[Gmod-gbrowse] Error 404 while running GBrowse Tutorial for Administrators

Discussion:

ThankGod E. Ebenezer

2014-09-18 10:59:59 UTC

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 [1] 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 [1] 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

Links:
------
[1] http://cloud.gmod.org/cgi-bin/gb2/gbrowse/volvox

Scott Cain

2014-09-18 14:05:55 UTC

Permalink

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

Post by ThankGod E. Ebenezer
Hello,

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html

Post by ThankGod E. Ebenezer
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
***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.

Post by ThankGod E. Ebenezer
LDS/GBrowse-2.55.tar.gz
sudo ./Build install -- OK

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html and followed
through all the steps, and everything worked fine.

Post by ThankGod E. Ebenezer
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.

Post by ThankGod E. Ebenezer
When I point my web browser at http://localhost/cgi-bin/gb2/gbrowse/volvox
Not Found
The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this

server.

Post by ThankGod E. Ebenezer
________________________________
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.

Post by ThankGod E. Ebenezer
Hoping to here from you
Regards,
ThankGod

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

Post by ThankGod E. Ebenezer
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

Post by ThankGod E. Ebenezer
_______________________________________________
Gmod-gbrowse mailing list
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

Scott Cain

2014-09-18 15:26:33 UTC

Permalink

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

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
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
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

Post by ThankGod E. Ebenezer
Hello,

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html

for users and custom tracks.

Post by ThankGod E. Ebenezer
LDS/GBrowse-2.55.tar.gz
sudo ./Build install -- OK

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html and followed
through all the steps, and everything worked fine.

Post by ThankGod E. Ebenezer
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.

Post by ThankGod E. Ebenezer
When I point my web browser at
Not Found
The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this

server.

Post by ThankGod E. Ebenezer
________________________________
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.

Post by ThankGod E. Ebenezer
Hoping to here from you
Regards,
ThankGod

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

Post by ThankGod E. Ebenezer
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

Post by ThankGod E. Ebenezer
_______________________________________________
Gmod-gbrowse mailing list
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

ThankGod E. Ebenezer

2014-09-18 16:13:18 UTC

Permalink

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/ [12]

Also, I discovered that there is a /var/www/ directory but not a
/var/www/GBROWSE2 i.e no /gbrowse subdirectory extension

Regards,

ThankGod

Post by 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 [1]? 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
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
Hi ThankGod,
git clone https://github.com/GMOD/GBrowse.git [2]
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 [1] 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 [3] to see a sample dataset. If that works, you should be able to proceed with the tutorial as well.
Scott

Post by ThankGod E. Ebenezer
Hello,
I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html [4]
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
***INSTALLATION COMPLETE***
Load http://localhost/htdocs [5] for demo and documentation.
Visit the http://gmod.org [6] 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 [4] 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 [7] and type in "ctgA" in the search box", I encountered some problems.
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 [8]
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse [9]

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [10]) 216-392-3087
Ontario Institute for Cancer Research

Links:
------
[1] http://localhost/gbrowse2
[2] https://github.com/GMOD/GBrowse.git
[3] http://localhost/cgi-bin/gb2/gbrowse/yeast
[4] http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
[5] http://localhost/htdocs
[6] http://gmod.org
[7] http://localhost/cgi-bin/gb2/gbrowse/volvox
[8]
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
[9] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
[10] http://gmod.org/
[11] tel:216-392-3087
[12] http://cloud.gmod.org/gbrowse2/tutorial/conf_files

Scott Cain

2014-09-19 13:12:31 UTC

Permalink

Post by 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 *
* gbgff gbrowse_details gbrowse_img gbrowse_logindas 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!).
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
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/
<http://cloud.gmod.org/gbrowse2/tutorial/conf_files>
Also, I discovered that there is a /var/www/ directory but not a /var/www*/gbrowse2
*i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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

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
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
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

Post by ThankGod E. Ebenezer
Hello,

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html

for users and custom tracks.

Post by ThankGod E. Ebenezer
LDS/GBrowse-2.55.tar.gz
sudo ./Build install -- OK

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html and followed
through all the steps, and everything worked fine.

Post by ThankGod E. Ebenezer
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.

Post by ThankGod E. Ebenezer
When I point my web browser at
Not Found
The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this

server.

Post by ThankGod E. Ebenezer
________________________________
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.

Post by ThankGod E. Ebenezer
Hoping to here from you
Regards,
ThankGod

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

Post by ThankGod E. Ebenezer
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

Post by ThankGod E. Ebenezer
_______________________________________________
Gmod-gbrowse mailing list
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

ThankGod E. Ebenezer

2014-09-23 10:29:25 UTC

Permalink

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 [3] 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

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
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 [1] and I can view the documentation page (Welcome to Generic Genome Browse!).
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"
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/ [2]
Also, I discovered that there is a /var/www/ directory but not a /var/www/GBROWSE2 i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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 [3]? 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
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
Hi ThankGod,
git clone https://github.com/GMOD/GBrowse.git [4]
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 [3] 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 [5] to see a sample dataset. If that works, you should be able to proceed with the tutorial as well.
Scott

Post by ThankGod E. Ebenezer
Hello,
I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html [6]
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
***INSTALLATION COMPLETE***
Load http://localhost/htdocs [7] for demo and documentation.
Visit the http://gmod.org [8] 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 [6] 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 [9] and type in "ctgA" in the search box", I encountered some problems.
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 [10]
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse [11]

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [12]) 216-392-3087 [13]
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [12]) 216-392-3087
Ontario Institute for Cancer Research

Links:
------
[1] http://localhost/gbrowse
[2] http://cloud.gmod.org/gbrowse2/tutorial/conf_files
[3] http://localhost/gbrowse2
[4] https://github.com/GMOD/GBrowse.git
[5] http://localhost/cgi-bin/gb2/gbrowse/yeast
[6] http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
[7] http://localhost/htdocs
[8] http://gmod.org
[9] http://localhost/cgi-bin/gb2/gbrowse/volvox
[10]
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
[11] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
[12] http://gmod.org/
[13] tel:216-392-3087

ThankGod E. Ebenezer

2014-09-23 12:53:41 UTC

Permalink

Hello scott,

I have now been able to access
http://localhost/cgi-bin/gb2/gbrowse/volvox [14]

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

Post by 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).
NOT FOUND
The requested URL /gbrowse2/ was not found on this server.
-------------------------
Apache/2.2.22 (Ubuntu) Server at localhost Port 80 Regards,ThankGod
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
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 [2] and I can view the documentation page (Welcome to Generic Genome Browse!).
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"
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/ [3]
Also, I discovered that there is a /var/www/ directory but not a /var/www/GBROWSE2 i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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 [1]? 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
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
Hi ThankGod,
git clone https://github.com/GMOD/GBrowse.git [4]
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 [1] 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 [5] to see a sample dataset. If that works, you should be able to proceed with the tutorial as well.
Scott

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [12]) 216-392-3087 [13]
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [12]) 216-392-3087
Ontario Institute for Cancer Research

Links:
------
[1] http://localhost/gbrowse2
[2] http://localhost/gbrowse
[3] http://cloud.gmod.org/gbrowse2/tutorial/conf_files
[4] https://github.com/GMOD/GBrowse.git
[5] http://localhost/cgi-bin/gb2/gbrowse/yeast
[6] http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
[7] http://localhost/htdocs
[8] http://gmod.org
[9] http://localhost/cgi-bin/gb2/gbrowse/volvox
[10]
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
[11] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
[12] http://gmod.org/
[13] tel:216-392-3087
[14] http://cloud.gmod.org/cgi-bin/gb2/gbrowse/volvox

ThankGod E. Ebenezer

2014-09-23 14:30:58 UTC

Permalink

Dear Scott,

I have encountered another problem. I discovered I was able to access:
http://localhost/cgi-bin/gb2/gbrowse/volvox [1]

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

Post by ThankGod E. Ebenezer
Hello scott,
I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox [1]
$ 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
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).
NOT FOUND
The requested URL /gbrowse2/ was not found on this server.
-------------------------
Apache/2.2.22 (Ubuntu) Server at localhost Port 80 Regards,ThankGod
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
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 [3] and I can view the documentation page (Welcome to Generic Genome Browse!).
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"
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/ [4]
Also, I discovered that there is a /var/www/ directory but not a /var/www/GBROWSE2 i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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 [2]? 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
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
Hi ThankGod,
git clone https://github.com/GMOD/GBrowse.git [5]
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 [2] 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 [6] to see a sample dataset. If that works, you should be able to proceed with the tutorial as well.
Scott

Post by ThankGod E. Ebenezer
Hello,
I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html [7]
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
***INSTALLATION COMPLETE***
Load http://localhost/htdocs [8] for demo and documentation.
Visit the http://gmod.org [9] 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 [7] 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 [10] and type in "ctgA" in the search box", I encountered some problems.
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 [11]
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse [12]

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [13]) 216-392-3087 [14]
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [13]) 216-392-3087
Ontario Institute for Cancer Research

Links:
------
[1] http://cloud.gmod.org/cgi-bin/gb2/gbrowse/volvox
[2] http://localhost/gbrowse2
[3] http://localhost/gbrowse
[4] http://cloud.gmod.org/gbrowse2/tutorial/conf_files
[5] https://github.com/GMOD/GBrowse.git
[6] http://localhost/cgi-bin/gb2/gbrowse/yeast
[7] http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
[8] http://localhost/htdocs
[9] http://gmod.org
[10] http://localhost/cgi-bin/gb2/gbrowse/volvox
[11]
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
[12] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
[13] http://gmod.org/
[14] tel:216-392-3087

Scott Cain

2014-09-23 14:45:22 UTC

Permalink

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

Post by ThankGod E. Ebenezer
Dear Scott,
http://localhost/cgi-bin/gb2/gbrowse/volvox
<http://cloud.gmod.org/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
Hello scott,
I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox
<http://cloud.gmod.org/cgi-bin/gb2/gbrowse/volvox>
$ 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
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'
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
Not Found
The requested URL /gbrowse2/ was not found on this server.
------------------------------
Apache/2.2.22 (Ubuntu) Server at localhost Port 80 Regards,ThankGod
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

Post by 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 *
* gbgff gbrowse_details gbrowse_img gbrowse_logindas 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!).
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
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/
<http://cloud.gmod.org/gbrowse2/tutorial/conf_files>
Also, I discovered that there is a /var/www/ directory but not a /var/www*/gbrowse2
*i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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

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
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
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

Post by ThankGod E. Ebenezer
Hello,

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html

databases for users and custom tracks.

Post by ThankGod E. Ebenezer
LDS/GBrowse-2.55.tar.gz
sudo ./Build install -- OK

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html and followed
through all the steps, and everything worked fine.

Post by ThankGod E. Ebenezer
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.

Post by ThankGod E. Ebenezer
When I point my web browser at
Not Found
The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this

server.

Post by ThankGod E. Ebenezer
________________________________
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.

Post by ThankGod E. Ebenezer
Hoping to here from you
Regards,
ThankGod

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

Post by ThankGod E. Ebenezer
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

Post by ThankGod E. Ebenezer
_______________________________________________
Gmod-gbrowse mailing list
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

ThankGod E. Ebenezer

2014-09-23 17:20:40 UTC

Permalink

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

Post by 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
Dear Scott,
I have encountered another problem. I discovered I was able to access: http://localhost/cgi-bin/gb2/gbrowse/volvox [2]
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
Hello scott,
I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox [2]
$ git clone https://github.com/GMOD/GBrowse [1]
$ 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
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).
NOT FOUND
The requested URL /gbrowse2/ was not found on this server.
-------------------------
Apache/2.2.22 (Ubuntu) Server at localhost Port 80 Regards,ThankGod
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
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 [4] and I can view the documentation page (Welcome to Generic Genome Browse!).
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"
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/ [5]
Also, I discovered that there is a /var/www/ directory but not a /var/www/GBROWSE2 i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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 [3]? 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
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
Hi ThankGod,
git clone https://github.com/GMOD/GBrowse.git [6]
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 [3] 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 [7] to see a sample dataset. If that works, you should be able to proceed with the tutorial as well.
Scott

Post by ThankGod E. Ebenezer
Hello,
I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html [8]
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
***INSTALLATION COMPLETE***
Load http://localhost/htdocs [9] for demo and documentation.
Visit the http://gmod.org [10] 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 [8] 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 [11] and type in "ctgA" in the search box", I encountered some problems.
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?
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When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk [12]
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse [13]

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [14]) 216-392-3087 [15]
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [14]) 216-392-3087 [15]
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [14]) 216-392-3087
Ontario Institute for Cancer Research

Links:
------
[1] https://github.com/GMOD/GBrowse
[2] http://cloud.gmod.org/cgi-bin/gb2/gbrowse/volvox
[3] http://localhost/gbrowse2
[4] http://localhost/gbrowse
[5] http://cloud.gmod.org/gbrowse2/tutorial/conf_files
[6] https://github.com/GMOD/GBrowse.git
[7] http://localhost/cgi-bin/gb2/gbrowse/yeast
[8] http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
[9] http://localhost/htdocs
[10] http://gmod.org
[11] http://localhost/cgi-bin/gb2/gbrowse/volvox
[12]
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
[13] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
[14] http://gmod.org/
[15] tel:216-392-3087

Scott Cain

2014-09-23 21:14:55 UTC

Permalink

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

Post by ThankGod E. Ebenezer
Dear Scott,
I think this is a permission problem. It's unable to fetch the files in
/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.
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
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

Post by ThankGod E. Ebenezer
Dear Scott,
http://localhost/cgi-bin/gb2/gbrowse/volvox
<http://cloud.gmod.org/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
Hello scott,
I have now been able to access
http://localhost/cgi-bin/gb2/gbrowse/volvox
<http://cloud.gmod.org/cgi-bin/gb2/gbrowse/volvox>
$ 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
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'
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
Not Found
The requested URL /gbrowse2/ was not found on this server.
------------------------------
Apache/2.2.22 (Ubuntu) Server at localhost Port 80 Regards,ThankGod
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

Post by 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 *
* gbgff gbrowse_details gbrowse_img gbrowse_logindas 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!).
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
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/
<http://cloud.gmod.org/gbrowse2/tutorial/conf_files>
Also, I discovered that there is a /var/www/ directory but not a /var/www*/gbrowse2
*i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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

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
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
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

Post by ThankGod E. Ebenezer
Hello,

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html

databases for users and custom tracks.

Post by ThankGod E. Ebenezer
LDS/GBrowse-2.55.tar.gz
sudo ./Build install -- OK

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html and followed
through all the steps, and everything worked fine.

Post by ThankGod E. Ebenezer
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.

Post by ThankGod E. Ebenezer
When I point my web browser at
Not Found
The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this

server.

Post by ThankGod E. Ebenezer
________________________________
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.

Post by ThankGod E. Ebenezer
Hoping to here from you
Regards,
ThankGod

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

Post by ThankGod E. Ebenezer
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

Post by ThankGod E. Ebenezer
_______________________________________________
Gmod-gbrowse mailing list
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

ThankGod E. Ebenezer

2014-10-13 22:56:37 UTC

Permalink

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

Post by Scott Cain
Hi ThankGod,
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
Dear Scott,
/gbrowse2/i/volvox/
/gbrowse2/images/buttons/
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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "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/ [2]" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
Regards,
ThankGod
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
Dear Scott,
I have encountered another problem. I discovered I was able to access: http://localhost/cgi-bin/gb2/gbrowse/volvox [3]
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
Hello scott,
I have now been able to access http://localhost/cgi-bin/gb2/gbrowse/volvox [3]
$ git clone https://github.com/GMOD/GBrowse [1]
$ 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
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).
NOT FOUND
The requested URL /gbrowse2/ was not found on this server.
-------------------------
Apache/2.2.22 (Ubuntu) Server at localhost Port 80 Regards,ThankGod
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
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 [5] and I can view the documentation page (Welcome to Generic Genome Browse!).
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"
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/ [6]
Also, I discovered that there is a /var/www/ directory but not a /var/www/GBROWSE2 i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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 [4]? 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
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
Hi ThankGod,
git clone https://github.com/GMOD/GBrowse.git [7]
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 [4] 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 [8] to see a sample dataset. If that works, you should be able to proceed with the tutorial as well.
Scott

Post by ThankGod E. Ebenezer
Hello,
I'm having problems running the GBrowse tutorial that I found here: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html [9]
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
***INSTALLATION COMPLETE***
Load http://localhost/htdocs [10] for demo and documentation.
Visit the http://gmod.org [11] 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 [9] 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 [12] and type in "ctgA" in the search box", I encountered some problems.
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 [13]
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse [14]

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [15]) 216-392-3087 [16]
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [15]) 216-392-3087 [16]
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [15]) 216-392-3087 [16]
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/ [15]) 216-392-3087
Ontario Institute for Cancer Research

Links:
------
[1] https://github.com/GMOD/GBrowse
[2] http://localhost/cgi-bin/gb2/gbrowse/volvox/
[3] http://cloud.gmod.org/cgi-bin/gb2/gbrowse/volvox
[4] http://localhost/gbrowse2
[5] http://localhost/gbrowse
[6] http://cloud.gmod.org/gbrowse2/tutorial/conf_files
[7] https://github.com/GMOD/GBrowse.git
[8] http://localhost/cgi-bin/gb2/gbrowse/yeast
[9] http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
[10] http://localhost/htdocs
[11] http://gmod.org
[12] http://localhost/cgi-bin/gb2/gbrowse/volvox
[13]
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
[14] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
[15] http://gmod.org/
[16] tel:216-392-3087

Scott Cain

2014-10-14 14:35:38 UTC

Permalink

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

Post by 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
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
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

Post by ThankGod E. Ebenezer
Dear Scott,
http://localhost/cgi-bin/gb2/gbrowse/volvox
<http://cloud.gmod.org/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
Hello scott,
I have now been able to access
http://localhost/cgi-bin/gb2/gbrowse/volvox
<http://cloud.gmod.org/cgi-bin/gb2/gbrowse/volvox>
$ 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
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'
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
Not Found
The requested URL /gbrowse2/ was not found on this server.
------------------------------
Apache/2.2.22 (Ubuntu) Server at localhost Port 80 Regards,ThankGod
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

Post by 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 *
* gbgff gbrowse_details gbrowse_img gbrowse_logindas 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!).
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
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/
<http://cloud.gmod.org/gbrowse2/tutorial/conf_files>
Also, I discovered that there is a /var/www/ directory but not a
/var/www*/gbrowse2 *i.e no /gbrowse subdirectory extension
Regards,
ThankGod
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

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
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
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

Post by ThankGod E. Ebenezer
Hello,

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html

databases for users and custom tracks.

Post by ThankGod E. Ebenezer
LDS/GBrowse-2.55.tar.gz
sudo ./Build install -- OK

http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html and followed
through all the steps, and everything worked fine.

Post by ThankGod E. Ebenezer
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.

Post by ThankGod E. Ebenezer
When I point my web browser at
Not Found
The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this

server.

Post by ThankGod E. Ebenezer
________________________________
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.

Post by ThankGod E. Ebenezer
Hoping to here from you
Regards,
ThankGod

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

Post by ThankGod E. Ebenezer
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Post by ThankGod E. Ebenezer
_______________________________________________
Gmod-gbrowse mailing list
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

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