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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Roberts Lab
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North Carolina State University

kpcoyle-e4nNhFGpWWo@public.gmane.org



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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,
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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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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
------------------------------------------------------------------------------
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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


The University of Dundee is a registered Scottish Charity, No: SC015096
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Sofia Robb | 19 Apr 16:06 2016
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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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Tevfik Hamdi Kitapci | 1 Apr 01:17 2016
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gbrowse problem

Hi,
I installed gbrowse following this:


I can see the main page when I point my browser to


I am trying to visualize the volvox data set as described here


I followed all the steps and double checked to make sure I did everything and set all the permissions when I point my browser to http://localhost/cgi-bin/gb2/gbrowse/volvox I got the following message:

I am running Ubuntu 14.04.4 LTS so I set the my_user_name to www-data 

Not Found

The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.

Apache/2.4.7 (Ubuntu) Server at localhost Port 80
I checked the error.log located at /var/log/apache2/error.log there is no message.
Then I tried to point my browser to: http://localhost/gb2/gbrowse/volvox this time I am getting the following:

Forbidden

You don't have permission to access /gb2/gbrowse/volvox on this server.

Apache/2.4.7 (Ubuntu) Server at localhost Port 80
this time I have this message added to the /var/log/apache2/error.log file
[Thu Mar 31 16:14:44.349626 2016] [authz_core:error] [pid 12936:tid 140590595376896] [client 127.0.0.1:58597] AH01630: client denied by server configuration: /usr/lib/cgi-bin/gbrowse/gbrowse

I will appreciate if you can help me with this problem
Thanks a lotBest RegardsT. Hamdi Kitapci
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Thomas LETELLIER | 23 Mar 14:16 2016
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SVG & PNG export failed

Hello,

I have a trouble with images export with my GBrowse, I saw in the 
documentation that it was a known bug, but I did not find any solution 
to this problem...

When I click on the export I get an "Internal server error" with this 
stack :

> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Can't locate
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \t/home/gbrowse/webapps/GBrowse-2.33/etc/gbrowse2/plugins/GFFDumper.pm 
> in  <at> INC ( <at> INC contains: 
> /home/gbrowse/webapps/GBrowse-2.33/etc/gbrowse2/plugins 
> /usr/local/lib64/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 
> /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl 
> /usr/lib64/perl5 /usr/share/perl5 .) at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/PluginSet.pm line 31 (#1)
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] (F) You 
> said to do (or require, or use) a file that couldn't be
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] found. 
> Perl looks for the file in all the locations mentioned in  <at> INC,
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] unless the 
> file name included the full path to the file.  Perhaps you
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] need to 
> set the PERL5LIB or PERL5OPT environment variable to say where
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] the extra 
> library is, or maybe the script needs to add the library name
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]     to 
>  <at> INC.  Or maybe you just misspelled the name of the file.  See
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> perlfunc/require and lib.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Can't call 
> method "seq_id" on an undefined value at
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \t/usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 
> 1971 (#2)
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] (F) You 
> used the syntax of a method call, but the slot filled by the
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] object 
> reference or package name contains an undefined value. Something
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] like this 
> will reproduce the error:
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]         
> $BADREF = undef;
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]         
> process $BADREF 1,2,3;
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]         
> $BADREF->process(1,2,3);
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Uncaught 
> exception from user code:
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] \tCan't 
> call method "seq_id" on an undefined value at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 1971.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]  at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 1971.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
>
\tBio::Graphics::Browser2::RenderPanels::create_panel_args(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), 
> HASH(0x56fb120)) called at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 259
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
>
\tBio::Graphics::Browser2::RenderPanels::make_requests(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), 
> HASH(0x56fb120)) called at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 130
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
>
\tBio::Graphics::Browser2::RenderPanels::request_panels(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), 
> HASH(0x56fb120)) called at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 219
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
>
\tBio::Graphics::Browser2::RenderPanels::render_track_images(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), 
> HASH(0x56fb120)) called at 
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img 
> line 311
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \tGBrowse_img::render_tracks(GBrowse_img=HASH(0x4e32de0), 
> Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), "GD", 0, undef) 
> called at 
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img 
> line 217
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \tGBrowse_img::render_image(GBrowse_img=HASH(0x4e32de0)) called at 
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img 
> line 139
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \tGBrowse_img::run(GBrowse_img=HASH(0x4e32de0)) called at 
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img line 73
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Premature 
> end of script headers: gbrowse_img

My GBrowse version is 2.33 and I saw that GFFDumper.pm was deprecated 
since 2.0, so the error message does not helped me a lot...

Best regards,

Thomas

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Scott Cain | 2 Mar 17:32 2016
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Call for Abstracts for BOSC

Hi All,

I'm forwarding this call for abstracts for BOSC (Bioinformatics Open Source Conference) this year in Orlando, Florida:

From Peter Cock (p.j.a.cock at googlemail.com):

As BOSC co-chair I would like to encourage you all to think about
attending BOSC 2016, and if you are working on your own open
source software for bioinformatics please consider submitting an
abstract. See the email below and:

http://news.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/

Also, as a member of the Open Bioinformatics Foundation (OBF)
Board of Directors, I am delighted to let you know about the new
OBF Travel Fellowship which could be used to attend BOSC:

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

In case you missed the earlier announcement last year, we finally
got rid of the paper forms for OBF membership, see:

http://news.open-bio.org/2015/12/10/online-membership-form/

Thank you,

Peter

[Biopython developer, BOSC co-chair, OBF Secretary, etc.]


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王敏晓 | 24 Feb 13:42 2016
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unable to load fasta sequences

Hi! I’d llke to make our genome dataset visible by gbrowse2. I’m now following the tutorial guide to understand the processing steps of the configuration. Everything seems to be successful except the part on DNA and 3-frame translations. Nothing appeared on the corresponding track. The volvax directory have been made writable worldwide following the instruction.
Thanks in advance.
Yours Wang Minxiao
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Scott Cain | 1 Mar 16:37 2016
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GMOD in Google Summer of Code 2016

Hello,

Very good news!  GMOD (as part of the Open Genome Informatics group along with Reactome) has been accepted into Google Summer of Code this year.  If you are or know of a student that might like to participate, please take a look at


where there are several really interesting project ideas.  It is also possible for students to suggest their own ideas and we will try hard to find them a mentor. 

Please let me know if you have any questions about GSoC.

Scott

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Ontario Institute for Cancer Research
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