gmane.science.biology.gmod.gbrowse

Can a region be too small to render with bigwig orbam?

Jim Hu — 2013-05-18T15:30:55

On our E. coli Gbrowse we're trying to show published high throughput data using bigwig tracksets. This:

http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Lrp_Exponential&t=Lrp_Stationary

Seems to work when I am zoomed to >2kbp, but not when I'm at 1kbp.  It times out on the smaller region with the dreaded pink track display. I get this in the logs

[Sat May 18 10:17:24 2013] [error] [client 74.197.139.252] [Sat May 18 10:17:24 2013] gbrowse: alarm clock at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RenderPanels.pm line 1508., referer: http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Lrp_Exponential&t=Lrp_Stationary
[Sat May 18 10:17:24 2013] [error] [client 74.197.139.252] [Sat May 18 10:17:24 2013] gbrowse: RenderPanels error: timeout at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RenderPanels.pm line 1508., referer: http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Lrp_Exponential&t=Lrp_Stationary
[Sat May 18 10:17:24 2013] [error] [client 74.197.139.252] [Sat May 18 10:17:24 2013] gbrowse: [14887] rendering error track: Timeout; Try turning off tracks or looking at a smaller region. at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Render.pm line 3651., referer: http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Lrp_Exponential&t=Lrp_Stationary

Counterintuitive!

To see if it's just us, I looked a modencode. I don't see that for what I am guessing is a bigwig track on the C. elegans gbrowse there (adult spe0 miRNA change), but I do see a problem at 1kb with Young Adult 25dC 46hrs. It displays this in the pink track messages:

can't locate object method tid via package Bio::DB::Bam::SplitAlignmentPart

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054



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multiple tracks via URL

Jim Hu — 2013-05-18T15:04:21

in gbrowse_img, you can tell it to show multiple tracks by using 

?t=track1+track2...

but this doesn't work in Gbrowse. Instead, you can do

?t=track1&t=track2...

Is the first syntax supposed to work in Gbrowse too?

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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new file upload options

Timothy Parnell — 2013-05-16T22:33:52

Hello,

I have done some work to extend the available file options for uploading custom user tracks that I would like to make available to the community.

The short list of changes include.
1. BigBed files are now supported via upload and URL. Both region and coverage tracks are generated.
2. Archives (ZIP or TAR) of two or more BigWig files are supported, resulting in a BigWigSet with each file set up as a subtrack selected by display name.
3. USeq archives are automatically converted to BigWig or BigBed tracks depending on context if support is enabled.

Additionally, uploaded Bam files are no longer sorted automatically but only when the Bam sort flag header is not set to coordinate. Samtools does not set this flag (you must do it manually), but Picard does.

You may checkout the additions here
https://github.com/tjparnell/GBrowse/tree/new_upload_options
They are sync'ed with the current GBrowse master.

I have tested these on the VBox and Amazon GBrowse virtual machines, as well as in house on Mac OS X. Please let me know if you find any problems.

Some additional notes:
The archives are extracted through a pipe directly to file to avoid issues with errant and non-sensible paths that may be stored in the archive.

The USeq format is native to the USeq analysis package developed here at the University of Utah. More information can be found at http://useq.sourceforge.net, including information about the file format. It requires the installation of java 1.6+ and the USeq package in a searchable path. It should fail gracefully if these are not found.

Upload file size limits may need to be increased for FCGI environments to avoid timeout issues. 

Tim


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Features on reverse strand

Joachim Baran — 2013-05-13T14:17:15

Hello,

Sorry, I have sent this question to the mailing list before, but I think
the email might have not made it through. I cannot see it showing up in the
archive. So, I am resending it here:

I have recently joined the WormBase development team and a lot of my work
centres around GBrowse.

Currently, I am struggling to make GBrowse show a feature on the reverse
strand. I am adding the feature as follows:

http://www.wormbase.org/tools/genome/gbrowse/c_briggsae/?name=chrV:13058784..13065097;add=chrV+Hits+Hits+13062147-13060275

The glyph for "Hits" denotes that the feature is on the forward strand.
That is fine. However, I would like to have "Hits" on the reverse strand,
i.e. the glyph should be flipped.

I tried:

1. reversing the coordinate (13060275-13062147), which does not change
anything
2. adding "flip=1" to the URL, which flips everything
3. adding "style=...", which breaks everything (the "Hits" track breaks)

Is there a way to add features via URI and have them on the reverse
strand?

Thanks,
Joachim
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Personal Genome SNP format or BigBed?

Zhang, Hongxin (MU-Student — 2013-05-09T15:20:45

Hi,

Did anyone have used personal genome SNP format coming from UCSC before? Thank Tim gave me suggest about BigBed format but looks like personal genome snp format is exactly what I want. Does GBrowse support this format already?

If I use BigBed, how should I store my data? Suppose I have:
chr position REFERENCE IA3023_ALLELE J105_3_4_ALLELE M20_2_5_2_ALLELE
Gm01 975 G G G

I changed the data into Bed format like this:
Gm01 975 975 Reference
Gm01 975 975 IA3023_ALLELE J105_3_4_ALLELE
Gm01 975 975 M20_2_5_2_ALLELE

But where should I put my alleles name if I want to put all information into one track?
These figures are my track using gff3 format and I don't think I will use this format anymore. Thank you for your help.

Best,
Hongxin
[cid:17c71f7f-94b6-0caa-0909-4daf781bbff2]

[cid:1529061a-9b7e-13ef-b6dc-57e237c6d821]

[cid:f2ac5606-bc53-b6e5-1dcd-c57f79c40d54]

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Download FASTA issue

Omar Darwish — 2013-05-08T23:09:04

Hello everyone,

I need to download the DNA sequence from the chromosome of the the
currently displayed area on GBrowse.
When I click the small save icon on one of the alignments SAM tracks (see
the attached snapshot) and then select FASTA and  click on Download track
data across region (LG5 ...... )
The file is downloaded, but it contains the header of the fasta only (*> LG5
*) nothing else
*
*
Id there any other ways to pull up this area from the chromosome? or
something is wrong with the GBrowse?

Added features on the reverse strand via URL

Joachim Baran — 2013-05-08T20:57:00

Hello,

  I have recently joined the WormBase development team and a lot of my work
centres around GBrowse.

  Currently, I am struggling to make GBrowse show a feature on the reverse
strand. I am adding the feature as follows:


http://www.wormbase.org/tools/genome/gbrowse/c_briggsae/?name=chrV:13058784..13065097;add=chrV+Hits+Hits+13062147-13060275

  The glyph for "Hits" denotes that the feature is on the forward strand.
That is fine. However, I would like to have "Hits" on the reverse strand,
i.e. the glyph should be flipped.

  I tried:

  1. reversing the coordinate (13060275-13062147), which does not change
anything
  2. adding "flip=1" to the URL, which flips everything
  3. adding "style=...", which breaks everything (the "Hits" track breaks)

  Is there a way to add features via URI and have them on the reverse
strand?

Thanks,
Joachim
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Problem with BigWig file

Youhuang BAI - 白有煌 — 2013-05-08T01:01:35

Hi,

I want to use Gbrowse to display the density of short reads mapped on Arabidopsis genome and BigWig file is supposed to be provided into Gbrowse.
However, only an example on configuration of Wiggle file is given on the tutorial of Gbrowse. Is any example of BigWig format is available for me?

And I tried to configurate it as fellow:
[BigWig:database]
 db_adaptor    = Bio::DB::BigWig
 db_args       = -bigwig /home/gb/ath/20130506.uniqueMapped.minus.chr.bw

[BigWigIntervals:region] 
 feature  = summary 
 database = BigWig 
 glyph    = wiggle_whiskers 
 min_score = 0 
 max_score = 80 
 key       = test bigWig 

It doesn't work.



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Need documentation on Gbrowse session handling

Michael Dondrup — 2013-05-07T11:31:53

Dear Gbrowse list,

I have, with a little desperation, started to search look for documentation on the Gbrowse2 Session module. In particular, I am 
interested in how to *correctly* initialize and build up a Gbrowse session which is fully authorized for a user. Let's assume the 
task is to: write a cgi script (in addition to the gbrowse cgi) to initialize a gbrowse session with an authenticated user, such that in
the next invocation of gbrowse, the user is authenticated and logged in. 

I found by reading through the source code and reverse
engineering a sequence of commands that will *almost* get me there. I am seemingly missing one step only:
- the example code below works in case I already have a Gbrowse session
- the example doesn't work when there is no session at all, because subsequent calls to gbrowse make a new session which then is not authenticated.

So, what is the correct way to initialize a Gbrowse2 Session programmatically? Am I missing something.

I'd really appreciate your help, because now I am definitely stuck.



Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen, 
Norway


#!/usr/bin/env perl

use strict;
use warnings;
use Net::SAML;
use CGI::Fast qw(:standard);

use Bio::Graphics::Browser2;
use Bio::Graphics::Browser2::Render::HTML;

while (my $q = CGI::Fast->new) {
my $username ="valid user"; 
# it's not really important where this comes from,
# the user information is coming from an authentication module using Net::SAML
my $fullname = "Fully Valid";
my $mail = "valid-O5WfVfzUwx8< at >public.gmane.org";

 if ($username) {

my $p = "https://url";
my $myurl = "https://url/gbrowse/lsalmonis/";
my $htmlhead = <<HTML
<script src="$p/gbrowse2/js/login.js" type="text/javascript"></script>
<script src="$p/gbrowse2/js/controller.js" type="text/javascript"></script>
HTML
;
       ## STEP 1:
        ## get the session and initialize it
       
        my $session = $render->session;
        $session->lock();
        $session->username($username);
        $session->flush;

## STEP 2:
        ## authorization handling:
my $userdb = $render->userdb;
        my $id = $userdb->check_or_add_named_session($session->id,$username);
        $userdb->set_fullname_from_username($username=>$fullname,$mail) if defined $fullname;
        warn "username ".$session->username. " stored in session ".$session->id();
        # now authenticate
        my ($sid, $nonce) = $render->authorize_user($username,$id, 1,undef);
        my $is_authorized = $render->user_authorized_for_source($username);

        ## STEP 3:
        ## prepare for JavaScript invocation
        ## seems like the final step is to invoke login_load_account to make the UI aware of the login

# convert the login data to json
        my $result = to_json { userOK  => 1,
                sessionid => $id,
                username  => $username,
                message   => 'login ok',
              };

## STEP 5:
        ## print an intermediate web page to invoke javascript 
print header(-type=>"text/html");
      print start_html(-head=>$htmlhead);
      print b("user $username". (($is_authorized)?" is ": "is not ") . "authorized!");
        print script({-type=>'text/javascript'},
<<SCRIPT      
var p = $result;
login_load_account("$myurl",p);
SCRIPT
);
$session->unlock();
print end_html();
 }








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What glyph to use for displaying a gene?

Barris, Wes — 2013-05-03T18:00:12

I have a gff3 file with gene defined using the parental nesting
described here: http://www.gmod.org/wiki/GFF3
The features include (with indentation representing the nesting):

gene
   mRNA
   transcript
      five_prime_UTR
      CDS
      three_prime_UTR
      exon

My question is: What glyph should be used to properly display this
gene description in gbrowse2?

I've tried transcript, transcript2, processed_transcript, cds.
None of them are showing what I think it should look like.

GBrowse 2.54 cannot display tracks on Mac, Firefox,Safari, Opera

184523479 — 2013-05-02T11:35:21

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Restricted access to tracks defined in conf files?

Jim Hu — 2013-05-01T13:59:50

I'm not sure if this is related to some of the recent messages about authentication...

We need to move some tracks uploaded by users from the user upload area to our sets of experimental data tracks defined in conf files.  Is there a way to make these invisible except to specific users defined in the conf file? In other words, I'd like to have the tracks behave like the uploaded/shared tracks, but within the main list of tracks.

Thanks,

Jim


=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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Autocomplete limit?

Hans Vasquez-Gross — 2013-04-30T19:47:14

Hi All,

     Is there a limit for the number of sequences autocomplete works with?
 Two example data sources are provided below, which work fine with
autocomplete.

http://dendrome.ucdavis.edu/fgb2/pita_bac_ann/?q=BAC3:1..1000000
http://dendrome.ucdavis.edu/fgb2/pita_fosmids/

    However, testing autocomplete on a new load of an early v0.8 assembly
of a ~22Gbp genome with ~16.5 million individual sequences has not been
successful.   If I try to type the first few characters of a scaffold (ie
jcf), a list never drops down.

I continued typing a sequence name reasoning that maybe there was a limit
to how many results could be returned, but it never autocompleted.  In
fact, I'm fairly certain when testing this assembly performance with
autocomplete in GBrowse caused my webserver to become unresponsive and had
to be restarted.  I'd like to have the autocomplete return a minimal number
of scaffolds (20+-) so it'll stay responsive and not crash the server, but
continue filtering that set as the user types more of the scaffold name.

   Any comments or suggestions would be greatly appreciated.

Thanks,
-Hans
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Issues with snapshot

Beau Desaulniers — 2013-04-27T21:10:08

Hi,

Every time I try and take a snapshot I end up with what Figure 1 looks like
when what I want is something like figure 2. I've tried a different
computer and operating system to check if it was my browser. Same thing.
This is the website I am accessing:

http://ascobase.cgrb.oregonstate.edu/cgi-bin/gb2/gbrowse/ncrassa_nargang/

 Can you please help.

Thanks,

beau.des
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option for language preference in Genome Browser 2

Kin — 2013-04-27T02:39:49

Hi,


I really like Genome Browser and especially the version 2 that just came
out. However, I have issues reading the text on the website. My computer is
a traditional Chinese windows 7 and the genome browser 2 automatically
detect my system as simplified Chinese. All I need is English! It will be
great if you have a button or something that I can switch back the genome
browser into English!

Thank you so much!!!

Best wishes,
Kin


------------------------------------------------------
Chikin Kuok(Kin)
Department of Molecular Genetics
University of Toronto
Tel:+1(647)821-6288
E-mail:kinkuok-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org
            kin.kuok-UsiKwlUuF4aeFQavDyXPBQ< at >public.gmane.org
            kuok-1i+9uMS5CLHqJdGyAr2GoA< at >public.gmane.org
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Problem with plugins in GBrowse2

Victor Strelets — 2013-04-23T19:04:57

Hi,

I was debugging strange output of FastaDumper
plugin and realized that probably I'm using
version which was not supposed to work with
current GBrowse2.

Visited CPAN - list of plugins contains FastaDumper,
but it is not connected to anything submitted.
Half of the plugins are that way on that page.

Links from GMOD wiki (to same CPAN) produces list
of something totally unrelated.

Checked how plugins work on other MODs and
realized that FastaDumper does proper color 
decoration only on WormBase site, on others 
(FlyBase too) it just dumps completely undecorated 
fasta (like txt instead of html).

Can somebody clarify what is the known
situation with plugins? Is it possible that
FastaDumper which comes packaged with GBrowse2
was somehow left unreplaced with current version?
It was dated 2005 coming with GBrowse2 2.54.

Any info will help.

Victor
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Phylogenetic Tree Glyph in GBrowse

Abraham Darius Llave (IRRI — 2013-04-23T09:21:38

Hello!

For the past two weeks, I have been trying to use the Phylogenetic Tree
Glyph feature as described in the link
http://urgi.versailles.inra.fr/gbrowse2/tutorial/tutorial.phyTreeEdit.html
(strangely
enough, I don't find anything that refers to it, on
http://gmod.org/wiki/GBrowse and its subpages ).

And yes, I can't get it to work. Indeed, I'm experiencing what is mentioned
in the link : "Note: the phylogenetic tree display appears to be broken in
GBrowse version 2.0. Help bringing it back would be much appreciated." .

What happens exactly on my part is, I get numerous tracks of assumed Perl
hash dumps, instead of those of the species as specified in the tree file.

[image: Inline image 1]

Am I doing something wrong? Or any dependencies I am forgetting to install?
Whatever it is, your generous assistance is really appreciated.

Cheers,

Abraham Darius S. Llave****

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute****

Los Baños, Laguna 4027****

Republic of the Philippines

a.llave-XBJXOCa7Bx8< at >public.gmane.org
+63-49-536-2701 extension 2643****

+639183981185

Parent feature in a callback

Doug Senalik — 2013-04-18T01:40:58

In version 2.50 of GBrowse, I was able to access parent feature values 
(/e.g./ score) in a call back with code that started like this:

bgcolor        = sub {
                  my 
($feature,$option_name,$part_no,$total_parts,$glyph) = < at >_;
                  my $parent = $glyph->parent_feature;
                  my $score = $parent->score;
                  ... (then I converted score to a color) ...
                  return $color;
                  }

When I upgraded to version 2.54, this stopped working, and with some 
debugging I find that I get an undefined value for $parent.
Has there been a change, is this a bug, or (most likely) I have been 
doing it wrong all along?
Thanks in advance
Doug

How can one cite Gbrowse2 ?

Omar Darwish — 2013-04-17T16:35:10

Hello all,

Quick question, how can I can cite GBrowse2?

VBox Gbrowse instance not reaching to the alignment files through a shared folder

Vipin TS — 2013-04-16T22:35:51

Hello dev-team,

I am working on displaying BAM files through a virtual image instance of
Gbrowse, I have shared the host path with BAM files and configured the BAM
files are symlinked to the Gbrowse htdocs directory. Now I tried to access
my alignment tracks and it is not showing up. the apache log says that

mod_fcgid: stderr: Could not open database:
/opt/gbrowse/htdocs/htseq/BT.bam does not exist at

I have checked, the symlinked file in the above folder which can be
accessed by root user

Any idea how can I fix the issue?

thanks,
--/Vipin
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analytics on semi-structured data. The platform includes APIs for building
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Need help regarding Gbrowse...

vindhya vatsyayan — 2013-04-15T05:53:55

Hi,

I have been trying to install Gbrowse2 in Ubuntu 11.04 but Gbrowse folders are not being created on my system. I have tried both manually and through sourceforge direct installation. Please help.

Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences Bioinformatics Infrastructure FacilityJamia Millia Islamia (Central University)       ------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse