Need help regarding Gbrowse

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Need help regarding Gbrowse

vindhya vatsyayan
Hi,

We have been trying to install gbrowse manually and  through sourceforge but Gbrowse folders are not not being created. I think its not being properly installed.

Kindly help.



Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)

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analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
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Re: Need help regarding Gbrowse

Scott Cain
Hi Vindhya,

Can you please provide more information?  What did you do and what messages did you get in response?

Scott



On Fri, Apr 12, 2013 at 7:19 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi,

We have been trying to install gbrowse manually and  through sourceforge but Gbrowse folders are not not being created. I think its not being properly installed.

Kindly help.



Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
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/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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Re: Need help regarding Gbrowse

Scott Cain
Hi Vindhya,

Let's make this the email thread will work on.

When you said you tried to install using sudo with the Build install command but you got a "different set of files" in the message, what do you mean?  Using sudo should give you permission to write anywhere on the file system.

Scott



On Mon, Apr 15, 2013 at 10:16 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi Scott,

I have been trying to install Gbrowse on my ubuntu 11.04 through CPAN but following error pops up everytime I run ./Build Install command.

ERROR: Can't create '/usr/local/lib/perl/5.14.2/Bio/DB/SeqFeature/Store'
Do not have write permissions on '/usr/local/lib/perl/5.14.2/Bio/DB/SeqFeature/Store'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 at /usr/share/perl/5.14/Module/Build/Base.pm line 3569


Besides this I have tried installing gbrowse through other means as well but Gbrowse and other relevant folders are not being created anywhere on my system.


 
I have tried giving out permissions also (using sudo)  but then it comes up with the same error only with a different set of  files and folders.

One more thing that when I installed Gbrowse from here http://gmod.org/wiki/GBrowse_Ubuntu_HOWTO... I was able to view  all the files and examples following this http://localhost/gbrowse2 but no files and folders were created on my system.

Please help.



Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)



Date: Mon, 15 Apr 2013 10:09:57 -0400
Subject: Re: [Gmod-gbrowse] Need help regarding Gbrowse
From: [hidden email]
To: [hidden email]
CC: [hidden email]


Hi Vindhya,

Can you please provide more information?  What did you do and what messages did you get in response?

Scott



On Fri, Apr 12, 2013 at 7:19 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi,

We have been trying to install gbrowse manually and  through sourceforge but Gbrowse folders are not not being created. I think its not being properly installed.

Kindly help.



Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
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/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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Re: Need help regarding Gbrowse

girlwithglasses
Hi Vindhya,

Further to Scott's comment, are you using 'sudo' for all the commands you run, not just the ./Build step?


On Mon, Apr 15, 2013 at 3:24 PM, Scott Cain <[hidden email]> wrote:
Hi Vindhya,

Let's make this the email thread will work on.

When you said you tried to install using sudo with the Build install command but you got a "different set of files" in the message, what do you mean?  Using sudo should give you permission to write anywhere on the file system.

Scott



On Mon, Apr 15, 2013 at 10:16 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi Scott,

I have been trying to install Gbrowse on my ubuntu 11.04 through CPAN but following error pops up everytime I run ./Build Install command.

ERROR: Can't create '/usr/local/lib/perl/5.14.2/Bio/DB/SeqFeature/Store'
Do not have write permissions on '/usr/local/lib/perl/5.14.2/Bio/DB/SeqFeature/Store'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 at /usr/share/perl/5.14/Module/Build/Base.pm line 3569


Besides this I have tried installing gbrowse through other means as well but Gbrowse and other relevant folders are not being created anywhere on my system.


 
I have tried giving out permissions also (using sudo)  but then it comes up with the same error only with a different set of  files and folders.

One more thing that when I installed Gbrowse from here http://gmod.org/wiki/GBrowse_Ubuntu_HOWTO... I was able to view  all the files and examples following this http://localhost/gbrowse2 but no files and folders were created on my system.

Please help.



Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)



Date: Mon, 15 Apr 2013 10:09:57 -0400
Subject: Re: [Gmod-gbrowse] Need help regarding Gbrowse
From: [hidden email]
To: [hidden email]
CC: [hidden email]


Hi Vindhya,

Can you please provide more information?  What did you do and what messages did you get in response?

Scott



On Fri, Apr 12, 2013 at 7:19 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi,

We have been trying to install gbrowse manually and  through sourceforge but Gbrowse folders are not not being created. I think its not being properly installed.

Kindly help.



Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
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

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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Gmod-gbrowse mailing list
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Re: Need help regarding Gbrowse

girlwithglasses
The problem now is that the files that GBrowse is expecting to find aren't in the places it expects them to be. Have you got your Apache server (i.e. localhost) configured correctly so that it looks for the cgi-bin at /usr/lib/cgi-bin? This is where GBrowse installs the files (in a default installation) - make sure Apache is looking in the right directories for the files.
  • /var/www/gbrowse2/: Holds the website files (HTML, etc.), Javascript & CSS files, and any databases.
  • /etc/gbrowse2/: Holds the language files for help, MobyServices, the themes & various configuration files.
  • /usr/local/lib/perl/[perl version]/Bio/Graphics/Browser2: The perl modules which make up the majority of the Gbrowse code.
  • /etc/apache2/conf.d/gbrowse2.conf: The apache configuration file.
  • /usr/lib/cgi-bin/: CGI scripts for use when the site is running (anything in the source /cgi-bin/ directory).
  • /var/tmp/gbrowse2/: Temporary files like sessions, user data, images, etc.


On Tue, Apr 16, 2013 at 9:59 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi,

I am now able to install gbrowse using sudo build command...but still i am able to run the volvox example. This is what it is showing

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, webmaster@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.

Apache/2.2.22 (Ubuntu) Server at localhost Port 80

And in error log files : [Tue Apr 16 11:32:42 2013] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Tue Apr 16 11:33:36 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox
[Tue Apr 16 11:33:41 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox
[Tue Apr 16 11:33:49 2013] [error] [client 127.0.0.1] No GBrowse configuration file at /var/www/vindhya/Outlookfinal/GBrowse-2.54/GBrowse.conf! at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2.pm line 31.

Now I also want to ask do we need any other file beside .gff3 and .conf . Does this procedure forms cgi-bin folder showed here http://localhost/cgi-bin/gb2/gbrowse/volvox because I am not able to locate this folder any where in the local host.

Please help.


Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)


--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Need help regarding Gbrowse

girlwithglasses
Hi Vindhya,

So the situation is that you've got the yeast example working, but can't get volvox running?

The locations of the various files that GBrowse uses are detailed here:

http://gmod.org/wiki/GBrowse_2.0_Install_Paths


On Tue, Apr 16, 2013 at 10:34 AM, vindhya vatsyayan <[hidden email]> wrote:
yes...we are using these locations only. One more thing that I am able to run all the examples of yeast and others but want to know where are these files located? in cgi-bin or where?


Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)



From: [hidden email]
Date: Tue, 16 Apr 2013 10:28:16 +0100

Subject: Re: [Gmod-gbrowse] Need help regarding Gbrowse
To: [hidden email]; [hidden email]


The problem now is that the files that GBrowse is expecting to find aren't in the places it expects them to be. Have you got your Apache server (i.e. localhost) configured correctly so that it looks for the cgi-bin at /usr/lib/cgi-bin? This is where GBrowse installs the files (in a default installation) - make sure Apache is looking in the right directories for the files.
  • /var/www/gbrowse2/: Holds the website files (HTML, etc.), Javascript & CSS files, and any databases.
  • /etc/gbrowse2/: Holds the language files for help, MobyServices, the themes & various configuration files.
  • /usr/local/lib/perl/[perl version]/Bio/Graphics/Browser2: The perl modules which make up the majority of the Gbrowse code.
  • /etc/apache2/conf.d/gbrowse2.conf: The apache configuration file.
  • /usr/lib/cgi-bin/: CGI scripts for use when the site is running (anything in the source /cgi-bin/ directory).
  • /var/tmp/gbrowse2/: Temporary files like sessions, user data, images, etc.


On Tue, Apr 16, 2013 at 9:59 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi,

I am now able to install gbrowse using sudo build command...but still i am able to run the volvox example. This is what it is showing

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, webmaster@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.

Apache/2.2.22 (Ubuntu) Server at localhost Port 80

And in error log files : [Tue Apr 16 11:32:42 2013] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Tue Apr 16 11:33:36 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox
[Tue Apr 16 11:33:41 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox
[Tue Apr 16 11:33:49 2013] [error] [client 127.0.0.1] No GBrowse configuration file at /var/www/vindhya/Outlookfinal/GBrowse-2.54/GBrowse.conf! at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2.pm line 31.

Now I also want to ask do we need any other file beside .gff3 and .conf . Does this procedure forms cgi-bin folder showed here http://localhost/cgi-bin/gb2/gbrowse/volvox because I am not able to locate this folder any where in the local host.

Please help.


Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)


--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject




--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Need help regarding Gbrowse

Scott Cain
Hi Vindhya,

Please keep all correspondence on the mailing list; I'm trying to piece together what state you're in but that is made more difficult by your responses not being on the mailing list.

When I looked back on one of your apache error log, I found this line:

[Tue Apr 16 11:33:36 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox

which makes it look like you're trying to go to this url:

That is not the typical URL for a GBrowse installation.  Typically, the url would look like this:

Scott



On Tue, Apr 16, 2013 at 1:20 PM, Amelia Ireland <[hidden email]> wrote:
Hi Vindhya,

So the situation is that you've got the yeast example working, but can't get volvox running?

The locations of the various files that GBrowse uses are detailed here:

http://gmod.org/wiki/GBrowse_2.0_Install_Paths


On Tue, Apr 16, 2013 at 10:34 AM, vindhya vatsyayan <[hidden email]> wrote:
yes...we are using these locations only. One more thing that I am able to run all the examples of yeast and others but want to know where are these files located? in cgi-bin or where?


Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)



From: [hidden email]
Date: Tue, 16 Apr 2013 10:28:16 +0100

Subject: Re: [Gmod-gbrowse] Need help regarding Gbrowse
To: [hidden email]; [hidden email]


The problem now is that the files that GBrowse is expecting to find aren't in the places it expects them to be. Have you got your Apache server (i.e. localhost) configured correctly so that it looks for the cgi-bin at /usr/lib/cgi-bin? This is where GBrowse installs the files (in a default installation) - make sure Apache is looking in the right directories for the files.
  • /var/www/gbrowse2/: Holds the website files (HTML, etc.), Javascript & CSS files, and any databases.
  • /etc/gbrowse2/: Holds the language files for help, MobyServices, the themes & various configuration files.
  • /usr/local/lib/perl/[perl version]/Bio/Graphics/Browser2: The perl modules which make up the majority of the Gbrowse code.
  • /etc/apache2/conf.d/gbrowse2.conf: The apache configuration file.
  • /usr/lib/cgi-bin/: CGI scripts for use when the site is running (anything in the source /cgi-bin/ directory).
  • /var/tmp/gbrowse2/: Temporary files like sessions, user data, images, etc.


On Tue, Apr 16, 2013 at 9:59 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi,

I am now able to install gbrowse using sudo build command...but still i am able to run the volvox example. This is what it is showing

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, webmaster@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.

Apache/2.2.22 (Ubuntu) Server at localhost Port 80

And in error log files : [Tue Apr 16 11:32:42 2013] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Tue Apr 16 11:33:36 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox
[Tue Apr 16 11:33:41 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox
[Tue Apr 16 11:33:49 2013] [error] [client 127.0.0.1] No GBrowse configuration file at /var/www/vindhya/Outlookfinal/GBrowse-2.54/GBrowse.conf! at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2.pm line 31.

Now I also want to ask do we need any other file beside .gff3 and .conf . Does this procedure forms cgi-bin folder showed here http://localhost/cgi-bin/gb2/gbrowse/volvox because I am not able to locate this folder any where in the local host.

Please help.


Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)


--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject




--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject




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

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Need help regarding Gbrowse

Scott Cain
Hi Vindhya,

No, I mean always "reply-all" so that the GBrowse mailing list is included so that people other than just the person you are corresponding with can read the thread.  That way the thread also gets archived so others can find it in the future if they're having the same problem.

You'll note that the message you are getting in the error log changed.  Before it couldn't find the gbrowse cgi; now apache does find it, but when it tries to execute it fails almost immediately since it can't find the GBrowse.conf file.  The gbrowse cgi is looking in /var/www/vindhya/Outlookfinal/GBrowse-2.54 for the conf file.  Any idea why?  Normally it would look for it in /etc/gbrowse2, but you must have changed the configuration directory when you installed it, and then maybe moved that directory?  Or perhaps it isn't readable by the webserver?  Hard to say.  Generally, I would say when you are new to a piece of software, it's a good idea to accept the defaults unless you have a good reason for not doing so.

Scott





On Thu, Apr 18, 2013 at 3:17 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi,

You mean I should reply to this email add only?

yeah after using the url 
http://localhost/cgi-bin/gb2/gbrowse/volvox  I m still getting this:

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, webmaster@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.

Apache/2.2.22 (Ubuntu) Server at localhost Port 80

and in error log file:

[Thu Apr 18 12:45:36 2013] [error] [client 127.0.0.1] No GBrowse configuration file at /var/www/vindhya/Outlookfinal/GBrowse-2.54/GBrowse.conf! at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2.pm line 31.
[Thu Apr 18 12:45:36 2013] [error] [client 127.0.0.1] Premature end of script headers: gbrowse



Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)



Date: Wed, 17 Apr 2013 16:01:22 -0400

Subject: Re: [Gmod-gbrowse] Need help regarding Gbrowse
From: [hidden email]
To: [hidden email]
CC: [hidden email]; [hidden email]


Hi Vindhya,

Please keep all correspondence on the mailing list; I'm trying to piece together what state you're in but that is made more difficult by your responses not being on the mailing list.

When I looked back on one of your apache error log, I found this line:

[Tue Apr 16 11:33:36 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox

which makes it look like you're trying to go to this url:

That is not the typical URL for a GBrowse installation.  Typically, the url would look like this:

Scott



On Tue, Apr 16, 2013 at 1:20 PM, Amelia Ireland <[hidden email]> wrote:
Hi Vindhya,

So the situation is that you've got the yeast example working, but can't get volvox running?

The locations of the various files that GBrowse uses are detailed here:

http://gmod.org/wiki/GBrowse_2.0_Install_Paths


On Tue, Apr 16, 2013 at 10:34 AM, vindhya vatsyayan <[hidden email]> wrote:
yes...we are using these locations only. One more thing that I am able to run all the examples of yeast and others but want to know where are these files located? in cgi-bin or where?


Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)



From: [hidden email]
Date: Tue, 16 Apr 2013 10:28:16 +0100

Subject: Re: [Gmod-gbrowse] Need help regarding Gbrowse
To: [hidden email]; [hidden email]


The problem now is that the files that GBrowse is expecting to find aren't in the places it expects them to be. Have you got your Apache server (i.e. localhost) configured correctly so that it looks for the cgi-bin at /usr/lib/cgi-bin? This is where GBrowse installs the files (in a default installation) - make sure Apache is looking in the right directories for the files.
  • /var/www/gbrowse2/: Holds the website files (HTML, etc.), Javascript & CSS files, and any databases.
  • /etc/gbrowse2/: Holds the language files for help, MobyServices, the themes & various configuration files.
  • /usr/local/lib/perl/[perl version]/Bio/Graphics/Browser2: The perl modules which make up the majority of the Gbrowse code.
  • /etc/apache2/conf.d/gbrowse2.conf: The apache configuration file.
  • /usr/lib/cgi-bin/: CGI scripts for use when the site is running (anything in the source /cgi-bin/ directory).
  • /var/tmp/gbrowse2/: Temporary files like sessions, user data, images, etc.


On Tue, Apr 16, 2013 at 9:59 AM, vindhya vatsyayan <[hidden email]> wrote:
Hi,

I am now able to install gbrowse using sudo build command...but still i am able to run the volvox example. This is what it is showing

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, webmaster@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.

Apache/2.2.22 (Ubuntu) Server at localhost Port 80

And in error log files : [Tue Apr 16 11:32:42 2013] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Tue Apr 16 11:33:36 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox
[Tue Apr 16 11:33:41 2013] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/gbrowse/volvox
[Tue Apr 16 11:33:49 2013] [error] [client 127.0.0.1] No GBrowse configuration file at /var/www/vindhya/Outlookfinal/GBrowse-2.54/GBrowse.conf! at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2.pm line 31.

Now I also want to ask do we need any other file beside .gff3 and .conf . Does this procedure forms cgi-bin folder showed here http://localhost/cgi-bin/gb2/gbrowse/volvox because I am not able to locate this folder any where in the local host.

Please help.


Regards,

Vindhya Vatsyayan
Msc.Bioinformatics (IV semester)
Department of Computer Sciences 
Bioinformatics Infrastructure Facility
Jamia Millia Islamia (Central University)


--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject




--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject




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