[Gmod-gbrowse] 500 internal server error

Discussion:

Ramesh krishnan Ramasamy

2015-07-12 04:06:04 UTC

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

Scott Cain

2015-07-13 13:41:12 UTC

Permalink

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 <

Post by 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.
[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
http://xx.x.xxx.xxx/gbrowse2/
I appreciate any sort of help.
Thanks
Ramesh
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Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Ramesh krishnan Ramasamy

2015-07-13 16:25:07 UTC

Permalink

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

Post by 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 <

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

Scott Cain

2015-07-13 16:32:51 UTC

Permalink

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 <

Post by 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

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

Ramesh krishnan Ramasamy

2015-07-13 16:37:20 UTC

Permalink

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

Post by 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 <

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

Scott Cain

2015-07-14 14:42:00 UTC

Permalink

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 <

Post by 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

Post by 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 <

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

Ramesh krishnan Ramasamy

2015-07-14 16:20:55 UTC

Permalink

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

Post by 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 <

Post by 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 <

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at
scottcain dot net
GMOD Coordinator (http://gmod.org/) 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