ThankGod Ebenezer | 30 Apr 21:32 2015
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GMOD Summer School 2015

Dear Scott,

I'm emailing to know if the GMOD Summer School will hold this year, and perhaps when applications will open for 2015? 

Regards,
ThankGod
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Scott Cain | 22 Apr 15:59 2015
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Re: gbrowse details

Hello,

Please give us *much* more information.  Where there any errors during loading? Are there any errors in the apache error log?  Does the rest of the GBrowse page load normally and you just don't get details tracks, or is it something else?

Scott


On Tue, Apr 21, 2015 at 10:07 PM, 黎志 <18987161688-9Onoh4P/yGk@public.gmane.org> wrote:
Hi:
    I use bp_seqfeature_load.pl to import gff3 files to mysql。Details parts  donn't display.


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Scott Cain | 22 Apr 15:51 2015
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Re: gbrowse error

Hi Ita,

Please keep the GBrowse mailing list cc'ed so other people can see and help.

The message about permission denied on /var/lib/gbrowse2/sessions/cgisess.db.lck is definitely a problem.  Check the ownership on the /var/lib/gbrowse2 directory and subdirectories.  It should be owned by the same owner that runs apache, which varies from system to system.  If you're using Ubuntu, I believe the owner should be www-data.  If you find that the sessions directory (or the other directories in the gbrowse2 directory) are not owned by www-data, do this:

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

If you're not using Ubuntu, please change the "www-data" parts to the appropriate owner's name.

Scott


On Wed, Apr 22, 2015 at 5:39 AM, Iti Gupta <iti.gupta-zSXK7qcHZLM@public.gmane.org> wrote:
Hey scott,
i do checked my javascript it was enabled and regarding the error log the errors are as follows: 

[root <at> localhost httpd]# tail error_log

[Tue Apr 21 22:44:21 2015] [error] [client ::1] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin)

[Tue Apr 21 22:44:21 2015] [error] [client ::1] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/local/share/perl5/CGI/Session/Driver/db_file.pm line 98.

[Tue Apr 21 22:44:22 2015] [error] [client ::1] CGI::param called in list context from package Bio::Graphics::Browser2::Render line 69, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/local/share/perl5/CGI.pm line 408., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2845., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2901., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/

[Tue Apr 21 22:44:22 2015] [error] [client ::1] Premature end of script headers: gbrowse, referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/


regards,

Iti gupta


On Tue, Apr 21, 2015 at 9:17 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hello Iti,

Please make sure that javascript is turned on, as that is what you'd see if it's not.  Also, can you please check the apache error log for messages?  If something is going wrong during the creation of that image, you'd see the message there.

Scott


On Tue, Apr 21, 2015 at 7:22 AM, Iti Gupta <iti.gupta-zSXK7qcHZLM@public.gmane.org> wrote:
Dear sir/mam,
I am having an error while following one of your tutorial: Generic Genome Browser Version 2: A Tutorial for Administrators.
In this i am able to see the genomic browser but not able to see the blue tracks of genes in my browser.
Have checked all the path and other related issues as mention in your tutorial.
Kindly help me to fix the issue.
I have attached a ppt containing screen shot of my browser.
Please find the attachment.

Thanks and Regards,
Iti Gupta


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Iti Gupta | 21 Apr 13:22 2015
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gbrowse error

Dear sir/mam,
I am having an error while following one of your tutorial: Generic Genome Browser Version 2: A Tutorial for Administrators.
In this i am able to see the genomic browser but not able to see the blue tracks of genes in my browser.
Have checked all the path and other related issues as mention in your tutorial.
Kindly help me to fix the issue.
I have attached a ppt containing screen shot of my browser.
Please find the attachment.

Thanks and Regards,
Iti Gupta

Attachment (New Microsoft Office PowerPoint Presentation.pptx): application/vnd.openxmlformats-officedocument.presentationml.presentation, 315 KiB
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Help with protein sequence of a CDS in gene details

Hello all:

I'm trying to display translation features of a CDS on the gene details page.

My GFF3 file was generated from a gbk file via bp_genbank2gff3.pl script, and looks like this:

CP000560    GenBank    CDS    412    1752    .    +    1    ID=RBAM_000010;Dbxref=GI:154350370;Name=dnaA;Note=COG0593%3B chromosomal replication initiatior protein;codon_start=1;locus_tag=RBAM_000010;product=DnaA;protein_id=ABS72449.1;transl_table=11;translation=length.446
CP000560    GenBank    gene    412    1752    .    +    1    ID=RBAM_000010.gene;Alias=RBAM_000010;Name=dnaA;locus_tag=RBAM_000010
CP000560    GenBank    CDS    1937    3073    .    +    1    ID=RBAM_000020;Dbxref=GI:154350371;eC_number=2.7.7.7;Name=dnaN;Note=smart00480%3B DNA polymerase III (beta subunit);codon_start=1;locus_tag=RBAM_000020;product=DnaN;protein_id=ABS72450.1;transl_table=11;translation=length.378

I have fasta protein sequences at the end of the file. They are named matching with the feature ID, like this:

>RBAM_000010
MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTITAPNEFARDW...
>RBAM_000020
MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDEGVSFTGSDSDISI...
>RBAM_000030
MANPISIDTEMITLGQFLKLADVIQSGGMAKWFLSEHEVTVNNEPDNRRGRKL...

In the gene details page I'm getting the "length.#" string instead of the protein sequence. What should I do in my config file in order to get the proper translation in the gene details page?

I really appreciate any help you can provide me.

Sincerely,
Nicolas
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Stephen Montgomery | 14 Apr 00:20 2015
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Error pulling Splice junction information from D. melanogaster browser

Hi –

We had a mysql/Perl DBI error which said “rendering error: Can’t call method “Prepared_cached” on unblessed reference. When trying to view splice junction information (for any track)

Seen below in the picture for your convenience.

Any help would be appreciated! Thanks.

All the best,
Stephen

 

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Thomas LETELLIER | 13 Apr 18:04 2015
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tracks displayed at wrong positions

Hi everyone,

I succesfully loaded a GFF3 file in a BioDBGFF database but I get some 
issues on GBrowse interface:

My GFF3 file contains contig, BAC and markers. When I search for a 
contig with the QuickSearch all is fine, I see the contig, BAC and marker.
But when I search for my marker in the quicksearch, these positions 
change and GBrowse displays the wrong area.

For example my marker is localized at position 368 641 and GBrowse 
changes it to 434 176 when I click on the "search" button.

Here are the GFF3 lines:

ctg2762 assembly        contig  65536   671744  .       . .       
Sequence "ctg2762"; Name "ctg2762"
ctg2762 FPC     BAC     65537   671745  .       .       .       BAC 
"146DhC741H22"; Name "146DhC741H22"; Marker_hit "AT6D5365 0 0"; 
Contig_hit "2762"
ctg2762 FPC     marker  368641  368641  .       .       . marker 
"AT6D5365"; Name "AT6D5365"; Contig_hit "ctg2762 - 1" (146DhC741H22)

I checked into the database and my marker positions seem good, it's weird.

Best regards,

Thomas

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Jeevan Karloss Antony Samy | 9 Apr 21:01 2015
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Passing More Values through "Link" in conf file

Hello, 

I want to pass more values through “link” option in “/etc/gbrowse/Test.conf” file.

I have uploaded GFF3 file with Alias for all the gene tracks into MySQL database. 

I couldn’t find a way to pass Alias values along with $ref, $start,$end,$name to another page when a track
is clicked.

Could someone suggest how to do that?

Thanks,
Jeevan
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starsyi | 29 Mar 15:19 2015

DNA/GC Content and 6-frame translation

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5713172/QQ%E6%88%AA%E5%9B%BE20150329211059.jpg> 

I configure my GBrowse as tutorial, but It display nothing in the part of
DNA and 3-frame translations. but other features is display normal. I have
examined many times, had't found any problem and errors.
no errors and other information to prompt me.

my GBrowse version is 2.55

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Scott Cain | 6 Apr 17:48 2015
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Re: security issues with app

Hi Ian,

GBrowse 1.70 is very old and development was stopped on it quite some time ago.  We've addressed several security issues in GBrowse2, the most current version of which is 2.54.

Scott


On Mon, Apr 6, 2015 at 10:40 AM, Ian Miller <ianm-t4+EzPmVLfD2fBVCVOL8/A@public.gmane.org> wrote:
Hi support,
Are security team has just notified us that the current version we are running has a 
Many security issues.  Here is the email we received today. 


The BSD Information Security Office performed web application vulnerability scans on publicly accessible web applications.
We have detected four (86) potential Cross Site Scripting (XSS) vulnerabilities on agdp.uchicago.edu

Do you have a fix for these in the latest version?
We are running 
Generic genome browser version 1.70

Ian Miller
Research Systems Administrator
773-702-5135
Ecology & Evolution
Organismal Biology and Anatomy
University of Chicago 




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Nathan Weeks | 3 Apr 19:03 2015

Re: Balloon click function

Hi Vaneet,

The issue may be that GBrowse configuration files are in the
Bio::Graphics::FeatureFile format, which needs one or more spaces in
the first column to continue the "value" (in this case, callback
definition) on multiple lines. See:

http://search.cpan.org/dist/Bio-Graphics-2.39/lib/Bio/Graphics/FeatureFile.pm#Formatting_Entries

You would need to indent the closing brace, as well as any code that
appears within:

balloon click = sub{
    }

Regards,

--
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/

> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 23 Mar 2015 22:54:00 +0000
> From: Vaneet Lotay <vaneet.lotay@...>
> Subject: [Gmod-gbrowse] Balloon click function
> To: gmod-gbrowse <gmod-gbrowse@...>
> Message-ID:
>         <DC7B0481E83B9041B5338B1BFE4498456FDF15@...>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello,
>
> I'm trying to add some links via tool tip for several tracks or as it's called normally in the code the
"balloon click" function.  These tracks are bigwig tracks.  For some reason simply trying to add that code
to the respective configuration files causes the whole genome browser page not to be displayed, returns
an "Internal Server error" page instead which I've seen before sometimes when some code cannot process
properly from the .conf file.
>
> Even when I add an empty function with no code like this it doesn't work:
>
> balloon click = sub{
> }
>
> This function and the same code that I'm trying to paste has worked for other types of tracks like gene model
tracks, so I'm just wondering whether the Bigwig tracks simply don't accept 'balloon click' as a function
or not?  Is it not possible to add balloons or tool tips to bigwig tracks, if so how is it properly done?
>
> Thanks,
>
> Vaneet
>
>
> Vaneet Lotay
>
> Xenbase Bioinformatician
>
> 724 ICT Building - University of Calgary
>
> 2500 University Drive NW
>
> Calgary AB T2N 1N4
>
> CANADA
>
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