to this post by Wes Barris
Hi Wes, et al.,

I've identified the problem in the GBrowse2 DAS client implementation and will have a fix out in the next couple of days. I'm also going to finish work on the DAS server code, which has long been on the TODO list.

Lincoln

On Thu, Jun 10, 2010 at 9:18 PM, Wes Barris <[hidden email]> wrote:
On 10/06/2010 10:59 PM, Matthias Gierth wrote:
> Hi all
>
> I have a problem with gbrowse as a das client.

I do as well.

> Installation (via netinstall) went fine, also the make_das_client.pl
>
> it cretaed a valid conf file. make_das_conf.pl
> http://genome.cse.ucsc.edu/cgi-bin/das/mm9>
> /etc/apache2/gbrowse.conf/mouse_ucsc.conf

I tried the same thing and successfully created a mm9.conf file.

> my problem is the browser shows no tracks and in the apache log I get
> the following Error:

For me, this error is shown in Gbrowse2 where the track would normally
be displayed:

Track rendering error: Abstract method "Bio::DasI::get_seq_stream" is
not implemented by package Bio::Das.

> Use of uninitialized value in hash element at
> /usr/local/share/perl/5.10.0/Bio/Das/Request/Features.pm line 127.

I get a boatload of errors in my apache error log:

[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ------------- EXCEPTION Bio::Root::NotImplemented -------------, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] MSG: Abstract method "Bio::DasI::get_seq_stream" is not implemented by package Bio::Das., referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] This is not your fault - author of Bio::Das should be blamed!, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Root::RootI::throw_not_implemented /usr/lib/perl5/site_perl/5.8.5/Bio/Root/RootI.pm:739, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::DasI::get_seq_stream /usr/lib/perl5/site_perl/5.8.5/Bio/DasI.pm:429, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::get_iterator
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1785, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1596, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK (eval) /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1371, referer:
https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:1336, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::RenderPanels::request_panels
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm:160, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::render_deferred
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:3186, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::background_track_render
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:390, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Action::ACTION_navigate
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Action.pm:66, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::asynchronous_event
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:330, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::run_asynchronous_event
/htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:262, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK Bio::Graphics::Browser2::Render::run /htdocs/gbrowse2/share/lib/perl5/i386-linux-thread-multi/Bio/Graphics/Browser2/Render.pm:199,
referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] STACK toplevel /htdocs/gbrowse2/cgi-bin/gbrowse:43, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] ---------------------------------------------------------------, referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10
[Fri Jun 11 11:13:29 2010] [error] [client 140.253.153.217] , referer: https://www.biolives.csiro.au/cgi-bin/gbrowse/mm9/?name=10


> the yeast sample is running fine for me.

The rest of gbrowse2 is working fine for me too.

> any Ideas on this?
>
> many Thanks
> Matthias
>


--
Wes Barris

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: DAS client Problems

Lincoln Stein
In reply to this post by Matthias Gierth
Hi All,

The GBrowse2 DAS client now works if you update to Bio::Das version 1.16, which I just uploaded to CPAN. 

I also noticed popup balloons don't display correctly in GBrowse2 when you run it on a DAS source. I've fixed these in GBrowse2 SVN, but haven't released it yet to CPAN because I'm hoping to have the GBrowse2-based DAS server working as well for the next official release.

Lincoln

On Thu, Jun 10, 2010 at 8:59 AM, Matthias Gierth <[hidden email]> wrote:
Hi all

I have a problem with gbrowse as a das client.

Installation (via netinstall) went fine, also the make_das_client.pl

it cretaed a valid conf file. make_das_conf.pl
http://genome.cse.ucsc.edu/cgi-bin/das/mm9 >
/etc/apache2/gbrowse.conf/mouse_ucsc.conf

my problem is the browser shows no tracks and in the apache log I get
the following Error:

Use of uninitialized value in hash element at
/usr/local/share/perl/5.10.0/Bio/Das/Request/Features.pm line 127.

the yeast sample is running fine for me.

any Ideas on this?

many Thanks
Matthias

--
Matthias Gierth
System Administrator
Bioinformatics Service
TU Dresden, Biotec
Tatzberg 47-51
01307 Dresden
Phone:   +49 (0)351 463 40020
Fax:     +49 (0)351 463 40087
Email:   [hidden email]



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: DAS client Problems

Wes Barris
On 22/06/2010 3:42 AM, Lincoln Stein wrote:
> Hi All,
>
> The GBrowse2 DAS client now works if you update to Bio::Das version
> 1.16, which I just uploaded to CPAN.

Thanks Lincoln!

> I also noticed popup balloons don't display correctly in GBrowse2 when
> you run it on a DAS source. I've fixed these in GBrowse2 SVN, but
> haven't released it yet to CPAN because I'm hoping to have the
> GBrowse2-based DAS server working as well for the next official release.
>
> Lincoln
>
> On Thu, Jun 10, 2010 at 8:59 AM, Matthias Gierth
> <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi all
>
>     I have a problem with gbrowse as a das client.
>
>     Installation (via netinstall) went fine, also the make_das_client.pl
>     <http://make_das_client.pl>
>
>     it cretaed a valid conf file. make_das_conf.pl <http://make_das_conf.pl>
>     http://genome.cse.ucsc.edu/cgi-bin/das/mm9 >
>     /etc/apache2/gbrowse.conf/mouse_ucsc.conf
>
>     my problem is the browser shows no tracks and in the apache log I get
>     the following Error:
>
>     Use of uninitialized value in hash element at
>     /usr/local/share/perl/5.10.0/Bio/Das/Request/Features.pm line 127.
>
>     the yeast sample is running fine for me.
>
>     any Ideas on this?
>
>     many Thanks
>     Matthias
>
>     --
>     Matthias Gierth
>     System Administrator
>     Bioinformatics Service
>     TU Dresden, Biotec
>     Tatzberg 47-51
>     01307 Dresden
>     Phone:   +49 (0)351 463 40020
>     Fax:     +49 (0)351 463 40087
>     Email: [hidden email]
>     <mailto:[hidden email]>
>
>
>
>     ------------------------------------------------------------------------------
>     ThinkGeek and WIRED's GeekDad team up for the Ultimate
>     GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>     lucky parental unit.  See the prize list and enter to win:
>     http://p.sf.net/sfu/thinkgeek-promo
>     _______________________________________________
>     Gmod-gbrowse mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]
> <mailto:[hidden email]>>


--
Wes Barris

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse