Joachim Baran | 23 Apr 00:35 2014
Picon

GBrowse 2.54 fake configuration context

Hello,

  I am wondering whether this email will go through to the list, because it appears that my unsubscribe requests to the mailman have not been very fruitful.

  To an admin: I would rather like to unsubscribe from this mailing list rather than setting a spam filter on this mailing list.

Joachim

------------------------------------------------------------------------------
Start Your Social Network Today - Download eXo Platform
Build your Enterprise Intranet with eXo Platform Software
Java Based Open Source Intranet - Social, Extensible, Cloud Ready
Get Started Now And Turn Your Intranet Into A Collaboration Platform
http://p.sf.net/sfu/ExoPlatform
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Jacqueline Lee | 22 Apr 20:01 2014
Picon

Displaying Peptide sequence in genome Details page

Hello,

 

Since our most recent gbrowse update (2.17->2.55), some of our users have noticed the peptide sequence and coding sequence are missing on our gene details pages. All that we see is the entire mRNA sequence, including introns. Is there something extra I need to configure in order to make the protein/CDS sequence visible?

 

Thanks,

Jacqueline Lee

------------------------------------------------------------------------------
Start Your Social Network Today - Download eXo Platform
Build your Enterprise Intranet with eXo Platform Software
Java Based Open Source Intranet - Social, Extensible, Cloud Ready
Get Started Now And Turn Your Intranet Into A Collaboration Platform
http://p.sf.net/sfu/ExoPlatform
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Robert Petera | 21 Apr 18:26 2014

Feature ID Call back

Hello,

I am a student at Bradley University working the TGD model organism database. I am having an issue with id callbacks in my subroutine. Here is my subroutine so far

sub  {
 my $f = shift;
 my $name = $f->name;
 my $ref = $f->ref;
 my $start = $f->start;
 my $end = $f->end;
 my $class = $f->class;
 my $id = $f->id;
 my $ttherm = "TTHERM_";
 my($first, $rest) = split(/_/, $name, 2);
 my $final = $ttherm . $rest;
 
 
 my $part2 = "\'>View This Gene\'s Page</a>";
 
 my $result = join "", $details, $part1, $final, $part2;
 
 return $result;
}

The issue I am currently having is the feature_id part of the url, it uses the feature name instead of the primary id from the database. I have tried load_id and it gives me the same result. Any help on this would be appreciated. You can ignore the part1 and part2 strings as they are not a part of the problem. 

The backend i am using is Bio::DB::SeqFeature::Store and here is a sample of the gff3 file

supercontig2.1 BROAD gene 37065 42616 . - . ID=TTHMIC_02655509;name=02655509;note=hypothetical protein
supercontig2.1 BROAD gene 43023 44543 . + . ID=TTHMIC_00290610;name=00290610;note=leishmanolysin family protein
supercontig2.1 BROAD gene 49932 50240 . + . ID=TTHMIC_00290620;name=00290620;note=hypothetical protein
supercontig2.1 BROAD gene 52924 54424 . + . ID=TTHMIC_02655510;name=02655510;note=leishmanolysin family protein
supercontig2.1 BROAD gene 65346 66180 . + . ID=TTHMIC_02655511;name=02655511;note=leishmanolysin-like protein


Thanks,

Robert Petera
------------------------------------------------------------------------------
Start Your Social Network Today - Download eXo Platform
Build your Enterprise Intranet with eXo Platform Software
Java Based Open Source Intranet - Social, Extensible, Cloud Ready
Get Started Now And Turn Your Intranet Into A Collaboration Platform
http://p.sf.net/sfu/ExoPlatform
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Nathan Weeks | 21 Apr 17:51 2014

Re: Gmod-gbrowse Digest, Vol 95, Issue 5

To augment Scott's response: from a quick reading of the the
Bio::Graphics::Glyph::gene code, it looks like if one specifies a
value for "sub_part", only subfeatures of that type will be rendered
(e.g., if one specifies "sub_part = exon", then UTRs won't be
rendered). Here's the relevant code (I think) in the
Bio::Graphics::Glyph::gene module:

======================================
  my  <at> subparts;
  if ($class->option('sub_part')) {
     <at> subparts = $feature->get_SeqFeatures($class->option('sub_part'));
  }
  elsif ($feature->primary_tag =~ /^mRNA/i) {
     <at> subparts = $feature->get_SeqFeatures(qw(CDS five_prime_UTR
three_prime_UTR UTR));
  }
  else {
     <at> subparts = $feature->get_SeqFeatures('exon');
  }
======================================

It would be nice if sub_part accepted a list of types.

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
Crop Genome Informatics Laboratory
Iowa State University
http://weeks.public.iastate.edu/

On Thu, Apr 17, 2014 at 4:48 PM,
<gmod-gbrowse-request@...> wrote:
> ------------------------------
>
> Message: 7
> Date: Thu, 17 Apr 2014 10:47:22 -0700 (PDT)
> From: John Portwood <portwoodii@...>
> Subject: [Gmod-gbrowse] Configuring Genes to show exons and UTRs
> To: gmod-gbrowse@...
> Message-ID: <1397756842181-5712467.post@...>
> Content-Type: text/plain; charset=us-ascii
>
> Hello,
>
> I'm having an issue trying to render exons and UTRs together. Here is a
> sample of the GFF3 I'm working with:
>
> /Chr10   Ensembl_AGPv3   gene    1720611 1722779 .       +       .
> Name=GRMZM2G129907;biotype=protein_coding;description=Uncharacterized%20protein%20%20[Source:UniProtKB/TrEMBL%3BAcc:B4FHQ6];logic_name=genebuilder;ID=GRMZM2G129907
> Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .
> Name=GRMZM2G129907_T02;Parent=GRMZM2G129907;biotype=protein_coding;description=cdna|est|omrna;logic_name=genebuilder;ID=GRMZM2G129907_T02
> Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .
> Name=GRMZM2G129907_T01;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T01
> Chr10   Ensembl_AGPv3   mRNA    1721887 1722779 .       +       .
> Name=GRMZM2G129907_T03;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T03
> Chr10   Ensembl_AGPv3   exon    1720611 1720931 .       +       .
> Name=GRMZM2G129907_E02;Parent=GRMZM2G129907_T01;ensembl_end_phase=2;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E02
> Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .
> Parent=GRMZM2G129907_T01;
> Chr10   Ensembl_AGPv3   CDS     1720714 1720931 .       +       0
> Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=1;ID=GRMZM2G129907_P01
> Chr10   Ensembl_AGPv3   CDS     1721395 1721501 .       +       0
> Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=2;ID=GRMZM2G129907_P01
> Chr10   Ensembl_AGPv3   exon    1721395 1721501 .       +       .
> Name=GRMZM2G129907_E04;Parent=GRMZM2G129907_T01;ensembl_end_phase=1;ensembl_phase=2;rank=2;ID=GRMZM2G129907_E04
> Chr10   Ensembl_AGPv3   CDS     1722296 1722459 .       +       0
> Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=3;ID=GRMZM2G129907_P01
> Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
> Name=GRMZM2G129907_E03;Parent=GRMZM2G129907_T01;ensembl_end_phase=-1;ensembl_phase=1;rank=3;ID=GRMZM2G129907_E03
> Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .
> Parent=GRMZM2G129907_T01;
> Chr10   Ensembl_AGPv3   exon    1720611 1721501 .       +       .
> Name=GRMZM2G129907_E06;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E06
> Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .
> Parent=GRMZM2G129907_T02;
> Chr10   Ensembl_AGPv3   CDS     1720714 1720935 .       +       0
> Name=GRMZM2G129907_P02;Parent=GRMZM2G129907_T02;rank=1;ID=GRMZM2G129907_P02
> Chr10   Ensembl_AGPv3   three_prime_UTR 1720936 1722779 .       +       .
> Parent=GRMZM2G129907_T02;
> Chr10   Ensembl_AGPv3   exon    1721994 1722055 .       +       .
> Name=GRMZM2G129907_E05;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E05
> Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
> Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=3;ID=GRMZM2G129907_E01
> Chr10   Ensembl_AGPv3   exon    1721887 1722055 .       +       .
> Name=GRMZM2G129907_E07;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E07
> Chr10   Ensembl_AGPv3   five_prime_UTR  1721887 1722363 .       +       .
> Parent=GRMZM2G129907_T03;
> Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
> Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E01
> Chr10   Ensembl_AGPv3   CDS     1722364 1722459 .       +       0
> Name=GRMZM2G129907_P03;Parent=GRMZM2G129907_T03;rank=1;ID=GRMZM2G129907_P03
> Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .
> Parent=GRMZM2G129907_T03;/
>
> Using the gene glyph produces this rendering:
> <http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/geneModelsv3_UTRs.png>
>
> This is close to what I want, but the inner exons aren't showing. When I use
> "sub_part=exon" in this track's stanza, the exons show but the gray UTRs
> disappear:
> <http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/genModelsv3_Exons.png>
>
> I want to render a display that looks exactly like the image above, but with
> the grayed UTR regions showing in the exons. Any help on accomplishing this
> would be greatly appreciated.
>
> Thanks,
> John
>
>
>
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Configuring-Genes-to-show-exons-and-UTRs-tp5712467.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Start Your Social Network Today - Download eXo Platform
Build your Enterprise Intranet with eXo Platform Software
Java Based Open Source Intranet - Social, Extensible, Cloud Ready
Get Started Now And Turn Your Intranet Into A Collaboration Platform
http://p.sf.net/sfu/ExoPlatform
Scott Cain | 18 Apr 16:43 2014
Picon

Re: features are not displayed

Hi Qisen,

Always reply-all so the GBrowse mailing list stays cc'ed.

How did you install GBrowse?  The beginning of your error log mentions a url that has "...gbrowse/gbrowse/volvox" in it, which is the url I would expect from a apt-get install, but the end of your conf file mentions the file path /var/lib/gbrowse2, which is a path I would expect if it were installed on the command line (either from a downloaded tarball, a git clone or the cpan shell).

My guess is that you initially installed via apt-get, had some problem, then installed via the cpan shell, and now you have both.  I agree that there is a permission problem on the session directory; you should make sure it's owned by the apache user:

  sudo chown www-data:www-data /var/lib/gbrowse2/sessions


Scott





On Mon, Apr 14, 2014 at 11:20 PM, Qisen Zhang <zhqisen-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Scott
Thank you for your reply. I have made thing worst now. I could not open the page any more. Just get following error:

'The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, webmaster <at> localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.'

and error log file has following contents:

-----------------------------------------------------------
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 15 12:07:25 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 15 12:10:32 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 15 12:15:56 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 15 12:39:33 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse"

I am not good on using Ubuntu system. I may have file access permission problems.

Would you help please?

Best Regards

Qisen



On Mon, Apr 14, 2014 at 11:25 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Qisen,

Can you please send a screenshot of what your browser looks like as well as anything in your apache error log that looks like it might be related to GBrowse?

Scott



On Sun, Apr 13, 2014 at 3:14 AM, Qisen Zhang <zhqisen-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi

I am new on using Gbrowse2. I have installed it on ubuntu and following the tutorial till view example data set (volvox). I am able to open the volvox page, but all displayed details are different from the figure showing on Toturial. There is no marked ruler nor features. Features are not displyed.

Why is that? where is the problem?
Best Regard
Qisen


------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
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
------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Hyunmin Kim | 18 Apr 10:42 2014
Picon

GBrowse ( bp_seqfeature_load.pl ) Error

Hi, all

I tried to upload gff into mysql database with bp_seqfeature_load.pl

I downloaded latest GBrowse version on Github.

I tried to search this problem on google. but I can’t find the solving method.



$ bp_seqfeature_load.pl -u **** -p ***** -c -f -d human chr2_ens_annots.gff chr2.fa 2>&1 | tee /tmp/bpsl.log1

===============================================================================================
START


...
...
...
. (not full list..)
12000 features loaded in  5.19s ( 0.45s/1000 features)...
13000 features loaded in  5.63s ( 0.45s/1000 features)...
14000 features loaded in  6.08s ( 0.45s/1000 features)...
15000 features loaded in  6.53s ( 0.45s/1000 features)...
16000 features loaded in  6.98s ( 0.45s/1000 features)...
17000 features loaded in  7.42s ( 0.45s/1000 features)...
Building object tree... 0.25s4s
Loading bulk data into database... 2.55s
load time: 10.65s
loading chr2.fa...
DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1501, <GEN5> line 1165401.

-------------------- EXCEPTION --------------------
MSG: MySQL server has gone away
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_insert_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/DBI/mysql.pm:1501
STACK Bio::DB::SeqFeature::Store::insert_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store.pm:1243
STACK Bio::DB::SeqFeature::Store::Loader::load_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:619
STACK Bio::DB::SeqFeature::Store::GFF3Loader::load_line /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm:396
STACK Bio::DB::SeqFeature::Store::Loader::do_load /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:433
STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:353
STACK Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:261
—————————————————————


END
===============================================================================================

Thanks,
Hyunmin
------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Hyunmin Kim | 18 Apr 06:53 2014
Picon

gbrowse DNA track no visible (tutorial)

Dear All,

Hi, 

I leaning the gbrowse with tutorial.

I success all tutorial except for DNA track.

What problem?

(This situation occur in example data too) (like : Yeast chromosomes 1+2 (advanced) )

Thanks,
Hyunmin
------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
John Portwood | 17 Apr 19:47 2014
Picon

Configuring Genes to show exons and UTRs

Hello,

I'm having an issue trying to render exons and UTRs together. Here is a
sample of the GFF3 I'm working with:

/Chr10   Ensembl_AGPv3   gene    1720611 1722779 .       +       .      
Name=GRMZM2G129907;biotype=protein_coding;description=Uncharacterized%20protein%20%20[Source:UniProtKB/TrEMBL%3BAcc:B4FHQ6];logic_name=genebuilder;ID=GRMZM2G129907
Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .      
Name=GRMZM2G129907_T02;Parent=GRMZM2G129907;biotype=protein_coding;description=cdna|est|omrna;logic_name=genebuilder;ID=GRMZM2G129907_T02
Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .      
Name=GRMZM2G129907_T01;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T01
Chr10   Ensembl_AGPv3   mRNA    1721887 1722779 .       +       .      
Name=GRMZM2G129907_T03;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T03
Chr10   Ensembl_AGPv3   exon    1720611 1720931 .       +       .      
Name=GRMZM2G129907_E02;Parent=GRMZM2G129907_T01;ensembl_end_phase=2;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E02
Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .      
Parent=GRMZM2G129907_T01;
Chr10   Ensembl_AGPv3   CDS     1720714 1720931 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=1;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   CDS     1721395 1721501 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=2;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   exon    1721395 1721501 .       +       .      
Name=GRMZM2G129907_E04;Parent=GRMZM2G129907_T01;ensembl_end_phase=1;ensembl_phase=2;rank=2;ID=GRMZM2G129907_E04
Chr10   Ensembl_AGPv3   CDS     1722296 1722459 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=3;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E03;Parent=GRMZM2G129907_T01;ensembl_end_phase=-1;ensembl_phase=1;rank=3;ID=GRMZM2G129907_E03
Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .      
Parent=GRMZM2G129907_T01;
Chr10   Ensembl_AGPv3   exon    1720611 1721501 .       +       .      
Name=GRMZM2G129907_E06;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E06
Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .      
Parent=GRMZM2G129907_T02;
Chr10   Ensembl_AGPv3   CDS     1720714 1720935 .       +       0      
Name=GRMZM2G129907_P02;Parent=GRMZM2G129907_T02;rank=1;ID=GRMZM2G129907_P02
Chr10   Ensembl_AGPv3   three_prime_UTR 1720936 1722779 .       +       .      
Parent=GRMZM2G129907_T02;
Chr10   Ensembl_AGPv3   exon    1721994 1722055 .       +       .      
Name=GRMZM2G129907_E05;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E05
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=3;ID=GRMZM2G129907_E01
Chr10   Ensembl_AGPv3   exon    1721887 1722055 .       +       .      
Name=GRMZM2G129907_E07;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E07
Chr10   Ensembl_AGPv3   five_prime_UTR  1721887 1722363 .       +       .      
Parent=GRMZM2G129907_T03;
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E01
Chr10   Ensembl_AGPv3   CDS     1722364 1722459 .       +       0      
Name=GRMZM2G129907_P03;Parent=GRMZM2G129907_T03;rank=1;ID=GRMZM2G129907_P03
Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .      
Parent=GRMZM2G129907_T03;/

Using the gene glyph produces this
rendering:
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/geneModelsv3_UTRs.png> 

This is close to what I want, but the inner exons aren't showing. When I use
"sub_part=exon" in this track's stanza, the exons show but the gray
UTRs
disappear:
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/genModelsv3_Exons.png> 

I want to render a display that looks exactly like the image above, but with
the grayed UTR regions showing in the exons. Any help on accomplishing this
would be greatly appreciated.

Thanks,
John

--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Configuring-Genes-to-show-exons-and-UTRs-tp5712467.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
Qisen Zhang | 13 Apr 09:14 2014
Picon

features are not displayed

Hi

I am new on using Gbrowse2. I have installed it on ubuntu and following the tutorial till view example data set (volvox). I am able to open the volvox page, but all displayed details are different from the figure showing on Toturial. There is no marked ruler nor features. Features are not displyed.

Why is that? where is the problem?
Best Regard
Qisen

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
John Portwood | 7 Apr 23:15 2014
Picon

Searching names loading incorrect section in gbrowse

Hello,

I'm having a problem with GBrowse2 (v 2.43) and the link to the archive mailing list wasn't working so I'm not able to see if this has been reported before. 

For only one track, when the name is searched in GBrowse the browser will navigate to a section that is slightly off from where the name is located. For example take this section from my GFF3 (rendered from grepping "GRMZM2G124745"):

Chr7    AGPv3   protein_coding_gene     176806695       176810119       .       +       .       Name=GRMZM2G124745;biotype=protein_coding;logic_name=genebuilder;ID=GRMZM2G124745
Chr7    AGPv3   transcript      176806695       176810119       .       +       .       Name=GRMZM2G124745_T01;Parent=GRMZM2G124745;biotype=protein_coding;description=est;logic_name=genebuilder;ID=GRMZM2G124745_T01
Chr7    AGPv3   exon    176806695       176806968       .       +       .       Name=GRMZM2G124745_E04;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;rank=1;ID=GRMZM2G124745_E04
Chr7    AGPv3   five_prime_UTR  176806695       176806706       .       +       .       Parent=GRMZM2G124745_T01;
Chr7    AGPv3   CDS     176806707       176806968       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=1;ID=GRMZM2G124745_P01
Chr7    AGPv3   CDS     176808089       176808340       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=2;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176808089       176808340       .       +       .       Name=GRMZM2G124745_E03;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;rank=2;ID=GRMZM2G124745_E03
Chr7    AGPv3   CDS     176808921       176809060       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=3;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176808921       176809060       .       +       .       Name=GRMZM2G124745_E01;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_phase=1;rank=3;ID=GRMZM2G124745_E01
Chr7    AGPv3   CDS     176810033       176810119       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=4;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176810033       176810119       .       +       .       Name=GRMZM2G124745_E02;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=-1;rank=4;ID=GRMZM2G124745_E02

Searching for "GRMZM2G124745" in GBrowse will bring me to this region:
Chr7:176,822,753..176,826,177

However, on the first line in the above snippet you can see this element is actually located between 176,806,695 and 176,810,119 on Chr7. All of the elements are being rendered at their correct positions specified in the gff -- It's only when you search for them by name the browser takes you to a region ahead of them. 

This problem is not occurring with other tracks that I have loaded, so I'm guessing there's a problem either with the gff or the config file but after much research I'm still unable to find the cause of this issue.

Any help is greatly appreciated. Thanks!

-John 

------------------------------------------------------------------------------
Put Bad Developers to Shame
Dominate Development with Jenkins Continuous Integration
Continuously Automate Build, Test & Deployment 
Start a new project now. Try Jenkins in the cloud.
http://p.sf.net/sfu/13600_Cloudbees
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Brad Covey | 10 Apr 16:44 2014
Picon

Problem With Custom Track Entries in the Uploads Table of the Users.SQLite Database

Hi Guys,

I'm uploading large files to GBrowse manually as custom tracks. I've written scripts to create the sqlite database for the upload, the proper folder structure under "userdata", and the entry in the users.sqlite database.

The directory structure that is created looks like this:
userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite  
                STATUS     
                feature_name.conf  
                SOURCES/
                    feature_name


The upload seems to work fine and the new track appears under "Custom Tracks" as shown in the following screenshot:


here "might-have-fixed-the-featurefile" is the new upload.

But the upload is not shown under "Select Tracks":


I've done a bit of troubleshooting to try to figure out why this is happening. I've narrowed the problem down to the entry in the "uploads" table of the "users.sqlite" database.
These are the current entries in the database:

"2","private","trying-again",                            "","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again",                            "0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile","0"

I included the "trying-again" entry as a working example for reference.
note: the trackid is 32 characters long for both


As far as I can tell there is no difference between the two entries, but if I point the working "trying-again" entry at the non-working "might-have-fixed-the-featurefile" path like so:

"2","private","might-have-fixed-the-featurefile","","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again showing might-have-fixed-the-featurefile","0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile",                               "0"

My initially non-working track is displayed properly:


Which tells me that the folder structure, sqlite sqlite database, and configuration for my new custom track are being created properly but there is some problem with the entry in the "uploads" table of the users.sqlite database preventing the track from being displayed properly.


Does anyone have any idea what may be wrong with the "uploads" entries that my script is creating?


Thanks,
Brad

------------------------------------------------------------------------------
Put Bad Developers to Shame
Dominate Development with Jenkins Continuous Integration
Continuously Automate Build, Test & Deployment 
Start a new project now. Try Jenkins in the cloud.
http://p.sf.net/sfu/13600_Cloudbees
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Gmane