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Razi Khaja | 3 Oct 2011 19:15
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BIgWigSet, metadata.txt, trailing spaces cause GBrowse2 not to render xyplot tracks.

All,

I've spent a few days trying to figure out why my BigWig files will not display in GBrowse2.  My metadata.txt file is copied below as an example.
It turns out that if there are trailing spaces on any of the lines of the metadata.txt file, that GBrowse2 will not render the tracks.

Can someone verify this bug by adding a space or two after the tag = value pairs for one of your bigwig data sources? 
These trailing spaces could be the source of  headaches for many folks trying to use BigWig files and hopefully should be fixed.

Best regards,

Razi

/**
 * Razi Khaja
 * Bioinformatics Specialist
 * Precollege and Undergraduate Science Education
 * Howard Hughes Medical Institute
 * 4000 Jones Bridge Road, Rm. S102
 * Chevy Chase, MD 20815
 * Email: khajar-5+GbW1xn1kU@public.gmane.org
 * Website: http://www.hhmi.org/grants/sea/
 * Mobile: 240-328-4985
 * Office: 301-215-8877
 */


[Wally_frame1.bw]
display_name = Frame +1
method = GeneMark_TB
source = Frame1

[Wally_frame2.bw]
display_name = Frame +2
method = GeneMark_TB
source = Frame2

[Wally_frame3.bw]
display_name = Frame +3
method = GeneMark_TB
source = Frame3

[Wally_frame4.bw]
display_name = Frame -1
method = GeneMark_TB
source = Frame4

[Wally_frame5.bw]
display_name = Frame -2
method = GeneMark_TB
source = Frame5

[Wally_frame6.bw]
display_name = Frame -3
method = GeneMark_TB
source = Frame6

------------------------------------------------------------------------------
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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Lincoln Stein | 3 Oct 2011 20:08
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Re: BIgWigSet, metadata.txt, trailing spaces cause GBrowse2 not to render xyplot tracks.

This is now fixed in Bio::DB::BigFile version 1.06, which should be appearing on CPAN within a few hours.


Lincoln

On Mon, Oct 3, 2011 at 1:15 PM, Razi Khaja <razi.khaja-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
All,

I've spent a few days trying to figure out why my BigWig files will not display in GBrowse2.  My metadata.txt file is copied below as an example.
It turns out that if there are trailing spaces on any of the lines of the metadata.txt file, that GBrowse2 will not render the tracks.

Can someone verify this bug by adding a space or two after the tag = value pairs for one of your bigwig data sources? 
These trailing spaces could be the source of  headaches for many folks trying to use BigWig files and hopefully should be fixed.

Best regards,

Razi

/**
 * Razi Khaja
 * Bioinformatics Specialist
 * Precollege and Undergraduate Science Education
 * Howard Hughes Medical Institute
 * 4000 Jones Bridge Road, Rm. S102
 * Chevy Chase, MD 20815
 * Email: khajar-5+GbW1xn1kU@public.gmane.org
 * Website: http://www.hhmi.org/grants/sea/
 * Mobile: 240-328-4985
 * Office: 301-215-8877
 */


[Wally_frame1.bw]
display_name = Frame +1
method = GeneMark_TB
source = Frame1

[Wally_frame2.bw]
display_name = Frame +2
method = GeneMark_TB
source = Frame2

[Wally_frame3.bw]
display_name = Frame +3
method = GeneMark_TB
source = Frame3

[Wally_frame4.bw]
display_name = Frame -1
method = GeneMark_TB
source = Frame4

[Wally_frame5.bw]
display_name = Frame -2
method = GeneMark_TB
source = Frame5

[Wally_frame6.bw]
display_name = Frame -3
method = GeneMark_TB
source = Frame6


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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--
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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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Erick Antezana | 4 Oct 2011 12:58
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look up for a region based on TWO landmarks?

Hi,

is there a way to configure (or hack) GBrowse in order to get a region
(a region of regions actually) by providing two landmarks:

   A .. B

where A and B are for instance two gene names, SNP names, etc ?

In the sample yeast track:

  A = YAL063C       with region:  24,001..27,969
  B =  NUT21          with region: 110,847..113,360

expected region to be shown: 24,001..113,360

thanks,
erick

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Parul Kudtarkar | 4 Oct 2011 23:38
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GBrowse details page error

Dear GBrowse community,

When I click on gbrowse feature details I get following error:
The server encountered an internal error or misconfiguration and was
unable to complete your request.

When I check server log file, following message is registered:
 Can't call method "uploadsid" on unblessed reference at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/UserTracks.pm
line 42.,

Any insight into this problem would be helpful.

Thanks and reagrs,
Parul Kudtarkar

--

-- 
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Parul Kudtarkar | 5 Oct 2011 19:35
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Re: GBrowse details page error

Dear GBrowse community,

Any solution to the aforementioned error?

Thanks,
Parul Kudtarkar

> Dear GBrowse community,
>
> When I click on gbrowse feature details I get following error:
> The server encountered an internal error or misconfiguration and was
> unable to complete your request.
>
> When I check server log file, following message is registered:
>  Can't call method "uploadsid" on unblessed reference at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/UserTracks.pm
> line 42.,
>
> Any insight into this problem would be helpful.
>
> Thanks and reagrs,
> Parul Kudtarkar
>
> --
> Parul Kudtarkar
> Scientific Programmer
> Center for Computational Regulatory Genomics
> Beckman Institute,
> California Institute of Technology
>
>

--

-- 
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Razi Khaja | 7 Oct 2011 00:23
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GBrowse2: Caching Tracks Independently?

In GBrowse2, how can I turn caching off completely?

More, importantly, is it possible to turn off "caching" for individual tracks?  If it is not possible to turn on/off caching for individual tracks, could this enhancement be put into the queue for future enhancements?

The reason, I request this enhancement is because, I have the following scenario:

Im using:
(1) GBrowse2,
(2) PostgreSQL with a chado database, and
(3) Apollo

I have a user, that selects a genomic region in GBrowse, and opens it in Apollo to call a gene.

With some magic (lots of code), the called gene is somehow entered into the chado database (not important how the called gene/annotation gets into the database, just that it does get into the database).

The user refreshes GBrowse, but the gene cannot be seen in the 'called Genes' track because 'caching' is turned ON.

Manually, the user selects the "Preferences" tab, un-checks the "Cache Tracks" box , and goes back to the "Browser".  The gene now appears in the 'called Genes' track.  If it were possible for the GBrowse Administrator to specify in the GBrowse conf files in the stanza for the 'called Genes' track, not to cache that particular track, then user would NOT have to manually uncheck 'caching', because we anticipate that the 'called Genes' track will be updated frequently and hence should not be cached.

This enhancement would give us the benefits of caching for the majority of tracks while providing a more user friendly 'end-user experience' (for a user who likely doesn't know what caching means! or which preferences to turn on/off.)  I hope this is a compelling reason to add this to the queue of enhancements.

In the meantime, I would be very appreciative, if someone could recommend settings for caching, or how to turn off caching completely.

Best regards,

Razi

/**
 * Razi Khaja
 * Bioinformatics Specialist
 * Precollege and Undergraduate Science Education
 * Howard Hughes Medical Institute
 * Janelia Farm Research Campus
 * 19700 Helix Drive, Rm. 3W.162
 * Ashburn, VA 20147
 * Email: khajar-5+GbW1xn1kU@public.gmane.org
 * Website: http://www.hhmi.org/grants/sea/
 * Mobile: 240-328-4985
 * Janelia Farm: 571-209-4693
 */
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-gbrowse mailing list
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Miquel Ràmia | 7 Oct 2011 17:56
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TrackDumper problem

Hi,

Need some advise about an odd behavior of the TrackDumper.pm (used from 
the floppy disk icon). Few days ago I could download track gff's without 
any problem, but today I can download track data but no from xy_plots or 
wiggle_plots of quantitative data. I have no problem downloading other 
features like gene, mrnas, ... I got this error when I try to dump 
quantitative tracks, any idea what could be the problem? :

[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] 
-------------------- EXCEPTION -------------------- , referer: 
localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] MSG: You 
have an error in your SQL syntax; check the manual that corresponds to 
your MySQL server version for the right syntax to use near '), referer: 
localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] )' at line 
12, referer: localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::DB::SeqFeature::Store::DBI::mysql::_features 
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm:865, 
referer: localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::DB::SeqFeature::Store::get_seq_stream 
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store.pm:738, referer: 
localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::Graphics::Browser2::TrackDumper::_dump_gff3 
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/TrackDumper.pm:113, 
referer: localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::Graphics::Browser2::TrackDumper::dump_gff3_autowig 
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/TrackDumper.pm:93, 
referer: localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::Graphics::Browser2::TrackDumper::dump_track 
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/TrackDumper.pm:88, 
referer: localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::Graphics::Browser2::TrackDumper::print_datafile 
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/TrackDumper.pm:414, 
referer: localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::Graphics::Browser2::Render::handle_gff_dump 
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1350, 
referer: localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::Graphics::Browser2::Render::render 
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:724, referer: 
localhost/gb2/gbrowse/dgrp/?name=2L
[Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
Bio::Graphics::Browser2::Render::run 
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:281, referer: 
localhost/gb2/gbrowse/dgrp/?name=2L

--

-- 
Miquel Ràmia Jesús
PhD. student (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Autònoma de Barcelona (UAB)
08193, Cerdanyola del Vallès
Barcelona (Spain)

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
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Lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org | 7 Oct 2011 18:15
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Re: TrackDumper problem

Did you update any software?

Lincoln

Sent from my iPad

On Oct 7, 2011, at 11:56 AM, Miquel Ràmia <miquel.ramia <at> uab.cat> wrote:

> Hi,
> 
> Need some advise about an odd behavior of the TrackDumper.pm (used from 
> the floppy disk icon). Few days ago I could download track gff's without 
> any problem, but today I can download track data but no from xy_plots or 
> wiggle_plots of quantitative data. I have no problem downloading other 
> features like gene, mrnas, ... I got this error when I try to dump 
> quantitative tracks, any idea what could be the problem? :
> 
> 
> 
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] 
> -------------------- EXCEPTION -------------------- , referer: 
> localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] MSG: You 
> have an error in your SQL syntax; check the manual that corresponds to 
> your MySQL server version for the right syntax to use near '), referer: 
> localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] )' at line 
> 12, referer: localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::DB::SeqFeature::Store::DBI::mysql::_features 
> /usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm:865, 
> referer: localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::DB::SeqFeature::Store::get_seq_stream 
> /usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store.pm:738, referer: 
> localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::Graphics::Browser2::TrackDumper::_dump_gff3 
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/TrackDumper.pm:113, 
> referer: localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::Graphics::Browser2::TrackDumper::dump_gff3_autowig 
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/TrackDumper.pm:93, 
> referer: localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::Graphics::Browser2::TrackDumper::dump_track 
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/TrackDumper.pm:88, 
> referer: localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::Graphics::Browser2::TrackDumper::print_datafile 
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/TrackDumper.pm:414, 
> referer: localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::Graphics::Browser2::Render::handle_gff_dump 
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1350, 
> referer: localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::Graphics::Browser2::Render::render 
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:724, referer: 
> localhost/gb2/gbrowse/dgrp/?name=2L
> [Fri Oct 07 18:50:18 2011] [error] [client 158.109.215.166] STACK 
> Bio::Graphics::Browser2::Render::run 
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:281, referer: 
> localhost/gb2/gbrowse/dgrp/?name=2L
> 
> 
> -- 
> Miquel Ràmia Jesús
> PhD. student (PIF)
> Evolutionary Bioinformatics Group
> (Genomics, Bioinformatics and Evolution Group)
> Lab MRB/014 - 93 586 89 58
> MRB - Institut de Biologia i Biomedicina (IBB)
> Universitat Autònoma de Barcelona (UAB)
> 08193, Cerdanyola del Vallès
> Barcelona (Spain)
> 
> 
> 
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2dcopy2
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse <at> lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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JINGJING JIN | 10 Oct 2011 02:07
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how to install the multiple gbrowse in one computer

Hi all,

Because I want to use two different gbrowse2 in one computer, one is
for public access and another for our lab access. Hence, the two
gbrowse will contain different mysql database.

Can some one give some suggestion about how to configure the gbrowse
configure file, or what others I should do?

Thanks!

jingjing

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Karthik | 10 Oct 2011 16:47
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Re: GBrowse 2.40 released

Hello Lincoln
Does the primer3 plugin work with gbrowse 2.40 ?
Also, when i installed gbrowse2.38, I got a black screen for the
authentication page and I had to revert to GBrowse2.23. Is that fixed now ?

Thanks
Karthik

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Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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