[Gmod-help] Gbrowse2

[Scott Cain]

Hi Bill,

I cc'ed this to the GBrowse mailing list; replies to this email can
trim the "help" email from the cc list.  The GBrowse mailing list
provides a much wider audience and makes it more likely your problems
will be solved quickly.

Clearly, just hitting "back" shouldn't break anything, but I don't
know what's going on either, because it doesn't do that for me.
Whenever you get a 500 error, you should look at the apache error_log,
located at /var/log/apache2/error_log on Ubuntu systems, for a hint at
what the problem is.  If it isn't obvious to you, you can copy what
you think is the relevant section of the log to the mailing list and
we'll take a look too.  So, right after you trigger the 500 error,
take a look at the bottom of the error_log to see what apache had to
say about the error.

About the back button: while it shouldn't cause an error, you also
shouldn't need to use it.  GBrowse is a very "AJAX-y" web application
that interacts with the webserver (redraws tracks, adds and removes
tracks) without redrawing the whole page, so the back button may not
be doing what you think it's doing in this context anyway.

About the 403 forbidden: It is in fact forbidden, whether it's
supposed to be or not.  The apache config that GBrowse uses (found in
/etc/apache2/other/gbrowse2.conf I think) explicitly disallows
displaying the contents of directories when there isn't an index.html
file present.  I think including a simple html page was just an
oversight, so I'll add one now.

Scott


On Thu, Apr 7, 2011 at 8:34 AM, William Belden <belden at aesop.rutgers.edu> wrote:
> Hello,
>
> I am attempting to run GBrowse2 on a desktop workstation running Ubuntu
> 10.04 (64 bit) and Apache 2.2.14 to analyze high throughput sequencing data.
>  I installed all the prerequisites and then used shell command (sudo perl
> -MCPAN -e 'install Bio::Graphics::Browser2').  The installation went fine
> and everything looks appropriate.  I can view /var/www/gbrowse2/tutorial on
> localhost using Firefox.  Initially, I was also able to view
> http://localhost/cgi-bin/gb2/gbrowse/yeast on my system when I clicked on
> it.   I then hit the back button and tried the link again (as well as some
> of the other links) and I receive a "500 server error".  I was only able to
> see the GBrowser once (but because I saw it once, I believe the installation
> is fine).  I was also able to type in my IP address in place of localhost
> and saw the Yeast Gbrowse again, but when I hit the back button again, and
> then tried the link again the "500 error" returned.  I am also receiving
> "403 Forbidden" error when I try to view /var/www/gbrowse3/example_scripts,
> saying I do not have permission.
>
> Can you please help with this problem.  And thank you in advance for your
> support.  It is greatly appreciated.
>
> Bill
>
>
> William J. Belden, Ph.D.
> Assistant Professor
> Department of Biochemistry and Microbiology
> Rutgers, The State University of New Jersey
> School of Environmental and Biological Sciences
> 76 Lipman Drive
> New Brunswick, NJ 08901-8525
> Tel 732-932-9763 ext. 121
> Fax 732-932-8965
>
> belden at aesop.rutgers.edu
>
>
>
>
>



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