Re: Error 404 while running GBrowse Tutorial for Administrators

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Re: Error 404 while running GBrowse Tutorial for Administrators

ThankGod E. Ebenezer

Hello,

I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html

I successfully installed GBrowse via the CPAN shell as so:

sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'


This is the installation message I got:

***INSTALLATION COMPLETE***

Load http://localhost/htdocs for demo and documentation.

Visit the http://gmod.org for more information on setting up databases for users and custom tracks.

LDS/GBrowse-2.55.tar.gz

sudo ./Build install -- OK

 

I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.

But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.

When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:

Not Found

The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 

I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.

Hoping to here from you

Regards,

ThankGod


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Re: Error 404 while running GBrowse Tutorial for Administrators

Scott Cain
Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.

Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> 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

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
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Re: Error 404 while running GBrowse Tutorial for Administrators

Scott Cain
Hi ThankGod,

Please always "reply-all" so your responses can stay on the GBrowse mailing list.

If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.

So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?

Scott


On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> 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

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Error 404 while running GBrowse Tutorial for Administrators

ThankGod E. Ebenezer

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> 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">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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Re: Error 404 while running GBrowse Tutorial for Administrators

Scott Cain
Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.

Scott


On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> 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" 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

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Re: Error 404 while running GBrowse Tutorial for Administrators

ThankGod E. Ebenezer

Dear Scott,

I have removed the directory as so:     sudo rm -rf apache/

And then forced install Gbrowse as so:    sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

This is the message I got after force re-installing Gbrowse:    Bio::Graphics::Browser2 is up to date (2.55).

I discovered I can no longer access http://localhost/gbrowse2  but was able to access it before the deleting /apache directory. This is the message that I got while trying to access it, and I was wondering if it means that Gbrowse didn't re-install?:

Not Found

The requested URL /gbrowse2/ was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 
 
Regards,
ThankGod
 
 

On 2014-09-19 14:12, Scott Cain wrote:

Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.
 
Scott
 

On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

 

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> 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">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">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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Re: Error 404 while running GBrowse Tutorial for Administrators

ThankGod E. Ebenezer

Hello scott,

I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox

What I did was to install GBrowse manually as so:

$ git clone https://github.com/GMOD/GBrowse
$ cd Gbrowse
$ perl Build.PL
$ ./Build installdeps
$ ./Build test
$ sudo ./Build install

This manual process had the automatic installation (sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2') overwritten and placed them in the right/default directories.

Regards,
ThankGod

On 2014-09-23 11:29, ThankGod E. Ebenezer wrote:

Dear Scott,

I have removed the directory as so:     sudo rm -rf apache/

And then forced install Gbrowse as so:    sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

This is the message I got after force re-installing Gbrowse:    Bio::Graphics::Browser2 is up to date (2.55).

I discovered I can no longer access http://localhost/gbrowse2  but was able to access it before the deleting /apache directory. This is the message that I got while trying to access it, and I was wondering if it means that Gbrowse didn't re-install?:

Not Found

The requested URL /gbrowse2/ was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 
 
Regards,
ThankGod
 
 

On 2014-09-19 14:12, Scott Cain wrote:

Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.
 
Scott
 

On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

 

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> 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">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">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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Re: Error 404 while running GBrowse Tutorial for Administrators

ThankGod E. Ebenezer

Dear Scott,

I have encountered another problem. I discovered I was able to access: http://localhost/cgi-bin/gb2/gbrowse/volvox

However, the image tracks for the volvox tutorial (including yeast) http site is not displaying. I've searched on google for possible solutions, but this hasn't been helpful at the moment.

I have also attached the screen shot per the current display for volvox. Please can you let me know how this can be fixed?

Regards,

ThankGod

On 2014-09-23 13:53, ThankGod E. Ebenezer wrote:

Hello scott,

I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox

What I did was to install GBrowse manually as so:

$ git clone https://github.com/GMOD/GBrowse
$ cd Gbrowse
$ perl Build.PL
$ ./Build installdeps
$ ./Build test
$ sudo ./Build install

This manual process had the automatic installation (sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2') overwritten and placed them in the right/default directories.

Regards,
ThankGod

On 2014-09-23 11:29, ThankGod E. Ebenezer wrote:

Dear Scott,

I have removed the directory as so:     sudo rm -rf apache/

And then forced install Gbrowse as so:    sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

This is the message I got after force re-installing Gbrowse:    Bio::Graphics::Browser2 is up to date (2.55).

I discovered I can no longer access http://localhost/gbrowse2  but was able to access it before the deleting /apache directory. This is the message that I got while trying to access it, and I was wondering if it means that Gbrowse didn't re-install?:

Not Found

The requested URL /gbrowse2/ was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 
 
Regards,
ThankGod
 
 

On 2014-09-19 14:12, Scott Cain wrote:

Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.
 
Scott
 

On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

 

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> 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">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">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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Screenshot from 2014-09-23 15:20:36.png (263K) Download Attachment
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Re: Error 404 while running GBrowse Tutorial for Administrators

Scott Cain
HI ThankGod,

If you look in the apache access log, you will probably see a series of 404 errors for images that it's trying to fetch but not finding.  The question is why isn't it finding them.  The two typical answers to that question is that there is a misconfiguration, where it's creating the files in one place and GBrowse is making them in another, or there is a permissions problem that is preventing the images from being created in the first place.  If it's the permissions problem, you should also see a series of errors in the apache error log about it.

Scott


On Tue, Sep 23, 2014 at 10:30 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I have encountered another problem. I discovered I was able to access: http://localhost/cgi-bin/gb2/gbrowse/volvox

However, the image tracks for the volvox tutorial (including yeast) http site is not displaying. I've searched on google for possible solutions, but this hasn't been helpful at the moment.

I have also attached the screen shot per the current display for volvox. Please can you let me know how this can be fixed?

Regards,

ThankGod

On 2014-09-23 13:53, ThankGod E. Ebenezer wrote:

Hello scott,

I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox

What I did was to install GBrowse manually as so:

$ git clone https://github.com/GMOD/GBrowse
$ cd Gbrowse
$ perl Build.PL
$ ./Build installdeps
$ ./Build test
$ sudo ./Build install

This manual process had the automatic installation (sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2') overwritten and placed them in the right/default directories.

Regards,
ThankGod

On 2014-09-23 11:29, ThankGod E. Ebenezer wrote:

Dear Scott,

I have removed the directory as so:     sudo rm -rf apache/

And then forced install Gbrowse as so:    sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

This is the message I got after force re-installing Gbrowse:    Bio::Graphics::Browser2 is up to date (2.55).

I discovered I can no longer access http://localhost/gbrowse2  but was able to access it before the deleting /apache directory. This is the message that I got while trying to access it, and I was wondering if it means that Gbrowse didn't re-install?:

Not Found

The requested URL /gbrowse2/ was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 
 
Regards,
ThankGod
 
 

On 2014-09-19 14:12, Scott Cain wrote:

Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.
 
Scott
 

On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

 

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" 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" 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

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Re: Error 404 while running GBrowse Tutorial for Administrators

ThankGod E. Ebenezer

Dear Scott,

I think this is a permission problem. It's unable to fetch the files in the following directories:

/gbrowse2/i/volvox/

/gbrowse2/images/buttons/

I was wondering if there is a work around the permission problem? I have access to root, and have changed the permissions of the above directories (as so: sudo chown user_name /gbrowse2/i/volvox   ...and did the same for /gbrowse2/images/buttons/ directory) to see if this works - but it didn't. This is the error message in apache.log:

127.0.0.1 - - [23/Sep/2014:17:02:27 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 302 206 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:28 +0100] "GET /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 8141 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/f204a79ef63ec70bc681817a2d735f79.png HTTP/1.1" 404 536 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/38aa55d4ef5424f25373579d020ce1fd.png HTTP/1.1" 404 534 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/open_open.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/f204a79ef63ec70bc681817a2d735f79.png HTTP/1.1" 404 535 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/38aa55d4ef5424f25373579d020ce1fd.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/open_open.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 1564 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 2291 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 7753 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/i/volvox/9ff0721a70ed802a3c3ab2c03a87936b.png HTTP/1.1" 404 534 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"

 

Regards,

ThankGod

On 2014-09-23 15:45, Scott Cain wrote:

HI ThankGod,
 
If you look in the apache access log, you will probably see a series of 404 errors for images that it's trying to fetch but not finding.  The question is why isn't it finding them.  The two typical answers to that question is that there is a misconfiguration, where it's creating the files in one place and GBrowse is making them in another, or there is a permissions problem that is preventing the images from being created in the first place.  If it's the permissions problem, you should also see a series of errors in the apache error log about it.
 
Scott
 

On Tue, Sep 23, 2014 at 10:30 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I have encountered another problem. I discovered I was able to access: http://localhost/cgi-bin/gb2/gbrowse/volvox

However, the image tracks for the volvox tutorial (including yeast) http site is not displaying. I've searched on google for possible solutions, but this hasn't been helpful at the moment.

I have also attached the screen shot per the current display for volvox. Please can you let me know how this can be fixed?

Regards,

ThankGod

On 2014-09-23 13:53, ThankGod E. Ebenezer wrote:

Hello scott,

I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox

What I did was to install GBrowse manually as so:

$ git clone https://github.com/GMOD/GBrowse
$ cd Gbrowse
$ perl Build.PL
$ ./Build installdeps
$ ./Build test
$ sudo ./Build install

This manual process had the automatic installation (sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2') overwritten and placed them in the right/default directories.

Regards,
ThankGod

On 2014-09-23 11:29, ThankGod E. Ebenezer wrote:

Dear Scott,

I have removed the directory as so:     sudo rm -rf apache/

And then forced install Gbrowse as so:    sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

This is the message I got after force re-installing Gbrowse:    Bio::Graphics::Browser2 is up to date (2.55).

I discovered I can no longer access http://localhost/gbrowse2  but was able to access it before the deleting /apache directory. This is the message that I got while trying to access it, and I was wondering if it means that Gbrowse didn't re-install?:

Not Found

The requested URL /gbrowse2/ was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 
 
Regards,
ThankGod
 
 

On 2014-09-19 14:12, Scott Cain wrote:

Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.
 
Scott
 

On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

 

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087">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">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">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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Re: Error 404 while running GBrowse Tutorial for Administrators

Scott Cain
Hi ThankGod,

The user that has to have read and write permissions on those directories is the user account that is running the webserver.  I'm pretty sure that user is "www-data" in Ubuntu, so you need to do something like:

chown -R www-data:www-data /gbrowse2/i

which will recursively change the ownership of the i directory and everything under it, so that the webserver will have permission to create directories and files as well as read them.  Fixing the permissions usually happens at install time, but sometimes (for reasons I never seem to find out), it doesn't happen.

Scott


On Tue, Sep 23, 2014 at 1:20 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I think this is a permission problem. It's unable to fetch the files in the following directories:

/gbrowse2/i/volvox/

/gbrowse2/images/buttons/

I was wondering if there is a work around the permission problem? I have access to root, and have changed the permissions of the above directories (as so: sudo chown user_name /gbrowse2/i/volvox   ...and did the same for /gbrowse2/images/buttons/ directory) to see if this works - but it didn't. This is the error message in apache.log:

127.0.0.1 - - [23/Sep/2014:17:02:27 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 302 206 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:28 +0100] "GET /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 8141 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/f204a79ef63ec70bc681817a2d735f79.png HTTP/1.1" 404 536 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/38aa55d4ef5424f25373579d020ce1fd.png HTTP/1.1" 404 534 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/open_open.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/f204a79ef63ec70bc681817a2d735f79.png HTTP/1.1" 404 535 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/38aa55d4ef5424f25373579d020ce1fd.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/open_open.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 1564 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 2291 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 7753 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/i/volvox/9ff0721a70ed802a3c3ab2c03a87936b.png HTTP/1.1" 404 534 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"

 

Regards,

ThankGod

On 2014-09-23 15:45, Scott Cain wrote:

HI ThankGod,
 
If you look in the apache access log, you will probably see a series of 404 errors for images that it's trying to fetch but not finding.  The question is why isn't it finding them.  The two typical answers to that question is that there is a misconfiguration, where it's creating the files in one place and GBrowse is making them in another, or there is a permissions problem that is preventing the images from being created in the first place.  If it's the permissions problem, you should also see a series of errors in the apache error log about it.
 
Scott
 

On Tue, Sep 23, 2014 at 10:30 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I have encountered another problem. I discovered I was able to access: http://localhost/cgi-bin/gb2/gbrowse/volvox

However, the image tracks for the volvox tutorial (including yeast) http site is not displaying. I've searched on google for possible solutions, but this hasn't been helpful at the moment.

I have also attached the screen shot per the current display for volvox. Please can you let me know how this can be fixed?

Regards,

ThankGod

On 2014-09-23 13:53, ThankGod E. Ebenezer wrote:

Hello scott,

I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox

What I did was to install GBrowse manually as so:

$ git clone https://github.com/GMOD/GBrowse
$ cd Gbrowse
$ perl Build.PL
$ ./Build installdeps
$ ./Build test
$ sudo ./Build install

This manual process had the automatic installation (sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2') overwritten and placed them in the right/default directories.

Regards,
ThankGod

On 2014-09-23 11:29, ThankGod E. Ebenezer wrote:

Dear Scott,

I have removed the directory as so:     sudo rm -rf apache/

And then forced install Gbrowse as so:    sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

This is the message I got after force re-installing Gbrowse:    Bio::Graphics::Browser2 is up to date (2.55).

I discovered I can no longer access http://localhost/gbrowse2  but was able to access it before the deleting /apache directory. This is the message that I got while trying to access it, and I was wondering if it means that Gbrowse didn't re-install?:

Not Found

The requested URL /gbrowse2/ was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 
 
Regards,
ThankGod
 
 

On 2014-09-19 14:12, Scott Cain wrote:

Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.
 
Scott
 

On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

 

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" 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" 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" 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

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Re: Error 404 while running GBrowse Tutorial for Administrators

ThankGod E. Ebenezer

Dear Scott,

I tried this out since the last email below - there seems to be some challenges with the permission issue. I'm considering not having to have Gbrowse with the permission option. What other options do you suggest?

I did a quick check on the web, and I found that Gbrowse does have a VM option: http://gmod.org/wiki/GBrowse2_VMs

I'm considering using this in the main to avoid the permission option, and I was wondering if you could let me know how efficient the VM flavour is for creating a database? Is this also suitable to give remote database access to guests/other individuals etc? Does it work as it would if I had Gbrowse installed directly on my server, or as I would normally would want to use the direct installed flavour? Would you recommend this as an alternative to direct installations? Do you know of anything default Gbrowse utility that wouldn't work in the VM flavour?

Regards,

ThankGod

On 2014-09-23 22:14, Scott Cain wrote:

Hi ThankGod,
 
The user that has to have read and write permissions on those directories is the user account that is running the webserver.  I'm pretty sure that user is "www-data" in Ubuntu, so you need to do something like:
 
chown -R www-data:www-data /gbrowse2/i
 
which will recursively change the ownership of the i directory and everything under it, so that the webserver will have permission to create directories and files as well as read them.  Fixing the permissions usually happens at install time, but sometimes (for reasons I never seem to find out), it doesn't happen.
 
Scott
 

On Tue, Sep 23, 2014 at 1:20 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I think this is a permission problem. It's unable to fetch the files in the following directories:

/gbrowse2/i/volvox/

/gbrowse2/images/buttons/

I was wondering if there is a work around the permission problem? I have access to root, and have changed the permissions of the above directories (as so: sudo chown user_name /gbrowse2/i/volvox   ...and did the same for /gbrowse2/images/buttons/ directory) to see if this works - but it didn't. This is the error message in apache.log:

127.0.0.1 - - [23/Sep/2014:17:02:27 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 302 206 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:28 +0100] "GET /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 8141 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/f204a79ef63ec70bc681817a2d735f79.png HTTP/1.1" 404 536 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/38aa55d4ef5424f25373579d020ce1fd.png HTTP/1.1" 404 534 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/open_open.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/f204a79ef63ec70bc681817a2d735f79.png HTTP/1.1" 404 535 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/38aa55d4ef5424f25373579d020ce1fd.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/open_open.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 1564 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 2291 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 7753 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/i/volvox/9ff0721a70ed802a3c3ab2c03a87936b.png HTTP/1.1" 404 534 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"

 

Regards,

ThankGod

On 2014-09-23 15:45, Scott Cain wrote:

HI ThankGod,
 
If you look in the apache access log, you will probably see a series of 404 errors for images that it's trying to fetch but not finding.  The question is why isn't it finding them.  The two typical answers to that question is that there is a misconfiguration, where it's creating the files in one place and GBrowse is making them in another, or there is a permissions problem that is preventing the images from being created in the first place.  If it's the permissions problem, you should also see a series of errors in the apache error log about it.
 
Scott
 

On Tue, Sep 23, 2014 at 10:30 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I have encountered another problem. I discovered I was able to access: http://localhost/cgi-bin/gb2/gbrowse/volvox

However, the image tracks for the volvox tutorial (including yeast) http site is not displaying. I've searched on google for possible solutions, but this hasn't been helpful at the moment.

I have also attached the screen shot per the current display for volvox. Please can you let me know how this can be fixed?

Regards,

ThankGod

On 2014-09-23 13:53, ThankGod E. Ebenezer wrote:

Hello scott,

I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox

What I did was to install GBrowse manually as so:

$ git clone https://github.com/GMOD/GBrowse
$ cd Gbrowse
$ perl Build.PL
$ ./Build installdeps
$ ./Build test
$ sudo ./Build install

This manual process had the automatic installation (sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2') overwritten and placed them in the right/default directories.

Regards,
ThankGod

On 2014-09-23 11:29, ThankGod E. Ebenezer wrote:

Dear Scott,

I have removed the directory as so:     sudo rm -rf apache/

And then forced install Gbrowse as so:    sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

This is the message I got after force re-installing Gbrowse:    Bio::Graphics::Browser2 is up to date (2.55).

I discovered I can no longer access http://localhost/gbrowse2  but was able to access it before the deleting /apache directory. This is the message that I got while trying to access it, and I was wondering if it means that Gbrowse didn't re-install?:

Not Found

The requested URL /gbrowse2/ was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 
 
Regards,
ThankGod
 
 

On 2014-09-19 14:12, Scott Cain wrote:

Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.
 
Scott
 

On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

 

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087">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">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">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">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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Re: Error 404 while running GBrowse Tutorial for Administrators

Scott Cain
Hi ThankGod,

I honestly don't know much about running a VirtualBox instance as a "real" server (that is, one that you have up all the time and available to the outside world).  You might have to talk to the IT people at your institution about what is involved in hosting it in a persistent state.

That said, using the virtual machines can make life a lot easier, though the version of GBrowse is a little old (2.52 versus 2.55); for most uses, this shouldn't make much of a difference.  Performance is also usually pretty good.

Scott


On Mon, Oct 13, 2014 at 6:56 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I tried this out since the last email below - there seems to be some challenges with the permission issue. I'm considering not having to have Gbrowse with the permission option. What other options do you suggest?

I did a quick check on the web, and I found that Gbrowse does have a VM option: http://gmod.org/wiki/GBrowse2_VMs

I'm considering using this in the main to avoid the permission option, and I was wondering if you could let me know how efficient the VM flavour is for creating a database? Is this also suitable to give remote database access to guests/other individuals etc? Does it work as it would if I had Gbrowse installed directly on my server, or as I would normally would want to use the direct installed flavour? Would you recommend this as an alternative to direct installations? Do you know of anything default Gbrowse utility that wouldn't work in the VM flavour?

Regards,

ThankGod

On 2014-09-23 22:14, Scott Cain wrote:

Hi ThankGod,
 
The user that has to have read and write permissions on those directories is the user account that is running the webserver.  I'm pretty sure that user is "www-data" in Ubuntu, so you need to do something like:
 
chown -R www-data:www-data /gbrowse2/i
 
which will recursively change the ownership of the i directory and everything under it, so that the webserver will have permission to create directories and files as well as read them.  Fixing the permissions usually happens at install time, but sometimes (for reasons I never seem to find out), it doesn't happen.
 
Scott
 

On Tue, Sep 23, 2014 at 1:20 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I think this is a permission problem. It's unable to fetch the files in the following directories:

/gbrowse2/i/volvox/

/gbrowse2/images/buttons/

I was wondering if there is a work around the permission problem? I have access to root, and have changed the permissions of the above directories (as so: sudo chown user_name /gbrowse2/i/volvox   ...and did the same for /gbrowse2/images/buttons/ directory) to see if this works - but it didn't. This is the error message in apache.log:

127.0.0.1 - - [23/Sep/2014:17:02:27 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 302 206 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:28 +0100] "GET /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 8141 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/f204a79ef63ec70bc681817a2d735f79.png HTTP/1.1" 404 536 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/38aa55d4ef5424f25373579d020ce1fd.png HTTP/1.1" 404 534 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/open_open.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/f204a79ef63ec70bc681817a2d735f79.png HTTP/1.1" 404 535 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/38aa55d4ef5424f25373579d020ce1fd.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/images/buttons/open_open.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:29 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 1564 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/e0ae04ae71b8b988ce21edd55ad26527.png HTTP/1.1" 404 532 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/63da62d5b1819c662de9b872aa1a8d66.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "GET /gbrowse2/i/volvox/8f9e8f5f7aa0f3ed3c2b7bd77fd76c11.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 2291 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:30 +0100] "POST /cgi-bin/gb2/gbrowse/volvox/ HTTP/1.1" 200 7753 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/images/buttons/pop_out.png HTTP/1.1" 404 516 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/i/volvox/9ff0721a70ed802a3c3ab2c03a87936b.png HTTP/1.1" 404 534 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [23/Sep/2014:17:02:31 +0100] "GET /gbrowse2/i/volvox/acb89b40b1d1c811734dd179989badf3.png HTTP/1.1" 404 533 "http://localhost/cgi-bin/gb2/gbrowse/volvox/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"

 

Regards,

ThankGod

On 2014-09-23 15:45, Scott Cain wrote:

HI ThankGod,
 
If you look in the apache access log, you will probably see a series of 404 errors for images that it's trying to fetch but not finding.  The question is why isn't it finding them.  The two typical answers to that question is that there is a misconfiguration, where it's creating the files in one place and GBrowse is making them in another, or there is a permissions problem that is preventing the images from being created in the first place.  If it's the permissions problem, you should also see a series of errors in the apache error log about it.
 
Scott
 

On Tue, Sep 23, 2014 at 10:30 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

I have encountered another problem. I discovered I was able to access: http://localhost/cgi-bin/gb2/gbrowse/volvox

However, the image tracks for the volvox tutorial (including yeast) http site is not displaying. I've searched on google for possible solutions, but this hasn't been helpful at the moment.

I have also attached the screen shot per the current display for volvox. Please can you let me know how this can be fixed?

Regards,

ThankGod

On 2014-09-23 13:53, ThankGod E. Ebenezer wrote:

Hello scott,

I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox

What I did was to install GBrowse manually as so:

$ git clone https://github.com/GMOD/GBrowse
$ cd Gbrowse
$ perl Build.PL
$ ./Build installdeps
$ ./Build test
$ sudo ./Build install

This manual process had the automatic installation (sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2') overwritten and placed them in the right/default directories.

Regards,
ThankGod

On 2014-09-23 11:29, ThankGod E. Ebenezer wrote:

Dear Scott,

I have removed the directory as so:     sudo rm -rf apache/

And then forced install Gbrowse as so:    sudo perl -MCPAN -e 'force install Bio::Graphics::Browser2'

This is the message I got after force re-installing Gbrowse:    Bio::Graphics::Browser2 is up to date (2.55).

I discovered I can no longer access http://localhost/gbrowse2  but was able to access it before the deleting /apache directory. This is the message that I got while trying to access it, and I was wondering if it means that Gbrowse didn't re-install?:

Not Found

The requested URL /gbrowse2/ was not found on this server.


Apache/2.2.22 (Ubuntu) Server at localhost Port 80
 
 
Regards,
ThankGod
 
 

On 2014-09-19 14:12, Scott Cain wrote:

Ah, I know what happened: you tried to install GBrowse before you installed apache.  When that happens, the installer assumes (usually incorrectly) that you'll be installing your own apache server from source and puts the server related files where they would typically end up, in /usr/local/apache.  What you should do, assuming you haven't actually installed a webserver in /usr/local/apache, is to completely remove that directory (rm -rf /usr/local/apache/) and install GBrowse again.  Now that you have a webserver installed, it should find the directory where cgi scripts should go and put them there.
 
Scott
 

On Thu, Sep 18, 2014 at 12:13 PM, ThankGod E. Ebenezer <[hidden email]> wrote:

Dear Scott,

1. /usr/lib/cgi-bin/gb2 does not exist, but /usr/lib/cgi-bin/. The /gb2 directory extension does not exist in the /usr/lib/cgi-bin/ directory.

Where GBrowse installed the files you mentioned (gbrowse, gbrowse_img) is in /usr/local/apache/cgi-bin

This has other files like: gbgff    gbrowse_details  gbrowse_img      gbrowse_login
das  gbrowse  gbrowse_gmap     gbrowse_key_img  gbrowse_syn

2. I can successfully get to http://localhost/gbrowse and I can view the documentation page (Welcome to Generic Genome Browse!).

This is the message for access.log file I found in /var/log/apache2:

127.0.0.1 - - [17/Sep/2014:13:35:32 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:43:30 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:05 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:13:45:07 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:19:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:20:36 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:22:53 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:27:41 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:28:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:33:25 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:42:37 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 539 "-" "Wget/1.13.4 (linux-gnu)"
127.0.0.1 - - [17/Sep/2014:14:56:51 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:56:54 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 510 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"
127.0.0.1 - - [17/Sep/2014:14:58:50 +0100] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 511 "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101 Firefox/31.0"

I also discovered that the installation locations changed slightly. For instance, the tutorial directory in my installation is found in /usr/local/apache/htdocs/tutorial with the following files and folders :

bin data_files  figures tutorial.html conf_files  dbgff tutorial.css  tutorial.phyTreeEdit.html

However, this is different from the directory where these tutorial documentation says the files/folders are located which is /var/www/gbrowse2/tutorial/

Also, I discovered that there is a /var/www/ directory but not a /var/www/gbrowse2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

 

On 2014-09-18 16:26, Scott Cain wrote:

Hi ThankGod,
 
Please always "reply-all" so your responses can stay on the GBrowse mailing list.
 
If you're using ubuntu 12.04, that's not your problem and there's not much point in installing from github (I'm reasonably sure you'd never be affected by the bug we fixed).  Also, there is not a "uninstall" option.  Typically perl-based tools don't have that, and they just install over the old files.  When it needs to install a new version of a configuration file (that is, something you might have edited), it will ask you if you want to keep the old one or replace it.
 
So, let's get back to your specific problem: does /usr/lib/cgi-bin/gb2 exist and does it have files in it named things like gbrowse, gbrowse_img, etc?  Can you successfully get to http://localhost/gbrowse2?  What exactly is the message related to gbrowse in the apache access log related to the not found problem (the access log is in /var/log/apache2)?
 
Scott
 

On Thu, Sep 18, 2014 at 11:14 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

Hello Scott.

Thanks. I'm actually using Ubuntu 12.04

However, I will progress to install GBrowse via GitHub. The problem now is that GBrowse does not have an uninstall option.

Should I just install via GitHub anyway? ...Will this replace the previous installation made via CPAN? Or how do I uninstall GBrowse if otherwise so I can install via GitHub?

Regards,

ThankGod

On 2014-09-18 15:05, Scott Cain wrote:

Hi ThankGod,

I'm guessing you're using Ubuntu 14.04.  While working on some minor bug fixes for GBrowse, we discovered that when Ubuntu 14.04 was released, they dramatically rearranged the file structure for system files, which broke the GBrowse installer.  The easiest way to install GBrowse correctly at the moment is to get a GitHub checkout of the current source and install that way.  It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL  #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though the links for sample data sets are written assuming you have fastcgi installed (which is a good idea to use, because it makes things faster), but if you don't have fastcgi, you should still be able to go to http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.  If that works, you should be able to proceed with the tutorial as well.
 
Scott




On Thu, Sep 18, 2014 at 6:59 AM, ThankGod E. Ebenezer <[hidden email]> wrote:

>
> Hello,
>
> I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
>
> I successfully installed GBrowse via the CPAN shell as so:
>
> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>
>
> This is the installation message I got:
>
> ***INSTALLATION COMPLETE***
>
> Load http://localhost/htdocs for demo and documentation.
>
> Visit the http://gmod.org for more information on setting up databases for users and custom tracks.
>
> LDS/GBrowse-2.55.tar.gz
>
> sudo ./Build install -- OK
>
>  
>
> I started to do the GBrowse tutorial for administrators here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html   and followed through all the steps, and everything worked fine.
>
> But when I got to the point that says: "You should now be able to view the data set. Point your web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox and type in "ctgA" in the search box", I encountered some problems.
>
> When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox   I got this error:
>
> Not Found
>
> The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.
>
> ________________________________
> Apache/2.2.22 (Ubuntu) Server at localhost Port 80
>
> I will be glad if you can let me know how to resolve this. I have checked this on google, but was unable to find any solution to this.
>
> Hoping to here from you
>
> Regards,
>
> ThankGod
>
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" 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" 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" 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" 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

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