Bérénice Benayoun | 29 Jul 04:43 2014
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lncRNA don't display correctly on GBrowse ?

Dear GBrowse developers,

I have been trying to display predicted lncRNA of my favorite species (a fish whose genome I am annotating). I am running Gbrowse out of an AWS machine using the public image as a starting point.

Everything is working well, except for lncRNAs: I can't get them to properly display the exon/intron structure (and the gene glyph doesn't look the same as for coding genes, through I configured everything identically save for the color). I attached a screen shot example...

I created a gff3 file derived from my Cufflinks results (I generated the gene, mRNA and exon features, similarly to my coding genes, but no CDS, since these are non-coding). I have loaded them using a SQLite backend.

Here is my invocation of the database in my conf file:

[lncRNA:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::SQLite
                -dsn     /opt/gbrowse/databases/NotFur/Nfur_lnc.sqlite
search options = default

Here is the track invocation:
[GenesNC]
database           = lncRNA
feature            = gene
glyph              = gene
#sub_part           = exon
height             = 15
bgcolor            = skyblue
connector_color    = midnightblue
decorate_introns   = 1
description        = 1
label              = 1
category           = Genes
key                = lncRNA genes
link               = AUTO

What am I doing wrong ? Is there any way to display non coding RNAs correctly ?

Thank you so much in advance for your help - I've spent hours on it without progress and this is driving me insane !!!

Best,

Berenice


--
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Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
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USA
Email: benayoun <at> stanford.edu
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Patricia Angelica Vera | 24 Jul 07:57 2014
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issues with eneric Genome Browser Version 2 tutorial for administrators

Dear GBrowse support staff,


I'm trying to work on the Genome Browser Version 2 tutorial and I'm having issues in the 1. "The Basics section", I can not visualize de data set on the web browser, when I type ctgA in the search box I got a "Not Found" message.

I tried the troubleshooting that is under and I can not find the yeast.conf file on my directory:


/var/www/gbrowse2/tutorial/conf_files


The other seems be ok, I would appreciate a hint to keep going through the tutorial,


Thank you for your time,

Patricia

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Scott Cain | 25 Jul 15:35 2014
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Re: help regarding invoking gbrowse

Hi Umay,

Please continue to cc the GBrowse mailing list (that is, please "reply-all").

When you installed gbrowse with apt-get, what command did you use?  Did you include the gbrowse-data package as well?  That's where you get the sample data. 

If you did include that package, is there anything in the apache error log that might indicate what the problem is?  The apache error log is probably in /var/log/apache2/error_log.

Scott



On Fri, Jul 25, 2014 at 1:36 AM, umay kulsum <kulsum.umay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Scott,

samplefile is actually the configuration file that i have created in etc/apache2/gbrowse....
if I go to

it gives: The requested URL /cgi-bin/gbrowse/gbrowse/yeast was not found on this server.

I am trying to run gbrowse on my local database that I have created...

I have samplefile.conf in etc/apache2/gbrowse/samplefile.conf  but how do I put an entry for it in etc/gbrowse/GBrowse.conf??
I have attached the samlefile which  now I have named as 114635370.conf

if the yeast is also not showing result is it that GBrowse is not installed properly??

Regards

Umay Kulsum
PhD Student
AIIMS
New Delhi


On Fri, Jul 25, 2014 at 12:30 AM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Umay,

It's best to ask these questions on the GBrowse mailing list; I'm cc'ing it here.

I'm a little confused about what it is you're trying to do; are you trying to go to this url:


What is "samplefile"?  Did you create a configuration file for it in /etc/gbrowse2 and put an entry for it in /etc/gbrowse2/GBrowse.conf?  Also, my recollection about the debian packaged GBrowse is that the url you have to use is a little goofy, you might have to use this one instead:


If that doesn't work, what happens if you go to:


Scott



On Wed, Jul 23, 2014 at 2:52 AM, umay kulsum <kulsum.umay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
I have installed gbrowse in my system having ubuntu 14.04 using:

sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2

now I want to invoke gbrowse using the url /localhost/cgi-bin/gbrowse/samplefile but it displays The requested URL /localhost/cgi-bin/gbrowse/samplefile was not found on this server.

the conf file and gff3 file has been created successfully.

even the example file of yeast is not present in usr/lib/cgi-bin/gbrowse.

please help on how to invoke gbrowse.



Regards

Umay Kulsum
Ph.D student
AIIMS
New Delhi



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research




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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Scott Cain | 24 Jul 21:00 2014
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Re: help regarding invoking gbrowse

Hi Umay,

It's best to ask these questions on the GBrowse mailing list; I'm cc'ing it here.

I'm a little confused about what it is you're trying to do; are you trying to go to this url:


What is "samplefile"?  Did you create a configuration file for it in /etc/gbrowse2 and put an entry for it in /etc/gbrowse2/GBrowse.conf?  Also, my recollection about the debian packaged GBrowse is that the url you have to use is a little goofy, you might have to use this one instead:


If that doesn't work, what happens if you go to:


Scott



On Wed, Jul 23, 2014 at 2:52 AM, umay kulsum <kulsum.umay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
I have installed gbrowse in my system having ubuntu 14.04 using:

sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2

now I want to invoke gbrowse using the url /localhost/cgi-bin/gbrowse/samplefile but it displays The requested URL /localhost/cgi-bin/gbrowse/samplefile was not found on this server.

the conf file and gff3 file has been created successfully.

even the example file of yeast is not present in usr/lib/cgi-bin/gbrowse.

please help on how to invoke gbrowse.



Regards

Umay Kulsum
Ph.D student
AIIMS
New Delhi



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Problems in accessing to the gene broswer

Hi I'm Valoroso Maria Carmen from Stazione Zoologica of Naples. I have problem 
to access on genome broswer because when I enter my credentials, these are not 
recognized, although they were entered correctly. How can I fix the problem? 
Thank you for your attention. 

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Fields, Christopher J | 9 Jul 16:55 2014

Bio-Samtools question

Hi all,

I’ve started working on a side project that implements low-level bindings to htslib and it’s kin
(including samtools and bcftools).  Part of this is to specifically target and optimize higher-level
code (particularly bioperl bindings) w/o being reliant on having any of those bindings directly installed.

However, I found that recent changes in samtools by Sanger appear to require a pre-compiled shared libhts
as well as libbam.  What I am thinking of doing is basically rewriting these to target specific versions of
hts/samtools/bcftools, possibly bundling them together in downstream distributions (they’re
really not large, particularly when compared to the current size of bioperl).  This can be done pretty
easily via submodules; to see a stub example:

    https://github.com/HPCBio/HTSSam-XS

I think It also may be easier to not have these be part of the GBrowse-Adaptors code base, but be a separate
‘fork’ of the code.  e.g. I could fork the current code, remove non-samtools stuff, strip out the
Bio-specific bindings (shouldn’t be hard), and then push up a new repo.  I could then add in support for
htslib, newer samtools, etc.

Does that seem reasonable?  Or would it be simpler to copy over relevant files and start from scratch in a repo
like the above?

chris
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Asma Riyaz | 7 Jul 20:04 2014
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Configure gbrowse_apache2.conf

Hi,

I am trying to set up GBrowse's apache configuration:

Here is the gbrowse_apache2.conf file:

Alias        "/gbrowse2/i/" "/var/cache/gbrowse/images/"
Alias        "/gbrowse2"    "/usr/share/gbrowse/htdocs"
ScriptAlias  "/gb2/gbrowse/"      "/usr/lib/cgi-bin/gb2/gbrowse"

<Directory "/usr/share/gbrowse/htdocs">
  AllowOverride Options
  Options -Indexes -MultiViews +FollowSymLinks
  Require all granted
</Directory>

<Directory "/usr/share/gbrowse/htdocs/tutorial">
  Options +Indexes
</Directory>

<Directory "/var/cache/gbrowse/images/">
  Require all granted
</Directory>

<Directory "/var/lib/gbrowse/databases">
  Require all granted
</Directory>

<Directory "/usr/lib/cgi-bin/gb2/gbrowse">

  Options ExecCGI
  SetEnv GBROWSE_CONF   "/etc/gbrowse2"
</Directory>

<IfModule mod_fcgid.c>
  Alias /fgb2 "/usr/lib/cgi-bin/gb2/gbrowse"
  <Location /fgb2>
    SetHandler   fcgid-script
  </Location>
  FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
  # these directives prevent idle/busy timeouts and may need to be
  # adjusted up or down
  FcgidMinProcessesPerClass 6
  FcgidIOTimeout   600
  FcgidBusyTimeout 600

</IfModule>

<IfModule mod_fastcgi.c>
  Alias /fgb2 "/usr/lib/cgi-bin/gb2/gbrowse"
  <Location /fgb2>
    SetHandler   fastcgi-script
  </Location>
  # Note: you may need to increase -idle-timeout if file uploads are timing out and returning server
  # errors.
  FastCgiConfig -idle-timeout 600 -maxClassProcesses 20  -initial-env GBROWSE_CONF=/etc/gbrowse2
</IfModule>
<IfModule mod_perl.c>
   Alias /mgb2 "/usr/lib/cgi-bin/gb2/gbrowse"

<IfModule mod_perl.c>
<Location /mgb2>
     SetHandler perl-script
     PerlResponseHandler ModPerl::Registry
     PerlOptions +ParseHeaders
   </Location>
</IfModule>


My iframe is set in this way:
<iframe src="/gb2/gbrowse/{% if organismId %}organismId{{ organismId }}{% endif %}{% if uniquename %}?uniquename={{ uniquename }}{% else %}{% if name %}?name={{ name }}{% endif %}{% endif %}" style="border: none; margin: 0 auto;" width="100%" height="100%"></iframe>

All this ends up displaying the gbrowse script under gb2 itself rather that the browser itself, any inputs to change this?

Thanks
Asma







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Hyunmin Kim | 1 Jul 06:01 2014
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Displaying Peptide sequence in gene Details page

Dear, all

I wonder how can I display the peptide sequence and amino acid sequence in detail page (click the one gene in
track and we can view the detail page.)

I tried to modify the cgi-bin/gbrowse_details, but I can’t proper modify it.

please consider to this.

Thanks,
Hyunmin

p.s I viewed http://gmod.org/wiki/GBrowse_2.0_HOWTO#Controlling_the_gbrowse_details_page. but I
can’t understand it exactly. no changed detail page.
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曲俊杰 | 30 Jun 09:20 2014
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question for GBrowse

Dear GBrowse author:

Sorry to trouble you. I met a problem when install GBrowse.
I point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box.But the result page is not as the turiual.
The log is attached.

hope you can help me. Thank you very much in advace.

Junjie Qu
Attachment (httpd.zip): application/zip, 21 KiB
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aum1816 | 23 Jun 19:34 2014
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Gbrowse help.

Dear all
I trying the Gbrowse tutorial and I follow all the instructions but when
I try to go at:
http://localhost/cgi-bin/gb2/gbrowse/volvox
I receive the following message

Internal Server 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.


________________________________________________________________________
Apache/2.2.14 (Ubuntu) Server at localhost Port 80

I check the error file and I see the next message:

[Mon Jun 23 10:15:49 2014] [error] [client ::1] File does not
exist: /var/www/favicon.ico
[Mon Jun 23 10:15:49 2014] [error] [client ::1] File does not
exist: /var/www/favicon.ico
[Mon Jun 23 10:22:58 2014] [notice] SIGUSR1 received.  Doing graceful
restart
apache2: Could not reliably determine the server's fully qualified
domain name, using 127.0.1.1 for ServerName
[Mon Jun 23 10:22:59 2014] [notice] Apache/2.2.14 (Ubuntu)
mod_fcgid/2.3.4 mod_perl/2.0.4 Perl/v5.10.1 configured -- resuming
normal operations
[Mon Jun 23 11:33:54 2014] [error] [client ::1] Can't locate
Bio/Graphics/Browser2.pm in <at> INC ( <at> INC contains:
lib /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /usr/lib/cgi-bin/gb2/gbrowse line 8., referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:33:54 2014] [error] [client ::1] BEGIN
failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.,
referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:33:54 2014] [error] [client ::1] Premature end of script
headers: gbrowse, referer:
http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:38:04 2014] [error] [client ::1] Can't locate
Bio/Graphics/Browser2.pm in <at> INC ( <at> INC contains:
lib /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /usr/lib/cgi-bin/gb2/gbrowse line 8., referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:38:04 2014] [error] [client ::1] BEGIN
failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.,
referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:38:04 2014] [error] [client ::1] Premature end of script
headers: gbrowse, referer:
http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:40:08 2014] [error] [client ::1] Can't locate
Bio/Graphics/Browser2.pm in <at> INC ( <at> INC contains:
lib /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /usr/lib/cgi-bin/gb2/gbrowse line 8., referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:40:08 2014] [error] [client ::1] BEGIN
failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.,
referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:40:08 2014] [error] [client ::1] Premature end of script
headers: gbrowse, referer:
http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:42:31 2014] [error] [client ::1] Can't locate
Bio/Graphics/Browser2.pm in <at> INC ( <at> INC contains:
lib /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /usr/lib/cgi-bin/gb2/gbrowse line 8., referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:42:31 2014] [error] [client ::1] BEGIN
failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.,
referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:42:31 2014] [error] [client ::1] Premature end of script
headers: gbrowse, referer:
http://localhost/gbrowse2/tutorial/tutorial.html
[Mon Jun 23 11:42:38 2014] [error] [client ::1] Can't locate
Bio/Graphics/Browser2.pm in <at> INC ( <at> INC contains:
lib /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /usr/lib/cgi-bin/gb2/gbrowse line 8.
[Mon Jun 23 11:42:38 2014] [error] [client ::1] BEGIN
failed--compilation aborted at /usr/lib/cgi-bin/gb2/gbrowse line 8.
[Mon Jun 23 11:42:38 2014] [error] [client ::1] Premature end of script
headers: gbrowse
[Mon Jun 23 11:42:47 2014] [error] [client ::1] attempt to invoke
directory as script: /usr/lib/cgi-bin/gb2/
[Mon Jun 23 11:42:59 2014] [error] [client ::1] attempt to invoke
directory as script: /usr/lib/cgi-bin/

Thanks in advance for your help.



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Mélanie Hachet | 5 Jun 14:56 2014
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Picon

configuration by default "packing" (auto, compact, expand, ...)

Hello,

I would like to know how to change the default "packing" value (auto, 
compact, expand, expand and label) with configuration file.
This modification is possible in "browser" tab cliking to "configure 
this track" icon.
I'm using Gbrowse 2.33.

If you need any further information, feel free to contact me.

Best regards.

Mélanie Hachet

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