Scott Cain | 14 Jul 20:46 2016
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Re: Regarding GBrowse installation

Hi Vijay,

Please reply all so the GBrowse mailing list will be included.

Have you tried looking for gbrowse in synaptic?  I haven't used it, but with apt-get on the command line you should be able to find it.  I would NOT suggest installing GBrowse via synaptic, since the version would be very old, but I imagine there is a way to install all of the prerequisites without installing GBrowse itself.  If you want to use the command line, I describe how I install on ubuntu with apt-get here:


Scott




On Thu, Jul 14, 2016 at 8:50 AM, Vijay Bhasker <uday4vijay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi Scott 

I have installed apache2,perl5 , libgd2 , and MySQL server from synaptic . Is there a different way I can install all the prerequisites and after installing the prerequisites which is the best way to install Gbrowse.

Regards
Vijaya Bhasker 



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Scott Cain | 11 Jul 19:51 2016
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Re: Regarding GBrowse installation

Hi Vijay,

I'm cc'ing the GBrowse mailing list so responses can be archived and other people can provide assistance too.

If when you're installing you get errors, it's not too surprising that you get 500 errors after the installation.  When happened when you installed prerequisites via Synaptic, because I know that there are apt packages for bioperl and biogaphics (and, I think pretty much every GBrowse prereq).  I think you should probably start with trying to solve that.

Scott


On Mon, Jul 11, 2016 at 1:42 PM, Vijay Bhasker <uday4vijay-Re5JQEeQqe8@public.gmane.orgm> wrote:
Hi Scott

I am pretty new to GBrowse and my instructor asked me to work on it.I have installed GBrowse using github in Ubuntu and ran perl script "Build.PL" which suggested me to run 1. ./Build test 2. ./Build demo 3. ./Build install. While running the perl script it gives me the errors, Bio::Graphics is not installed and Bio::Root::version is not installed. Also, when I try to open the example databases I come across the 500 internal server error. Could you please help me out how to install Gbrowse and what are the prerequisities to be installed and how to do them because I have installed all the prerequisities in Ubuntu using Synaptic package manager but I guess some of them were missing.So can I have a detailed description of how to follow the installation. Thanks in advance.

Regards
Vijaya Bhasker.

On Sun, Jul 10, 2016 at 10:19 PM, Scott Cain <scott <at> scottcain.net> wrote:
Hi Vijay,

How wedded are you to GBrowse? It is getting a little old; if you can use it, I'd suggest JBrowse instead. If not, please send  an email to the GBrowse mailing list with a more thorough description of the problem with excerpts of your Apache log files that might shed light on what's going on.

Scott


Sent from my iPhone

> On Jul 10, 2016, at 8:02 PM, Vijay Bhasker <uday4vijay-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
>
> Hi Scott
>
> I am a graduate student from Delaware State University and my majors is in bioinformatics and my research project is installing and adding genome sequence in the GBrowse. I face a lot of errors while going across the tutorial. In the tutorial after adding the features for DNA and 6-frames translation tracks, I am not able to view anything in those tracks. Later when I tried installing it again it shows me other errors which I haven't come across while installing earlier. So, please can you let me know what the error is. Thanks in advance.
>
> Regards
> Vijaya Bhasker.




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Barris, Wes | 20 Jun 23:02 2016

Message in GBrowse error log: Can't store GLOB items at ...

I have just installed GBrowse 2.54 (Bio::Graphics 2.39) on a new CentOS 7.2 system.  Although the software appears to be working properly, I am seeing many messages in the error_log of the following form:

 

Can't store GLOB items at /usr/lib64/perl5/vendor_perl/Storable.pm line 258, at /usr/local/share/perl5/Bio/Graphics/FeatureFile.pm line 445.

Use of uninitialized value in numeric ge (>=) at /usr/local/www/gbrowse2/share/lib/perl5/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 769.

Use of uninitialized value in numeric ge (>=) at /usr/local/www/gbrowse2/share/lib/perl5/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 769.

 

I’ve spent a lot of time searching the web but have not found a resolution.  Can anyone help me troubleshoot this?

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Scott Cain | 10 Jun 22:12 2016
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Re: Assist in GMOD

Hi Ahmad,

I'm guessing that since you sent me another email with a question after this one that the database connectivity problems have been solved, yes?

Scott


On Sat, Jun 4, 2016 at 11:40 AM, Seyed Ahmad Mousavi <ahmad.moousavi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Dr. Cain,

Thanks for helping me .

I could not solve the image render  problem, I remove fedora 23 and install it again but nothing has changed,
GMOD does not show any grid and could not render images.

When I want to run new human chr 2 and 22 project I saw following errors, I don't know why?

-------------------- EXCEPTION -------------------- MSG: Access denied for user 'apache' <at> 'localhost' (using password: NO) STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:217 STACK Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:388 STACK (eval) /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44 STACK Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44 STACK Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:997 STACK Bio::Graphics::Browser2::Render::region /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1110 STACK Bio::Graphics::Browser2::Render::segment /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1191 STACK Bio::Graphics::Browser2::Render::_update_state /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1926 STACK Bio::Graphics::Browser2::Render::update_state /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1916 STACK Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:290 STACK toplevel /var/www/cgi-bin/gb2/gbrowse:50 -------------------------------------------


I searched and changed number of issues but It seems there is no escape from them.

How can I fix these problems?


Kind regards,
Ahmad

On Wed, May 25, 2016 at 10:20 AM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Sayed,

This problem sounds very similar to another just posted to the mailing list (for which there is not a resolution yet but there are suggestions):


Also, people have had issues with newer versions of apache (2.4) discussed here:


Scott


On Wed, May 25, 2016 at 10:09 AM, Seyed Ahmad Mousavi <ahmad.moousavi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi

I've installed gbrowse 2.54 on Fedora 23, but during working with human sample chr 22 and chr2 the GBrowse does not show rulers and grids. You could see my page I got from screen.

How can I fix the problem?


Kind regards,
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Scott Cain | 10 Jun 22:10 2016
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Re: GMOD gives : "not found" error

Hi Seyed,

Please always cc the gbrowse mailing list (as I've done here).

The GBrowse "not found" message is usually the result of a problem with the GFF, and that problem is usually not having defined the reference sequence in the GFF.  In your example, you're looking for a reference sequence called chr20.  Is there a line in your GFF that looks something like:

chr20  .   chromosome   1    1243456788   .   .   .   Name=chr20

where the big number is the length of the feature?  The important bit is that the Name attribute match the name in the first column.

Scott


On Tue, Jun 7, 2016 at 7:24 AM, Seyed Ahmad Mousavi <ahmad.moousavi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Dr. Cain,

I've install last version of GMOD in Ubuntu 16.04 , it works nicely for sample and template but when I wanted to run GMOD on Chr2 and Chr20 (using Mysql) based on following tutorial :

http://gmod.org/wiki/GBrowse_NGS_Tutorial#Displaying_Human_Data_in_GBrowse

Inserting fasta and gff file by bp_seqfeature_load.pl tool has done correctly.
I gave all privilages to www-data in mysql and in human.conf I changed :

[annotations:database]
db_adaptor     = Bio::DB::SeqFeature::Store
db_args        = -adaptor DBI::mysql
                 -dsn human
          -user www-data
                 -pass pass1


But I got "Not found" red error at the top of the page, I could not found any thing in apache2 error_log.
You can see error page of GMOD at browser  below image.

How can I fix this problem?


Kind regards,
Ahmad



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Scott Cain | 25 May 16:21 2016
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Re: GBrowse2 tracks not rendering correctly

Hi Kate,

This sounds similar to what's discussed here:


Scott


On Tue, May 24, 2016 at 5:35 PM, kate coyle <kpcoyle-e4nNhFGpWWo@public.gmane.org> wrote:
Hi Scott,

Thanks for the prompt reply!

Here's my apache error log. I restarted apache earlier today for something unrelated to this. The last few errors are from while I was doing the tutorial--I think there's a typo that directs users to http://localhost/cgi-bin/gbrowse2/gbrowse/volvox when it should be directing to http://localhost/cgi-bin/gb2/gbrowse/volvox. I don't see anything here that would indicate where it's getting hung up...

[Mon May 23 07:51:25.504076 2016] [mpm_prefork:notice] [pid 32466] AH00163: Apache/2.4.7 (Ubuntu) mod_fcgid/2.3.9 PHP/5.5.9-1ubuntu4.16 mod_perl/2.0.8 Perl/v5.18.2 configured -- resuming normal operations
[Mon May 23 07:51:25.504096 2016] [core:notice] [pid 32466] AH00094: Command line: '/usr/sbin/apache2'
[Tue May 24 14:30:23.379923 2016] [mpm_prefork:notice] [pid 32466] AH00173: SIGHUP received.  Attempting to restart
[Tue May 24 14:30:23.658590 2016] [mpm_prefork:notice] [pid 32466] AH00163: Apache/2.4.7 (Ubuntu) mod_fcgid/2.3.9 PHP/5.5.9-1ubuntu4.16 mod_perl/2.0.8 Perl/v5.18.2 configured -- resuming normal operations
[Tue May 24 14:30:23.658607 2016] [core:notice] [pid 32466] AH00094: Command line: '/usr/sbin/apache2'
[Tue May 24 14:39:38.937569 2016] [cgi:error] [pid 3284] [client 127.0.0.1:54828] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse2
[Tue May 24 14:39:54.511123 2016] [cgi:error] [pid 3291] [client 127.0.0.1:54829] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse2
[Tue May 24 14:52:57.657444 2016] [cgi:error] [pid 3291] [client 127.0.0.1:54852] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse2

Configuration files are attached.

I was poking around in chrome and "Inspecting" the running site, and it looks like it's pulling images from gbrowse2/i/volvox, which is in /var/www/html. I can see the png files in that folder. 
I also noticed that the features in the Example Features track are still there and clickable (the info bubble even pops up when I hover over them). It's just not rendering the image itself.

Thanks!

On Tue, May 24, 2016 at 4:42 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Kate,

I would say that GBrowse/apache can't find where the images are, or they aren't being created.  Please take a look at the apache error log (probably /var/log/apache2/error_log) and go to the bottom of it and look for 404 errors that would indicate that it can't find the images, and then you/we will need to sort out why they aren't getting created there.  When you reply, you can included the last several lines of your apache error log and the configuration files you're using (GBrowse.conf and volvox.conf) so we can take a look at those too.

Scott


On Tue, May 24, 2016 at 3:19 PM, kate coyle <kpcoyle-e4nNhFGpWWo@public.gmane.org> wrote:
Hello,

I'm trying to set up GBrowse2 on my computer. I was working through the Tutorial for Administrators, but have run into an issue I can't seem to solve. The tracks aren't rendering properly--see attached. 

I've gone through all the suggested steps to ensure that all the necessary files are universally accessible. There are no new entries in my apache error log file. I've also accessed the web server from another computer (a Windows machine) to check if it was an issue with graphics on my ubuntu server, but the tracks look the same. 

Do you have any suggestions as to how to proceed or what might be going wrong?

Thanks!

Kate Coyle


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Program in Genetics
North Carolina State University

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--
Kaitlin Coyle
PhD Candidate
Roberts Lab
Program in Genetics
North Carolina State University

kpcoyle-e4nNhFGpWWo@public.gmane.org



--
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Ontario Institute for Cancer Research
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Seyed Ahmad Mousavi | 25 May 16:09 2016
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Assist in GMOD

Hi

I've installed gbrowse 2.54 on Fedora 23, but during working with human sample chr 22 and chr2 the GBrowse does not show rulers and grids. You could see my page I got from screen.

How can I fix the problem?


Kind regards,
--
Ahmad Mousavi
Royan Institute,
Tehran, Iran
------------------------------------------------------------------------------
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Scott Cain | 24 May 22:42 2016
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Re: GBrowse2 tracks not rendering correctly

Hi Kate,

I would say that GBrowse/apache can't find where the images are, or they aren't being created.  Please take a look at the apache error log (probably /var/log/apache2/error_log) and go to the bottom of it and look for 404 errors that would indicate that it can't find the images, and then you/we will need to sort out why they aren't getting created there.  When you reply, you can included the last several lines of your apache error log and the configuration files you're using (GBrowse.conf and volvox.conf) so we can take a look at those too.

Scott


On Tue, May 24, 2016 at 3:19 PM, kate coyle <kpcoyle-e4nNhFGpWWo@public.gmane.org> wrote:
Hello,

I'm trying to set up GBrowse2 on my computer. I was working through the Tutorial for Administrators, but have run into an issue I can't seem to solve. The tracks aren't rendering properly--see attached. 

I've gone through all the suggested steps to ensure that all the necessary files are universally accessible. There are no new entries in my apache error log file. I've also accessed the web server from another computer (a Windows machine) to check if it was an issue with graphics on my ubuntu server, but the tracks look the same. 

Do you have any suggestions as to how to proceed or what might be going wrong?

Thanks!

Kate Coyle


--
Kaitlin Coyle
PhD Candidate
Roberts Lab
Program in Genetics
North Carolina State University

kpcoyle-e4nNhFGpWWo@public.gmane.org
(973) 270-3951

------------------------------------------------------------------------------
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restrictions. Mobile Device Manager Plus allows you to control only the
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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kate coyle | 24 May 21:19 2016
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GBrowse2 tracks not rendering correctly

Hello,

I'm trying to set up GBrowse2 on my computer. I was working through the Tutorial for Administrators, but have run into an issue I can't seem to solve. The tracks aren't rendering properly--see attached. 

I've gone through all the suggested steps to ensure that all the necessary files are universally accessible. There are no new entries in my apache error log file. I've also accessed the web server from another computer (a Windows machine) to check if it was an issue with graphics on my ubuntu server, but the tracks look the same. 

Do you have any suggestions as to how to proceed or what might be going wrong?

Thanks!

Kate Coyle


--
Kaitlin Coyle
PhD Candidate
Roberts Lab
Program in Genetics
North Carolina State University

kpcoyle-e4nNhFGpWWo@public.gmane.org
(973) 270-3951
------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
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Shi-Qi An (Staff | 19 Apr 13:20 2016
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Gbrowse error_log

Dear GBrowse support,

 

I have been trying to setup GBrowse, my localhost address is 134.36.66.185.

It seems like the GBrowse has been installed and I have been trying to go through the tutorial. Unfortunately, after tried a few things I still had no luck even go through the first basic step. I have attached the my error_log. Could you please help me with this?

 

Many thanks.

 

Kind regards,

 

Shi-qi


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Sofia Robb | 19 Apr 16:06 2016
Gravatar

require valid-user

Hello,

I would like to require that a specific track is only viewable from a specific IP range or from a valid user. The IP range works great. When I am not in the IP range, i would like the apache login box to pop up and ask for the user and pasword. I set up my .httpd.conf and passwords file, but i am not getting the box asking me to log in when i have a link that contains a region with this track to be displayed, and the snp track is not being displayed.

[snps]
restrict = Order deny,allow
                  deny from all
                  Allow from 172.16.[9-63]
                  require valid-user

How do I properly set up "require valid-user" ?

Thanks,
Sofia
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