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500 internal server error

Ramesh krishnan Ramasamy
Hello everyone,

Today, I have installed GBrowse2 in my Ubuntu server 14.04.2. I used automatic installation and followed defaults in directory selection. None of the given example links are working, which returns 500 internal server error.

Error.log shows following error:

[Sun Jul 12 03:53:50.734165 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] AH01215:  at /usr/local/lib/perl/5.18.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 22., referer: http://xx.x.xxx.xxx/gbrowse2/
[Sun Jul 12 03:53:50.738689 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] End of script output before headers: gbrowse, referer: http://xx.x.xxx.xxx/gbrowse2/

I appreciate any sort of help.

Thanks
Ramesh

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Re: 500 internal server error

Scott Cain
Hi Ramesh,

My recollection that when you use apt-get to install GBrowse, the url to access GBrowse is http://xxxxxx/gbrowse/gbrowse, or perhaps http://xxxxx/gbrowse2/gbrowse2, but I think it's the first one (the Debian people don't like having version numbers in the application names).

Scott


On Sun, Jul 12, 2015 at 12:06 AM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hello everyone,

Today, I have installed GBrowse2 in my Ubuntu server 14.04.2. I used automatic installation and followed defaults in directory selection. None of the given example links are working, which returns 500 internal server error.

Error.log shows following error:

[Sun Jul 12 03:53:50.734165 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] AH01215:  at /usr/local/lib/perl/5.18.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 22., referer: http://xx.x.xxx.xxx/gbrowse2/
[Sun Jul 12 03:53:50.738689 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] End of script output before headers: gbrowse, referer: http://xx.x.xxx.xxx/gbrowse2/

I appreciate any sort of help.

Thanks
Ramesh

------------------------------------------------------------------------------
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Ontario Institute for Cancer Research

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Re: 500 internal server error

Ramesh krishnan Ramasamy
Hi Scott,

Many thanks for your prompt response. 

I have used sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' as explained in GBrowse installation page http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO

Thanks again,
Ramesh

On Mon, Jul 13, 2015 at 6:41 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

My recollection that when you use apt-get to install GBrowse, the url to access GBrowse is http://xxxxxx/gbrowse/gbrowse, or perhaps http://xxxxx/gbrowse2/gbrowse2, but I think it's the first one (the Debian people don't like having version numbers in the application names).

Scott


On Sun, Jul 12, 2015 at 12:06 AM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hello everyone,

Today, I have installed GBrowse2 in my Ubuntu server 14.04.2. I used automatic installation and followed defaults in directory selection. None of the given example links are working, which returns 500 internal server error.

Error.log shows following error:

[Sun Jul 12 03:53:50.734165 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] AH01215:  at /usr/local/lib/perl/5.18.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 22., referer: http://xx.x.xxx.xxx/gbrowse2/
[Sun Jul 12 03:53:50.738689 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] End of script output before headers: gbrowse, referer: http://xx.x.xxx.xxx/gbrowse2/

I appreciate any sort of help.

Thanks
Ramesh

------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
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Re: 500 internal server error

Scott Cain
Hi Ramesh,

That's good to know, but doesn't directly related to what I wrote: does using the different url have any effect?

Scott


On Mon, Jul 13, 2015 at 12:25 PM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hi Scott,

Many thanks for your prompt response. 

I have used sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' as explained in GBrowse installation page http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO

Thanks again,
Ramesh

On Mon, Jul 13, 2015 at 6:41 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

My recollection that when you use apt-get to install GBrowse, the url to access GBrowse is http://xxxxxx/gbrowse/gbrowse, or perhaps http://xxxxx/gbrowse2/gbrowse2, but I think it's the first one (the Debian people don't like having version numbers in the application names).

Scott


On Sun, Jul 12, 2015 at 12:06 AM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hello everyone,

Today, I have installed GBrowse2 in my Ubuntu server 14.04.2. I used automatic installation and followed defaults in directory selection. None of the given example links are working, which returns 500 internal server error.

Error.log shows following error:

[Sun Jul 12 03:53:50.734165 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] AH01215:  at /usr/local/lib/perl/5.18.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 22., referer: http://xx.x.xxx.xxx/gbrowse2/
[Sun Jul 12 03:53:50.738689 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] End of script output before headers: gbrowse, referer: http://xx.x.xxx.xxx/gbrowse2/

I appreciate any sort of help.

Thanks
Ramesh

------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
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[hidden email]
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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

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you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
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Re: 500 internal server error

Ramesh krishnan Ramasamy
Hi Scott,

Sorry, I forgot to mention this in my mail. No, it has no effect, I ended up with "404 Not found". In my computer, HTML files are in  /var/www/html/gbrowse2/

Thanks
Ramesh

On Mon, Jul 13, 2015 at 9:32 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

That's good to know, but doesn't directly related to what I wrote: does using the different url have any effect?

Scott


On Mon, Jul 13, 2015 at 12:25 PM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hi Scott,

Many thanks for your prompt response. 

I have used sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' as explained in GBrowse installation page http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO

Thanks again,
Ramesh

On Mon, Jul 13, 2015 at 6:41 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

My recollection that when you use apt-get to install GBrowse, the url to access GBrowse is http://xxxxxx/gbrowse/gbrowse, or perhaps http://xxxxx/gbrowse2/gbrowse2, but I think it's the first one (the Debian people don't like having version numbers in the application names).

Scott


On Sun, Jul 12, 2015 at 12:06 AM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hello everyone,

Today, I have installed GBrowse2 in my Ubuntu server 14.04.2. I used automatic installation and followed defaults in directory selection. None of the given example links are working, which returns 500 internal server error.

Error.log shows following error:

[Sun Jul 12 03:53:50.734165 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] AH01215:  at /usr/local/lib/perl/5.18.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 22., referer: http://xx.x.xxx.xxx/gbrowse2/
[Sun Jul 12 03:53:50.738689 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] End of script output before headers: gbrowse, referer: http://xx.x.xxx.xxx/gbrowse2/

I appreciate any sort of help.

Thanks
Ramesh

------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
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Re: 500 internal server error

Scott Cain
Hi Ramesh,

I'm trying to recreate the problem you're having and so I'm creating an Ubuntu 14.04 instance.  Before you got the to point where you were getting the error message, did you have to spend some time fiddling with the apache configuration?  I'm finding apache 2.4 to be fairly frustrating (due to unfamiliarity mostly), and I'm wondering what the total of issues related to GBrowse will be with regard to apache 2.4.  It might be much easier to move to Ubuntu 12.04. 

Scott


On Mon, Jul 13, 2015 at 12:37 PM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hi Scott,

Sorry, I forgot to mention this in my mail. No, it has no effect, I ended up with "404 Not found". In my computer, HTML files are in  /var/www/html/gbrowse2/

Thanks
Ramesh

On Mon, Jul 13, 2015 at 9:32 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

That's good to know, but doesn't directly related to what I wrote: does using the different url have any effect?

Scott


On Mon, Jul 13, 2015 at 12:25 PM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hi Scott,

Many thanks for your prompt response. 

I have used sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' as explained in GBrowse installation page http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO

Thanks again,
Ramesh

On Mon, Jul 13, 2015 at 6:41 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

My recollection that when you use apt-get to install GBrowse, the url to access GBrowse is http://xxxxxx/gbrowse/gbrowse, or perhaps http://xxxxx/gbrowse2/gbrowse2, but I think it's the first one (the Debian people don't like having version numbers in the application names).

Scott


On Sun, Jul 12, 2015 at 12:06 AM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hello everyone,

Today, I have installed GBrowse2 in my Ubuntu server 14.04.2. I used automatic installation and followed defaults in directory selection. None of the given example links are working, which returns 500 internal server error.

Error.log shows following error:

[Sun Jul 12 03:53:50.734165 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] AH01215:  at /usr/local/lib/perl/5.18.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 22., referer: http://xx.x.xxx.xxx/gbrowse2/
[Sun Jul 12 03:53:50.738689 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] End of script output before headers: gbrowse, referer: http://xx.x.xxx.xxx/gbrowse2/

I appreciate any sort of help.

Thanks
Ramesh

------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
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Re: 500 internal server error

Ramesh krishnan Ramasamy
Hi Scott,

Many thanks for your efforts. I haven't played around with apache2 configuration. Initially, I was getting "Not Found" error, then I wrapped path '/var/lib/gbrowse2/databases/volvox' in single quotes as explained in your cloud admin page (http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html). After wrapping, I ended up with "Internal server error". 

Yes, I was not having problem with Ubuntu 12.04. Since, we moved our other webpages to 14, I thought to install and check GBrowse in Ubuntu 14.04. 

Thanks again,
Ramesh 

On Tue, Jul 14, 2015 at 7:42 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

I'm trying to recreate the problem you're having and so I'm creating an Ubuntu 14.04 instance.  Before you got the to point where you were getting the error message, did you have to spend some time fiddling with the apache configuration?  I'm finding apache 2.4 to be fairly frustrating (due to unfamiliarity mostly), and I'm wondering what the total of issues related to GBrowse will be with regard to apache 2.4.  It might be much easier to move to Ubuntu 12.04. 

Scott


On Mon, Jul 13, 2015 at 12:37 PM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hi Scott,

Sorry, I forgot to mention this in my mail. No, it has no effect, I ended up with "404 Not found". In my computer, HTML files are in  /var/www/html/gbrowse2/

Thanks
Ramesh

On Mon, Jul 13, 2015 at 9:32 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

That's good to know, but doesn't directly related to what I wrote: does using the different url have any effect?

Scott


On Mon, Jul 13, 2015 at 12:25 PM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hi Scott,

Many thanks for your prompt response. 

I have used sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' as explained in GBrowse installation page http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO

Thanks again,
Ramesh

On Mon, Jul 13, 2015 at 6:41 AM, Scott Cain <[hidden email]> wrote:
Hi Ramesh,

My recollection that when you use apt-get to install GBrowse, the url to access GBrowse is http://xxxxxx/gbrowse/gbrowse, or perhaps http://xxxxx/gbrowse2/gbrowse2, but I think it's the first one (the Debian people don't like having version numbers in the application names).

Scott


On Sun, Jul 12, 2015 at 12:06 AM, Ramesh krishnan Ramasamy <[hidden email]> wrote:
Hello everyone,

Today, I have installed GBrowse2 in my Ubuntu server 14.04.2. I used automatic installation and followed defaults in directory selection. None of the given example links are working, which returns 500 internal server error.

Error.log shows following error:

[Sun Jul 12 03:53:50.734165 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] AH01215:  at /usr/local/lib/perl/5.18.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 22., referer: http://xx.x.xxx.xxx/gbrowse2/
[Sun Jul 12 03:53:50.738689 2015] [cgi:error] [pid 1320] [client xx.xxx.xxx.xx:52657] End of script output before headers: gbrowse, referer: http://xx.x.xxx.xxx/gbrowse2/

I appreciate any sort of help.

Thanks
Ramesh

------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
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