Invoking gbrowse

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Invoking gbrowse

navillusol
Hello, I am new to Gbrowse I have completed the tutorial and have now got my
own GFF3 file that I want to invoke. However I am at a loss as to how to do
this.

I have created a configuration file for it in /etc/gbrowse2 and put an entry
for it in /etc/gbrowse2/GBrowse.conf. But I do not know where to go from
there!?

I am sorry this is prob a very bad question but how do I proceed?

Thank you for your time



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Re: Invoking gbrowse

Scott Cain
Hello,

Can you give us some more information?  What have you tried, what isn't working, and is there anything in the apache error log that might indicate what the problem is?  Also, what os are you using?

Scott

Sent from my iPhone

> On Jul 30, 2014, at 6:09 PM, navillusol <[hidden email]> wrote:
>
> Hello, I am new to Gbrowse I have completed the tutorial and have now got my
> own GFF3 file that I want to invoke. However I am at a loss as to how to do
> this.
>
> I have created a configuration file for it in /etc/gbrowse2 and put an entry
> for it in /etc/gbrowse2/GBrowse.conf. But I do not know where to go from
> there!?
>
> I am sorry this is prob a very bad question but how do I proceed?
>
> Thank you for your time
>
>
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Invoking-gbrowse-tp5712665.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
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> Build a bridge from your legacy apps to the future.
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Re: Invoking gbrowse

navillusol
Hello Scott,
I point my browser to http://localhost/cgi-bin/gb2/gbrowse/N_div/ and it
displays the page but no glyphs, I have also noticed that in the Data Source
drop down menu the same issue occurs with the other databases.

My OS is Bio-Linux 12.04. I checked the log file and the following error was
generated;

GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Did not receive a reply. Possible causes include: the remote application did
not send a reply, the message bus security policy blocked the reply, the
reply timeout expired, or the network connection was broken.
GConf Error: No D-BUS daemon running

I assume this is a permission issue?



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Re: Invoking gbrowse

navillusol
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712673/14.png>



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Re: Invoking gbrowse

Scott Cain
In reply to this post by navillusol
Hello,

That warning doesn't have anything to do with GBrowse; in fact, I'm pretty sure that's not even an apache warning.  Are you sure you're looking in the correct log file?  I think biolinux is based on Ubuntu, so the apache error_log would be in /var/log/apache2/error_log.

The image you posted looks like what happens when the tmp image directory isn't configured correctly.  For ubuntu, a typical configuration for this would be:

tmp_base = /var/tmp/gbrowse2

and that would be be in the /etc/GBrowse.conf file. What directory is that configured for in your GBrowse.conf file, and what are the permissions on that directory?  For a quick way to see that, try doing this:

ls -ld /var/tmp/gbrowse2

and you can copy and paste that output.

Scott



On Mon, Aug 4, 2014 at 6:56 AM, navillusol <[hidden email]> wrote:
Hello Scott,
I point my browser to http://localhost/cgi-bin/gb2/gbrowse/N_div/ and it
displays the page but no glyphs, I have also noticed that in the Data Source
drop down menu the same issue occurs with the other databases.

My OS is Bio-Linux 12.04. I checked the log file and the following error was
generated;

GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Did not receive a reply. Possible causes include: the remote application did
not send a reply, the message bus security policy blocked the reply, the
reply timeout expired, or the network connection was broken.
GConf Error: No D-BUS daemon running

I assume this is a permission issue?



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Re: Invoking gbrowse

navillusol
Sure the output from your suggested command is as follows;

drwxr-xr-x 5 www-data www-data 4096 Jul 17 15:11 /var/tmp/gbrowse2



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Re: Invoking gbrowse

Scott Cain
OK, good, so the directory exists and has appropriate permissions.  Is that what directory is set for tmp_base in GBrowse.conf?  What about your apache error log?  Are there any 404/file not found messages in it?


On Mon, Aug 4, 2014 at 9:56 AM, navillusol <[hidden email]> wrote:
Sure the output from your suggested command is as follows;

drwxr-xr-x 5 www-data www-data 4096 Jul 17 15:11 /var/tmp/gbrowse2



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Re: Invoking gbrowse

Scott Cain
Hi Liam,

Would be reluctant to say anything definitely :-)

The fact that there are no errors in the apache log makes me think you're not looking in the right log file.  Apache can be configured to use more than one log file, so it's possible that the GBrowse logs are going elsewhere.  Did you install this instance of GBrowse or did it come with biolinux?

Also, is there an images directory in /var/tmp/gbrowse2, and is there anything in that directory?

Scott



On Mon, Aug 4, 2014 at 11:52 AM, Liam O'Sullivan <[hidden email]> wrote:
Yes that is the directory set for tmp_base in the .conf file, nope no errors regarding 404/file not found. So it definitely isn't a permission issue? 


On Mon, Aug 4, 2014 at 4:08 PM, Scott Cain <[hidden email]> wrote:
OK, good, so the directory exists and has appropriate permissions.  Is that what directory is set for tmp_base in GBrowse.conf?  What about your apache error log?  Are there any 404/file not found messages in it?


On Mon, Aug 4, 2014 at 9:56 AM, navillusol <[hidden email]> wrote:
Sure the output from your suggested command is as follows;

drwxr-xr-x 5 www-data www-data 4096 Jul 17 15:11 /var/tmp/gbrowse2



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Re: Invoking gbrowse

navillusol
Yup var/temp/Gbrowse2 contains an images folder with popdemo, yeast, yeast_advanced and volvox. I installed Gbrowse2 myself on this machine, but I do believe that the original GBrowse was already installed, would that have something to do with it perhaps?


The var/log/apache2 directory contains the following;

dan@dan-GPU[apache2] ls -l                                            [11:56AM]
total 364
-rw-r----- 1 root adm  90287 Aug  5 11:48 access.log
-rw-r----- 1 root adm  29261 Aug  4 11:50 access.log.1
-rw-r----- 1 root adm   1037 Jul 29 12:50 access.log.2.gz
-rw-r----- 1 root adm    737 Jul 21 12:49 access.log.3.gz
-rw-r----- 1 root adm   6174 Jul 18 10:46 access.log.4.gz
-rw-r----- 1 root adm    319 Feb  5 16:20 access.log.5.gz
-rw-r----- 1 root adm    185 Sep  6  2013 access.log.6.gz
-rw-r----- 1 root adm    372 Aug 23  2013 access.log.7.gz
-rw-r----- 1 root adm    515 Apr 25  2013 access.log.8.gz
-rw-r----- 1 root adm  34399 Aug  5 11:48 error.log
-rw-r----- 1 root adm  16543 Aug  4 11:59 error.log.1
-rw-r----- 1 root adm    222 Apr 10 14:38 error.log.10.gz
-rw-r----- 1 root adm    238 Mar 28 14:57 error.log.11.gz
-rw-r----- 1 root adm    302 Feb  5 16:28 error.log.12.gz
-rw-r----- 1 root adm    277 Jan 17  2014 error.log.13.gz
-rw-r----- 1 root adm    236 Dec  3  2013 error.log.14.gz
-rw-r----- 1 root adm    182 Nov  3  2013 error.log.15.gz
-rw-r----- 1 root adm    229 Nov  1  2013 error.log.16.gz
-rw-r----- 1 root adm    229 Oct 25  2013 error.log.17.gz
-rw-r----- 1 root adm    285 Oct  3  2013 error.log.18.gz
-rw-r----- 1 root adm    231 Sep  6  2013 error.log.19.gz
-rw-r----- 1 root adm    316 Aug 29  2013 error.log.20.gz
-rw-r----- 1 root adm    252 Aug 21  2013 error.log.21.gz
-rw-r----- 1 root adm    248 Aug 12  2013 error.log.22.gz
-rw-r----- 1 root adm    324 Aug  6  2013 error.log.23.gz
-rw-r----- 1 root adm    301 Jul 29  2013 error.log.24.gz
-rw-r----- 1 root adm    229 Jul 16  2013 error.log.25.gz
-rw-r----- 1 root adm    254 Jul  4  2013 error.log.26.gz
-rw-r----- 1 root adm    332 Jun 19  2013 error.log.27.gz
-rw-r----- 1 root adm    322 Jun 10  2013 error.log.28.gz
-rw-r----- 1 root adm    235 Jun  3  2013 error.log.29.gz
-rw-r----- 1 root adm    640 Jul 29 13:15 error.log.2.gz
-rw-r----- 1 root adm    268 May 26  2013 error.log.30.gz
-rw-r----- 1 root adm    229 May 21  2013 error.log.31.gz
-rw-r----- 1 root adm    254 May 15  2013 error.log.32.gz
-rw-r----- 1 root adm    271 May  7  2013 error.log.33.gz
-rw-r----- 1 root adm    415 Apr 29  2013 error.log.34.gz
-rw-r----- 1 root adm    245 Apr 22  2013 error.log.35.gz
-rw-r----- 1 root adm    442 Apr 16  2013 error.log.36.gz
-rw-r----- 1 root adm   1765 Jul 21 12:49 error.log.3.gz
-rw-r----- 1 root adm    234 Jul 15 12:16 error.log.4.gz
-rw-r----- 1 root adm    182 Jun 29 07:54 error.log.5.gz
-rw-r----- 1 root adm    227 Jun 25 10:56 error.log.6.gz
-rw-r----- 1 root adm    230 Jun  4 12:34 error.log.7.gz
-rw-r----- 1 root adm    223 May 28 11:58 error.log.8.gz
-rw-r----- 1 root adm    177 May 21 12:29 error.log.9.gz
-rw-r--r-- 1 root root     0 Apr 11  2013 other_vhosts_access.log





On Mon, Aug 4, 2014 at 7:41 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

Would be reluctant to say anything definitely :-)

The fact that there are no errors in the apache log makes me think you're not looking in the right log file.  Apache can be configured to use more than one log file, so it's possible that the GBrowse logs are going elsewhere.  Did you install this instance of GBrowse or did it come with biolinux?

Also, is there an images directory in /var/tmp/gbrowse2, and is there anything in that directory?

Scott



On Mon, Aug 4, 2014 at 11:52 AM, Liam O'Sullivan <[hidden email]> wrote:
Yes that is the directory set for tmp_base in the .conf file, nope no errors regarding 404/file not found. So it definitely isn't a permission issue? 


On Mon, Aug 4, 2014 at 4:08 PM, Scott Cain <[hidden email]> wrote:
OK, good, so the directory exists and has appropriate permissions.  Is that what directory is set for tmp_base in GBrowse.conf?  What about your apache error log?  Are there any 404/file not found messages in it?


On Mon, Aug 4, 2014 at 9:56 AM, navillusol <[hidden email]> wrote:
Sure the output from your suggested command is as follows;

drwxr-xr-x 5 www-data www-data 4096 Jul 17 15:11 /var/tmp/gbrowse2



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Re: Invoking gbrowse

navillusol
In reply to this post by Scott Cain
Apologies, when I did ~less error.log i get the following errors;

[Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist: /var/cache
/gbrowse/images, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/

[Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist: /var/cache/gbrowse/images, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/

[Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist: /var/cache/gbrowse/images, referer: http://localhost/cgi-bin/gb2/gbrowse/N_div/

but when I use gnome-open I get this error;

(gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken.
GConf Error: No D-BUS daemon running






On Tue, Aug 5, 2014 at 11:57 AM, Liam O'Sullivan <[hidden email]> wrote:
Yup var/temp/Gbrowse2 contains an images folder with popdemo, yeast, yeast_advanced and volvox. I installed Gbrowse2 myself on this machine, but I do believe that the original GBrowse was already installed, would that have something to do with it perhaps?


The var/log/apache2 directory contains the following;

dan@dan-GPU[apache2] ls -l                                            [11:56AM]
total 364
-rw-r----- 1 root adm  90287 Aug  5 11:48 access.log
-rw-r----- 1 root adm  29261 Aug  4 11:50 access.log.1
-rw-r----- 1 root adm   1037 Jul 29 12:50 access.log.2.gz
-rw-r----- 1 root adm    737 Jul 21 12:49 access.log.3.gz
-rw-r----- 1 root adm   6174 Jul 18 10:46 access.log.4.gz
-rw-r----- 1 root adm    319 Feb  5 16:20 access.log.5.gz
-rw-r----- 1 root adm    185 Sep  6  2013 access.log.6.gz
-rw-r----- 1 root adm    372 Aug 23  2013 access.log.7.gz
-rw-r----- 1 root adm    515 Apr 25  2013 access.log.8.gz
-rw-r----- 1 root adm  34399 Aug  5 11:48 error.log
-rw-r----- 1 root adm  16543 Aug  4 11:59 error.log.1
-rw-r----- 1 root adm    222 Apr 10 14:38 error.log.10.gz
-rw-r----- 1 root adm    238 Mar 28 14:57 error.log.11.gz
-rw-r----- 1 root adm    302 Feb  5 16:28 error.log.12.gz
-rw-r----- 1 root adm    277 Jan 17  2014 error.log.13.gz
-rw-r----- 1 root adm    236 Dec  3  2013 error.log.14.gz
-rw-r----- 1 root adm    182 Nov  3  2013 error.log.15.gz
-rw-r----- 1 root adm    229 Nov  1  2013 error.log.16.gz
-rw-r----- 1 root adm    229 Oct 25  2013 error.log.17.gz
-rw-r----- 1 root adm    285 Oct  3  2013 error.log.18.gz
-rw-r----- 1 root adm    231 Sep  6  2013 error.log.19.gz
-rw-r----- 1 root adm    316 Aug 29  2013 error.log.20.gz
-rw-r----- 1 root adm    252 Aug 21  2013 error.log.21.gz
-rw-r----- 1 root adm    248 Aug 12  2013 error.log.22.gz
-rw-r----- 1 root adm    324 Aug  6  2013 error.log.23.gz
-rw-r----- 1 root adm    301 Jul 29  2013 error.log.24.gz
-rw-r----- 1 root adm    229 Jul 16  2013 error.log.25.gz
-rw-r----- 1 root adm    254 Jul  4  2013 error.log.26.gz
-rw-r----- 1 root adm    332 Jun 19  2013 error.log.27.gz
-rw-r----- 1 root adm    322 Jun 10  2013 error.log.28.gz
-rw-r----- 1 root adm    235 Jun  3  2013 error.log.29.gz
-rw-r----- 1 root adm    640 Jul 29 13:15 error.log.2.gz
-rw-r----- 1 root adm    268 May 26  2013 error.log.30.gz
-rw-r----- 1 root adm    229 May 21  2013 error.log.31.gz
-rw-r----- 1 root adm    254 May 15  2013 error.log.32.gz
-rw-r----- 1 root adm    271 May  7  2013 error.log.33.gz
-rw-r----- 1 root adm    415 Apr 29  2013 error.log.34.gz
-rw-r----- 1 root adm    245 Apr 22  2013 error.log.35.gz
-rw-r----- 1 root adm    442 Apr 16  2013 error.log.36.gz
-rw-r----- 1 root adm   1765 Jul 21 12:49 error.log.3.gz
-rw-r----- 1 root adm    234 Jul 15 12:16 error.log.4.gz
-rw-r----- 1 root adm    182 Jun 29 07:54 error.log.5.gz
-rw-r----- 1 root adm    227 Jun 25 10:56 error.log.6.gz
-rw-r----- 1 root adm    230 Jun  4 12:34 error.log.7.gz
-rw-r----- 1 root adm    223 May 28 11:58 error.log.8.gz
-rw-r----- 1 root adm    177 May 21 12:29 error.log.9.gz
-rw-r--r-- 1 root root     0 Apr 11  2013 other_vhosts_access.log





On Mon, Aug 4, 2014 at 7:41 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

Would be reluctant to say anything definitely :-)

The fact that there are no errors in the apache log makes me think you're not looking in the right log file.  Apache can be configured to use more than one log file, so it's possible that the GBrowse logs are going elsewhere.  Did you install this instance of GBrowse or did it come with biolinux?

Also, is there an images directory in /var/tmp/gbrowse2, and is there anything in that directory?

Scott



On Mon, Aug 4, 2014 at 11:52 AM, Liam O'Sullivan <[hidden email]> wrote:
Yes that is the directory set for tmp_base in the .conf file, nope no errors regarding 404/file not found. So it definitely isn't a permission issue? 


On Mon, Aug 4, 2014 at 4:08 PM, Scott Cain <[hidden email]> wrote:
OK, good, so the directory exists and has appropriate permissions.  Is that what directory is set for tmp_base in GBrowse.conf?  What about your apache error log?  Are there any 404/file not found messages in it?


On Mon, Aug 4, 2014 at 9:56 AM, navillusol <[hidden email]> wrote:
Sure the output from your suggested command is as follows;

drwxr-xr-x 5 www-data www-data 4096 Jul 17 15:11 /var/tmp/gbrowse2



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Re: Invoking gbrowse

Raymond Wan

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running


I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.

For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Re: Invoking gbrowse

navillusol
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.

For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Re: Invoking gbrowse

Raymond Wan

Hi,


Quoting navillusol <[hidden email]>:

> Thanks Raymond, I found that post yesterday and made the relevant changes
> to no success. But I now know that the above issue is causing the problem.


You're welcome!  I don't use gnome-open, so maybe the reason why you're seeing
it differs from why I see it on occasion on my system...


> Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall
> Gbrowse2 and go from there?


My personal opinion is that there isn't a need to have both.  You might have
more problems later on...  The trick is to remove everything, though...I'm not
sure if everything resides in a single directory?

But, before you go and uninstall them, you might want to wait for a more
authoritive opinion than me!  :-)

Ray




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Re: Invoking gbrowse

Scott Cain
In reply to this post by navillusol
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.

For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Re: Invoking gbrowse

navillusol
Sure, the error in the apache log file seems to indicate to me that it is trying to use GBrowse vanilla rather than GBrowse 2 files. Also I should state that when I use http://localhost/cgi-bin/gbrowse2/gbrowse/volvox i get an error saying file not found, but when I use http://localhost/cgi-bin/gb2/gbrowse/volvox i get onto the page but without the glyphs (as above)

.Conf file is as follows,

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /var/tmp/gbrowse2
persistent_base        = /var/lib/gbrowse2
userdata_base          = /var/lib/gbrowse2/userdata
db_base                = /var/lib/gbrowse2/databases

# These paths are relative to the url base
buttons       = images/buttons
balloons      = images/balloons
openid        = images/openid
gbrowse_help  = .
js            = js

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# session settings
session lock type = default

# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver    = driver:file;serializer:default
#session args      = Directory /var/lib/gbrowse2/sessions

# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args   = FileName /var/lib/gbrowse2/sessions.db

# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.

# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.

# For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!

# for SQLite
#upload_db_adaptor = DBI::SQLite

# for Berkeleydb
#upload_db_adaptor = berkeleydb

# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host    = localhost
#upload_db_user    = www-data
#upload_db_pass    = foobar

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
slave_timeout          = 45
global_timeout         = 60
search_timeout         = 15
max_render_processes   = 4   # try double number of CPU/cores

# Renderfarm settings
#include renderfarm.conf

# Clean up settings (used by the gbrowse_clean script)
expire session  = 1M  # expire unused sessions after a month
expire cache    = 2h  # expire cached data if unmodified for >2 hours
expire uploads  = 6w  # expire uploaded data if unused for >6 weeks

# Appearance settings
truecolor     =  1   # better appearance at the expense of larger image files
# truetype    =  1   # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server.

# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.

#include "themes/warm_colors"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_colors"

balloon tips        = 1
titles are balloons = 1
plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid       = 0
region grid         = 0
detail grid         = 1
image widths        = 450 640 800 1024
default width       = 800
pad_left            = 60
pad_right           = 30
too many landmarks  = 100
track listing style = categories   # either "categories" or "facets"

# Loads more details image data than can fit on the screen.  This lets the user drag and drop the details
# tracks, without loading more data from the server.  A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3

# where to link to when user clicks in detailed view
link          = AUTO

# HTML to insert inside the <head></head> section
head =

# At the top of the HTML...
header =

# At the footer
footer = <hr />
         <p style="font-size:small">The Generic Genome Browser. For questions about the data
         at this site, please contact its webmaster. For support of the
         browser software <i>only</i>, send email to
         <a href="mailto:[hidden email]">[hidden email]</a>
         or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
         </p>

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =

# Limits on genomic regions (can be overridden in datasource config files)
region segment         = 200000
max segment            = 5000000
default segment        = 5000
zoom levels            = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 500000 1000000
region sizes           = 1000 5000 10000 20000
default region         = 5000
fine zoom              = 10%

# keyword search maxima
max keyword results    = 1000

###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate


####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts               = 1
user_accounts_registration  = 1
user_accounts_openid        = 1

# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.

user_account_db          = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For SQLite
# user_account_db        = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For MySQL
# user_account_db        = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse

# The number of public files to display
public_files       = 10

# What email gateway to use for outgoing registration confirmation messages.
# The full format is
#      <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
#    The port is assumed to be 25 unless ssl encryption is specified, in
#               which case it defaults to 465.
#    protocol is either "plain" or "ssl", "plain" assumed.
#    username and password may be required by the gateway for authentication
#
# here are some common options
# smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
# smtp_gateway         = smtp.oicr.on.ca                           # indicated machine will forward email for you
# smtp_gateway         = smtp.gmail.com:465:ssl:joe.user:secret    # use gmail with account "joe.user" and password "secret"
# smtp_gateway         = none                                      # disable outgoing email
smtp_gateway           = none  # disable outgoing email

# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name       = GBrowse
application_name_long  = The Generic Genome Browser
email_address          = [hidden email]

# name of the "superuser" who can add public tracks
admin_account          = admin
admin_dbs              = /var/lib/gbrowse2/databases/admin_uploads


######## DEFAULT DATASOURCE #########
default source = yeast

###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################

[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse

###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeast_advanced]
description   = Yeast chromosomes 1+2 (advanced)
path          = yeast_chr1+2.conf

[yeast_renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

[pop_demo]
description   = Population Display Demo
path          = pop_demo.conf

[volvox]
description  = Tutorial database
path         = volvox.conf

[N_div]
description  = N_div database
path         = N_div.conf


On Tue, Aug 5, 2014 at 2:08 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.

For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Re: Invoking gbrowse

Scott Cain
Hi Liam,

I'm not interested in the GBrowse.conf file, since it seems to be working (yeast and tutorial databases are working, right?).  I'm meant the conf file for your new dataset.

Scott



On Tue, Aug 5, 2014 at 9:18 AM, navillusol <[hidden email]> wrote:
Sure, the error in the apache log file seems to indicate to me that it is trying to use GBrowse vanilla rather than GBrowse 2 files. Also I should state that when I use http://localhost/cgi-bin/gbrowse2/gbrowse/volvox i get an error saying file not found, but when I use http://localhost/cgi-bin/gb2/gbrowse/volvox i get onto the page but without the glyphs (as above)

.Conf file is as follows,

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /var/tmp/gbrowse2
persistent_base        = /var/lib/gbrowse2
userdata_base          = /var/lib/gbrowse2/userdata
db_base                = /var/lib/gbrowse2/databases

# These paths are relative to the url base
buttons       = images/buttons
balloons      = images/balloons
openid        = images/openid
gbrowse_help  = .
js            = js

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# session settings
session lock type = default

# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver    = driver:file;serializer:default
#session args      = Directory /var/lib/gbrowse2/sessions

# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args   = FileName /var/lib/gbrowse2/sessions.db

# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.

# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.

# For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!

# for SQLite
#upload_db_adaptor = DBI::SQLite

# for Berkeleydb
#upload_db_adaptor = berkeleydb

# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host    = localhost
#upload_db_user    = www-data
#upload_db_pass    = foobar

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
slave_timeout          = 45
global_timeout         = 60
search_timeout         = 15
max_render_processes   = 4   # try double number of CPU/cores

# Renderfarm settings
#include renderfarm.conf

# Clean up settings (used by the gbrowse_clean script)
expire session  = 1M  # expire unused sessions after a month
expire cache    = 2h  # expire cached data if unmodified for >2 hours
expire uploads  = 6w  # expire uploaded data if unused for >6 weeks

# Appearance settings
truecolor     =  1   # better appearance at the expense of larger image files
# truetype    =  1   # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server.

# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.

#include "themes/warm_colors"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_colors"

balloon tips        = 1
titles are balloons = 1
plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid       = 0
region grid         = 0
detail grid         = 1
image widths        = 450 640 800 1024
default width       = 800
pad_left            = 60
pad_right           = 30
too many landmarks  = 100
track listing style = categories   # either "categories" or "facets"

# Loads more details image data than can fit on the screen.  This lets the user drag and drop the details
# tracks, without loading more data from the server.  A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3

# where to link to when user clicks in detailed view
link          = AUTO

# HTML to insert inside the <head></head> section
head =

# At the top of the HTML...
header =

# At the footer
footer = <hr />
         <p style="font-size:small">The Generic Genome Browser. For questions about the data
         at this site, please contact its webmaster. For support of the
         browser software <i>only</i>, send email to
         <a href="mailto:[hidden email]">[hidden email]</a>
         or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
         </p>

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =

# Limits on genomic regions (can be overridden in datasource config files)
region segment         = 200000
max segment            = 5000000
default segment        = 5000
zoom levels            = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 500000 1000000
region sizes           = 1000 5000 10000 20000
default region         = 5000
fine zoom              = 10%

# keyword search maxima
max keyword results    = 1000

###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate


####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts               = 1
user_accounts_registration  = 1
user_accounts_openid        = 1

# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.

user_account_db          = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For SQLite
# user_account_db        = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For MySQL
# user_account_db        = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse

# The number of public files to display
public_files       = 10

# What email gateway to use for outgoing registration confirmation messages.
# The full format is
#      <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
#    The port is assumed to be 25 unless ssl encryption is specified, in
#               which case it defaults to 465.
#    protocol is either "plain" or "ssl", "plain" assumed.
#    username and password may be required by the gateway for authentication
#
# here are some common options
# smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
# smtp_gateway         = smtp.oicr.on.ca                           # indicated machine will forward email for you
# smtp_gateway         = smtp.gmail.com:465:ssl:joe.user:secret    # use gmail with account "joe.user" and password "secret"
# smtp_gateway         = none                                      # disable outgoing email
smtp_gateway           = none  # disable outgoing email

# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name       = GBrowse
application_name_long  = The Generic Genome Browser
email_address          = [hidden email]

# name of the "superuser" who can add public tracks
admin_account          = admin
admin_dbs              = /var/lib/gbrowse2/databases/admin_uploads


######## DEFAULT DATASOURCE #########
default source = yeast

###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################

[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse

###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeast_advanced]
description   = Yeast chromosomes 1+2 (advanced)
path          = yeast_chr1+2.conf

[yeast_renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

[pop_demo]
description   = Population Display Demo
path          = pop_demo.conf

[volvox]
description  = Tutorial database
path         = volvox.conf

[N_div]
description  = N_div database
path         = N_div.conf


On Tue, Aug 5, 2014 at 2:08 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.

For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Re: Invoking gbrowse

navillusol
Apologies Scott, no they are not working on this machine (the image that I posted earlier displays what I see when I try to invoke them).


On Tue, Aug 5, 2014 at 3:21 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

I'm not interested in the GBrowse.conf file, since it seems to be working (yeast and tutorial databases are working, right?).  I'm meant the conf file for your new dataset.

Scott



On Tue, Aug 5, 2014 at 9:18 AM, navillusol <[hidden email]> wrote:
Sure, the error in the apache log file seems to indicate to me that it is trying to use GBrowse vanilla rather than GBrowse 2 files. Also I should state that when I use http://localhost/cgi-bin/gbrowse2/gbrowse/volvox i get an error saying file not found, but when I use http://localhost/cgi-bin/gb2/gbrowse/volvox i get onto the page but without the glyphs (as above)

.Conf file is as follows,

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /var/tmp/gbrowse2
persistent_base        = /var/lib/gbrowse2
userdata_base          = /var/lib/gbrowse2/userdata
db_base                = /var/lib/gbrowse2/databases

# These paths are relative to the url base
buttons       = images/buttons
balloons      = images/balloons
openid        = images/openid
gbrowse_help  = .
js            = js

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# session settings
session lock type = default

# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver    = driver:file;serializer:default
#session args      = Directory /var/lib/gbrowse2/sessions

# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args   = FileName /var/lib/gbrowse2/sessions.db

# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.

# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.

# For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!

# for SQLite
#upload_db_adaptor = DBI::SQLite

# for Berkeleydb
#upload_db_adaptor = berkeleydb

# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host    = localhost
#upload_db_user    = www-data
#upload_db_pass    = foobar

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
slave_timeout          = 45
global_timeout         = 60
search_timeout         = 15
max_render_processes   = 4   # try double number of CPU/cores

# Renderfarm settings
#include renderfarm.conf

# Clean up settings (used by the gbrowse_clean script)
expire session  = 1M  # expire unused sessions after a month
expire cache    = 2h  # expire cached data if unmodified for >2 hours
expire uploads  = 6w  # expire uploaded data if unused for >6 weeks

# Appearance settings
truecolor     =  1   # better appearance at the expense of larger image files
# truetype    =  1   # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server.

# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.

#include "themes/warm_colors"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_colors"

balloon tips        = 1
titles are balloons = 1
plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid       = 0
region grid         = 0
detail grid         = 1
image widths        = 450 640 800 1024
default width       = 800
pad_left            = 60
pad_right           = 30
too many landmarks  = 100
track listing style = categories   # either "categories" or "facets"

# Loads more details image data than can fit on the screen.  This lets the user drag and drop the details
# tracks, without loading more data from the server.  A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3

# where to link to when user clicks in detailed view
link          = AUTO

# HTML to insert inside the <head></head> section
head =

# At the top of the HTML...
header =

# At the footer
footer = <hr />
         <p style="font-size:small">The Generic Genome Browser. For questions about the data
         at this site, please contact its webmaster. For support of the
         browser software <i>only</i>, send email to
         <a href="mailto:[hidden email]">[hidden email]</a>
         or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
         </p>

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =

# Limits on genomic regions (can be overridden in datasource config files)
region segment         = 200000
max segment            = 5000000
default segment        = 5000
zoom levels            = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 500000 1000000
region sizes           = 1000 5000 10000 20000
default region         = 5000
fine zoom              = 10%

# keyword search maxima
max keyword results    = 1000

###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate


####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts               = 1
user_accounts_registration  = 1
user_accounts_openid        = 1

# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.

user_account_db          = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For SQLite
# user_account_db        = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For MySQL
# user_account_db        = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse

# The number of public files to display
public_files       = 10

# What email gateway to use for outgoing registration confirmation messages.
# The full format is
#      <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
#    The port is assumed to be 25 unless ssl encryption is specified, in
#               which case it defaults to 465.
#    protocol is either "plain" or "ssl", "plain" assumed.
#    username and password may be required by the gateway for authentication
#
# here are some common options
# smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
# smtp_gateway         = smtp.oicr.on.ca                           # indicated machine will forward email for you
# smtp_gateway         = smtp.gmail.com:465:ssl:joe.user:secret    # use gmail with account "joe.user" and password "secret"
# smtp_gateway         = none                                      # disable outgoing email
smtp_gateway           = none  # disable outgoing email

# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name       = GBrowse
application_name_long  = The Generic Genome Browser
email_address          = [hidden email]


# name of the "superuser" who can add public tracks
admin_account          = admin
admin_dbs              = /var/lib/gbrowse2/databases/admin_uploads


######## DEFAULT DATASOURCE #########
default source = yeast

###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################

[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse

###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeast_advanced]
description   = Yeast chromosomes 1+2 (advanced)
path          = yeast_chr1+2.conf

[yeast_renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

[pop_demo]
description   = Population Display Demo
path          = pop_demo.conf

[volvox]
description  = Tutorial database
path         = volvox.conf

[N_div]
description  = N_div database
path         = N_div.conf


On Tue, Aug 5, 2014 at 2:08 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.
For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Re: Invoking gbrowse

navillusol
The person on this thread seems to have the exact same problem as myself, however there is no solution in the end?


On Tue, Aug 5, 2014 at 3:26 PM, navillusol <[hidden email]> wrote:
Apologies Scott, no they are not working on this machine (the image that I posted earlier displays what I see when I try to invoke them).


On Tue, Aug 5, 2014 at 3:21 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

I'm not interested in the GBrowse.conf file, since it seems to be working (yeast and tutorial databases are working, right?).  I'm meant the conf file for your new dataset.

Scott



On Tue, Aug 5, 2014 at 9:18 AM, navillusol <[hidden email]> wrote:
Sure, the error in the apache log file seems to indicate to me that it is trying to use GBrowse vanilla rather than GBrowse 2 files. Also I should state that when I use http://localhost/cgi-bin/gbrowse2/gbrowse/volvox i get an error saying file not found, but when I use http://localhost/cgi-bin/gb2/gbrowse/volvox i get onto the page but without the glyphs (as above)

.Conf file is as follows,

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /var/tmp/gbrowse2
persistent_base        = /var/lib/gbrowse2
userdata_base          = /var/lib/gbrowse2/userdata
db_base                = /var/lib/gbrowse2/databases

# These paths are relative to the url base
buttons       = images/buttons
balloons      = images/balloons
openid        = images/openid
gbrowse_help  = .
js            = js

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# session settings
session lock type = default

# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver    = driver:file;serializer:default
#session args      = Directory /var/lib/gbrowse2/sessions

# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args   = FileName /var/lib/gbrowse2/sessions.db

# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.

# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.

# For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!

# for SQLite
#upload_db_adaptor = DBI::SQLite

# for Berkeleydb
#upload_db_adaptor = berkeleydb

# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host    = localhost
#upload_db_user    = www-data
#upload_db_pass    = foobar

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
slave_timeout          = 45
global_timeout         = 60
search_timeout         = 15
max_render_processes   = 4   # try double number of CPU/cores

# Renderfarm settings
#include renderfarm.conf

# Clean up settings (used by the gbrowse_clean script)
expire session  = 1M  # expire unused sessions after a month
expire cache    = 2h  # expire cached data if unmodified for >2 hours
expire uploads  = 6w  # expire uploaded data if unused for >6 weeks

# Appearance settings
truecolor     =  1   # better appearance at the expense of larger image files
# truetype    =  1   # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server.

# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.

#include "themes/warm_colors"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_colors"

balloon tips        = 1
titles are balloons = 1
plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid       = 0
region grid         = 0
detail grid         = 1
image widths        = 450 640 800 1024
default width       = 800
pad_left            = 60
pad_right           = 30
too many landmarks  = 100
track listing style = categories   # either "categories" or "facets"

# Loads more details image data than can fit on the screen.  This lets the user drag and drop the details
# tracks, without loading more data from the server.  A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3

# where to link to when user clicks in detailed view
link          = AUTO

# HTML to insert inside the <head></head> section
head =

# At the top of the HTML...
header =

# At the footer
footer = <hr />
         <p style="font-size:small">The Generic Genome Browser. For questions about the data
         at this site, please contact its webmaster. For support of the
         browser software <i>only</i>, send email to
         <a href="mailto:[hidden email]">[hidden email]</a>
         or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
         </p>

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =

# Limits on genomic regions (can be overridden in datasource config files)
region segment         = 200000
max segment            = 5000000
default segment        = 5000
zoom levels            = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 500000 1000000
region sizes           = 1000 5000 10000 20000
default region         = 5000
fine zoom              = 10%

# keyword search maxima
max keyword results    = 1000

###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate


####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts               = 1
user_accounts_registration  = 1
user_accounts_openid        = 1

# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.

user_account_db          = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For SQLite
# user_account_db        = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For MySQL
# user_account_db        = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse

# The number of public files to display
public_files       = 10

# What email gateway to use for outgoing registration confirmation messages.
# The full format is
#      <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
#    The port is assumed to be 25 unless ssl encryption is specified, in
#               which case it defaults to 465.
#    protocol is either "plain" or "ssl", "plain" assumed.
#    username and password may be required by the gateway for authentication
#
# here are some common options
# smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
# smtp_gateway         = smtp.oicr.on.ca                           # indicated machine will forward email for you
# smtp_gateway         = smtp.gmail.com:465:ssl:joe.user:secret    # use gmail with account "joe.user" and password "secret"
# smtp_gateway         = none                                      # disable outgoing email
smtp_gateway           = none  # disable outgoing email

# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name       = GBrowse
application_name_long  = The Generic Genome Browser
email_address          = [hidden email]


# name of the "superuser" who can add public tracks
admin_account          = admin
admin_dbs              = /var/lib/gbrowse2/databases/admin_uploads


######## DEFAULT DATASOURCE #########
default source = yeast

###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################

[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse

###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeast_advanced]
description   = Yeast chromosomes 1+2 (advanced)
path          = yeast_chr1+2.conf

[yeast_renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

[pop_demo]
description   = Population Display Demo
path          = pop_demo.conf

[volvox]
description  = Tutorial database
path         = volvox.conf

[N_div]
description  = N_div database
path         = N_div.conf


On Tue, Aug 5, 2014 at 2:08 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.
For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Re: Invoking gbrowse

Scott Cain
In reply to this post by navillusol
Hi Liam,

Can we back up several steps?  You're using BioLinux 12.04, right?  That comes with GBrowse 2.38 already installed.  Did you then install another version of GBrowse2 on top of that?  Ugh.  That's a mess.  How attached are you to this instance of Biolinux?  If it's a vm or AWS instance, it might be easier for you to pitch it and start over.

It's fairly easy to remove the gbrowse installed by apt-get and install a newer version, but it requires a few commands.

Scott



On Tue, Aug 5, 2014 at 10:26 AM, navillusol <[hidden email]> wrote:
Apologies Scott, no they are not working on this machine (the image that I posted earlier displays what I see when I try to invoke them).


On Tue, Aug 5, 2014 at 3:21 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

I'm not interested in the GBrowse.conf file, since it seems to be working (yeast and tutorial databases are working, right?).  I'm meant the conf file for your new dataset.

Scott



On Tue, Aug 5, 2014 at 9:18 AM, navillusol <[hidden email]> wrote:
Sure, the error in the apache log file seems to indicate to me that it is trying to use GBrowse vanilla rather than GBrowse 2 files. Also I should state that when I use http://localhost/cgi-bin/gbrowse2/gbrowse/volvox i get an error saying file not found, but when I use http://localhost/cgi-bin/gb2/gbrowse/volvox i get onto the page but without the glyphs (as above)

.Conf file is as follows,

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /var/tmp/gbrowse2
persistent_base        = /var/lib/gbrowse2
userdata_base          = /var/lib/gbrowse2/userdata
db_base                = /var/lib/gbrowse2/databases

# These paths are relative to the url base
buttons       = images/buttons
balloons      = images/balloons
openid        = images/openid
gbrowse_help  = .
js            = js

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# session settings
session lock type = default

# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver    = driver:file;serializer:default
#session args      = Directory /var/lib/gbrowse2/sessions

# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args   = FileName /var/lib/gbrowse2/sessions.db

# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.

# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.

# For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!

# for SQLite
#upload_db_adaptor = DBI::SQLite

# for Berkeleydb
#upload_db_adaptor = berkeleydb

# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host    = localhost
#upload_db_user    = www-data
#upload_db_pass    = foobar

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
slave_timeout          = 45
global_timeout         = 60
search_timeout         = 15
max_render_processes   = 4   # try double number of CPU/cores

# Renderfarm settings
#include renderfarm.conf

# Clean up settings (used by the gbrowse_clean script)
expire session  = 1M  # expire unused sessions after a month
expire cache    = 2h  # expire cached data if unmodified for >2 hours
expire uploads  = 6w  # expire uploaded data if unused for >6 weeks

# Appearance settings
truecolor     =  1   # better appearance at the expense of larger image files
# truetype    =  1   # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server.

# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.

#include "themes/warm_colors"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_colors"

balloon tips        = 1
titles are balloons = 1
plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid       = 0
region grid         = 0
detail grid         = 1
image widths        = 450 640 800 1024
default width       = 800
pad_left            = 60
pad_right           = 30
too many landmarks  = 100
track listing style = categories   # either "categories" or "facets"

# Loads more details image data than can fit on the screen.  This lets the user drag and drop the details
# tracks, without loading more data from the server.  A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3

# where to link to when user clicks in detailed view
link          = AUTO

# HTML to insert inside the <head></head> section
head =

# At the top of the HTML...
header =

# At the footer
footer = <hr />
         <p style="font-size:small">The Generic Genome Browser. For questions about the data
         at this site, please contact its webmaster. For support of the
         browser software <i>only</i>, send email to
         <a href="mailto:[hidden email]">[hidden email]</a>
         or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
         </p>

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =

# Limits on genomic regions (can be overridden in datasource config files)
region segment         = 200000
max segment            = 5000000
default segment        = 5000
zoom levels            = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 500000 1000000
region sizes           = 1000 5000 10000 20000
default region         = 5000
fine zoom              = 10%

# keyword search maxima
max keyword results    = 1000

###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate


####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts               = 1
user_accounts_registration  = 1
user_accounts_openid        = 1

# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.

user_account_db          = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For SQLite
# user_account_db        = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For MySQL
# user_account_db        = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse

# The number of public files to display
public_files       = 10

# What email gateway to use for outgoing registration confirmation messages.
# The full format is
#      <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
#    The port is assumed to be 25 unless ssl encryption is specified, in
#               which case it defaults to 465.
#    protocol is either "plain" or "ssl", "plain" assumed.
#    username and password may be required by the gateway for authentication
#
# here are some common options
# smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
# smtp_gateway         = smtp.oicr.on.ca                           # indicated machine will forward email for you
# smtp_gateway         = smtp.gmail.com:465:ssl:joe.user:secret    # use gmail with account "joe.user" and password "secret"
# smtp_gateway         = none                                      # disable outgoing email
smtp_gateway           = none  # disable outgoing email

# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name       = GBrowse
application_name_long  = The Generic Genome Browser
email_address          = [hidden email]


# name of the "superuser" who can add public tracks
admin_account          = admin
admin_dbs              = /var/lib/gbrowse2/databases/admin_uploads


######## DEFAULT DATASOURCE #########
default source = yeast

###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################

[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse

###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeast_advanced]
description   = Yeast chromosomes 1+2 (advanced)
path          = yeast_chr1+2.conf

[yeast_renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

[pop_demo]
description   = Population Display Demo
path          = pop_demo.conf

[volvox]
description  = Tutorial database
path         = volvox.conf

[N_div]
description  = N_div database
path         = N_div.conf


On Tue, Aug 5, 2014 at 2:08 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.
For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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Re: Invoking gbrowse

Scott Cain
If you are attached to your instance, you could try this:

  sudo apt-get remove --purge gbrowse

however, this may also remove several packages that GBrowse depends on, which will be a hassle but not insurmountable.  This command will remove the gbrowse files that were installed from the debian package.  Then you may have to reinstall GBrowse2 on the command line to replace anything the it needs that apt-get may have removed.

Scott



On Tue, Aug 5, 2014 at 12:45 PM, Scott Cain <[hidden email]> wrote:
Hi Liam,

Can we back up several steps?  You're using BioLinux 12.04, right?  That comes with GBrowse 2.38 already installed.  Did you then install another version of GBrowse2 on top of that?  Ugh.  That's a mess.  How attached are you to this instance of Biolinux?  If it's a vm or AWS instance, it might be easier for you to pitch it and start over.

It's fairly easy to remove the gbrowse installed by apt-get and install a newer version, but it requires a few commands.

Scott



On Tue, Aug 5, 2014 at 10:26 AM, navillusol <[hidden email]> wrote:
Apologies Scott, no they are not working on this machine (the image that I posted earlier displays what I see when I try to invoke them).


On Tue, Aug 5, 2014 at 3:21 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

I'm not interested in the GBrowse.conf file, since it seems to be working (yeast and tutorial databases are working, right?).  I'm meant the conf file for your new dataset.

Scott



On Tue, Aug 5, 2014 at 9:18 AM, navillusol <[hidden email]> wrote:
Sure, the error in the apache log file seems to indicate to me that it is trying to use GBrowse vanilla rather than GBrowse 2 files. Also I should state that when I use http://localhost/cgi-bin/gbrowse2/gbrowse/volvox i get an error saying file not found, but when I use http://localhost/cgi-bin/gb2/gbrowse/volvox i get onto the page but without the glyphs (as above)

.Conf file is as follows,

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /var/tmp/gbrowse2
persistent_base        = /var/lib/gbrowse2
userdata_base          = /var/lib/gbrowse2/userdata
db_base                = /var/lib/gbrowse2/databases

# These paths are relative to the url base
buttons       = images/buttons
balloons      = images/balloons
openid        = images/openid
gbrowse_help  = .
js            = js

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# session settings
session lock type = default

# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver    = driver:file;serializer:default
#session args      = Directory /var/lib/gbrowse2/sessions

# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args   = FileName /var/lib/gbrowse2/sessions.db

# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.

# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.

# For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!

# for SQLite
#upload_db_adaptor = DBI::SQLite

# for Berkeleydb
#upload_db_adaptor = berkeleydb

# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host    = localhost
#upload_db_user    = www-data
#upload_db_pass    = foobar

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
slave_timeout          = 45
global_timeout         = 60
search_timeout         = 15
max_render_processes   = 4   # try double number of CPU/cores

# Renderfarm settings
#include renderfarm.conf

# Clean up settings (used by the gbrowse_clean script)
expire session  = 1M  # expire unused sessions after a month
expire cache    = 2h  # expire cached data if unmodified for >2 hours
expire uploads  = 6w  # expire uploaded data if unused for >6 weeks

# Appearance settings
truecolor     =  1   # better appearance at the expense of larger image files
# truetype    =  1   # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server.

# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.

#include "themes/warm_colors"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_colors"

balloon tips        = 1
titles are balloons = 1
plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid       = 0
region grid         = 0
detail grid         = 1
image widths        = 450 640 800 1024
default width       = 800
pad_left            = 60
pad_right           = 30
too many landmarks  = 100
track listing style = categories   # either "categories" or "facets"

# Loads more details image data than can fit on the screen.  This lets the user drag and drop the details
# tracks, without loading more data from the server.  A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3

# where to link to when user clicks in detailed view
link          = AUTO

# HTML to insert inside the <head></head> section
head =

# At the top of the HTML...
header =

# At the footer
footer = <hr />
         <p style="font-size:small">The Generic Genome Browser. For questions about the data
         at this site, please contact its webmaster. For support of the
         browser software <i>only</i>, send email to
         <a href="mailto:[hidden email]">[hidden email]</a>
         or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
         </p>

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =

# Limits on genomic regions (can be overridden in datasource config files)
region segment         = 200000
max segment            = 5000000
default segment        = 5000
zoom levels            = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 500000 1000000
region sizes           = 1000 5000 10000 20000
default region         = 5000
fine zoom              = 10%

# keyword search maxima
max keyword results    = 1000

###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate


####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts               = 1
user_accounts_registration  = 1
user_accounts_openid        = 1

# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.

user_account_db          = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For SQLite
# user_account_db        = DBI:SQLite:/var/lib/gbrowse2/databases/users.sqlite

# For MySQL
# user_account_db        = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse

# The number of public files to display
public_files       = 10

# What email gateway to use for outgoing registration confirmation messages.
# The full format is
#      <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
#    The port is assumed to be 25 unless ssl encryption is specified, in
#               which case it defaults to 465.
#    protocol is either "plain" or "ssl", "plain" assumed.
#    username and password may be required by the gateway for authentication
#
# here are some common options
# smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
# smtp_gateway         = smtp.oicr.on.ca                           # indicated machine will forward email for you
# smtp_gateway         = smtp.gmail.com:465:ssl:joe.user:secret    # use gmail with account "joe.user" and password "secret"
# smtp_gateway         = none                                      # disable outgoing email
smtp_gateway           = none  # disable outgoing email

# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name       = GBrowse
application_name_long  = The Generic Genome Browser
email_address          = [hidden email]


# name of the "superuser" who can add public tracks
admin_account          = admin
admin_dbs              = /var/lib/gbrowse2/databases/admin_uploads


######## DEFAULT DATASOURCE #########
default source = yeast

###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################

[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse

###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeast_advanced]
description   = Yeast chromosomes 1+2 (advanced)
path          = yeast_chr1+2.conf

[yeast_renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

[pop_demo]
description   = Population Display Demo
path          = pop_demo.conf

[volvox]
description  = Tutorial database
path         = volvox.conf

[N_div]
description  = N_div database
path         = N_div.conf


On Tue, Aug 5, 2014 at 2:08 PM, Scott Cain [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Liam,

While it is certainly possible to run GBrowse 1 and 2 side by side on the same machine, it does add more complexity than I expect you want.  There isn't an uninstall tool, so it isn't exactly easy to uninstall.  I don't see that as a problem, though, as you just have to be sure to use the right files and directories.

So let's back up a few steps: you said you successfully completed the tutorial and the yeast datasets are working, right?  I suspect that means there is something wrong with your configuration file; why don't you show us that?

Scott



On Tue, Aug 5, 2014 at 8:53 AM, navillusol <[hidden email]> wrote:
Ok I think I may have found the problem. I have both Gbrowse and Gbrowse2 installed, both with separate conf files. It seems to be using the .conf from Gbrowse vanilla rather than GBrowse2 when I point Firefox to http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/ .

Thanks Raymond, I found that post yesterday and made the relevant changes to no success. But I now know that the above issue is causing the problem.


Should I just uninstall both Gbrowse and Gbrowse2 and then reinstall Gbrowse2 and go from there?


On Tue, Aug 5, 2014 at 12:10 PM, Raymond Wan [via Generic Model Organism System Database] <[hidden email]> wrote:

Hi,


Quoting navillusol <[hidden email]>:

> Apologies, when I did ~less error.log i get the following errors;
>
> [Mon Aug 04 12:01:21 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache
> /gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/yeast/
>
> [Mon Aug 04 12:13:38 2014] [error] [client 127.0.0.1] File does not exist:
> /var/cache/gbrowse/images, referer:
> http://localhost/cgi-bin/gb2/gbrowse/N_div/
>
> but when I use gnome-open I get this error;
>
> (gnome-open:5929): GConf-WARNING **: Client failed to connect to the D-BUS
> daemon:
> Did not receive a reply. Possible causes include: the remote application
> did not send a reply, the message bus security policy blocked the reply,
> the reply timeout expired, or the network connection was broken.
> GConf Error: No D-BUS daemon running
I'm not an expert with GBrowse, but I would suggest that you separate the first
problem above with your second one.  They may be unrelated.
For the second one, you can just take the error message and copy and paste it
into Google.  The first link (not necessarily the one that addresses your
problem) is this:

http://askubuntu.com/questions/135573/gconf-error-no-d-bus-daemon-running-how-to-reinstall-or-fix

thus, it seems to affect users who aren't using GBrowse.  (I've seen it myself
on Ubuntu and it usually is related to root owning a file...much like what this
link is talking about.)

The first problem says that you have directories missing.  You should see if
they are indeed missing or whether or not they exist but permissions are
incorrect.

Also, a previous message from Scott seemed to indicate that your Linux
distribution is Ubuntu-based?  Ubuntu has a GBrowse package.  Did you use that
or did you install from source?  If you installed from source, you might want
to consider erasing it (or moving it somewhere) and giving the GBrowse package
(if it exists for your distribution) a try.  As far as I can remember, that
worked with no problems.

Ray




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