Re: help regarding invoking gbrowse

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Re: help regarding invoking gbrowse

Scott Cain
Hi Umay,

It's best to ask these questions on the GBrowse mailing list; I'm cc'ing it here.

I'm a little confused about what it is you're trying to do; are you trying to go to this url:


What is "samplefile"?  Did you create a configuration file for it in /etc/gbrowse2 and put an entry for it in /etc/gbrowse2/GBrowse.conf?  Also, my recollection about the debian packaged GBrowse is that the url you have to use is a little goofy, you might have to use this one instead:


If that doesn't work, what happens if you go to:


Scott



On Wed, Jul 23, 2014 at 2:52 AM, umay kulsum <[hidden email]> wrote:
I have installed gbrowse in my system having ubuntu 14.04 using:

sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2

now I want to invoke gbrowse using the url /localhost/cgi-bin/gbrowse/samplefile but it displays The requested URL /localhost/cgi-bin/gbrowse/samplefile was not found on this server.

the conf file and gff3 file has been created successfully.

even the example file of yeast is not present in usr/lib/cgi-bin/gbrowse.

please help on how to invoke gbrowse.



Regards

Umay Kulsum
Ph.D student
AIIMS
New Delhi



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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

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Re: help regarding invoking gbrowse

Scott Cain
Hi Umay,

Please continue to cc the GBrowse mailing list (that is, please "reply-all").

When you installed gbrowse with apt-get, what command did you use?  Did you include the gbrowse-data package as well?  That's where you get the sample data. 

If you did include that package, is there anything in the apache error log that might indicate what the problem is?  The apache error log is probably in /var/log/apache2/error_log.

Scott



On Fri, Jul 25, 2014 at 1:36 AM, umay kulsum <[hidden email]> wrote:
Dear Scott,

samplefile is actually the configuration file that i have created in etc/apache2/gbrowse....
if I go to

it gives: The requested URL /cgi-bin/gbrowse/gbrowse/yeast was not found on this server.

I am trying to run gbrowse on my local database that I have created...

I have samplefile.conf in etc/apache2/gbrowse/samplefile.conf  but how do I put an entry for it in etc/gbrowse/GBrowse.conf??
I have attached the samlefile which  now I have named as 114635370.conf

if the yeast is also not showing result is it that GBrowse is not installed properly??

Regards

Umay Kulsum
PhD Student
AIIMS
New Delhi


On Fri, Jul 25, 2014 at 12:30 AM, Scott Cain <[hidden email]> wrote:
Hi Umay,

It's best to ask these questions on the GBrowse mailing list; I'm cc'ing it here.

I'm a little confused about what it is you're trying to do; are you trying to go to this url:


What is "samplefile"?  Did you create a configuration file for it in /etc/gbrowse2 and put an entry for it in /etc/gbrowse2/GBrowse.conf?  Also, my recollection about the debian packaged GBrowse is that the url you have to use is a little goofy, you might have to use this one instead:


If that doesn't work, what happens if you go to:


Scott



On Wed, Jul 23, 2014 at 2:52 AM, umay kulsum <[hidden email]> wrote:
I have installed gbrowse in my system having ubuntu 14.04 using:

sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2

now I want to invoke gbrowse using the url /localhost/cgi-bin/gbrowse/samplefile but it displays The requested URL /localhost/cgi-bin/gbrowse/samplefile was not found on this server.

the conf file and gff3 file has been created successfully.

even the example file of yeast is not present in usr/lib/cgi-bin/gbrowse.

please help on how to invoke gbrowse.



Regards

Umay Kulsum
Ph.D student
AIIMS
New Delhi



--
------------------------------------------------------------------------
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

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse