Query regarding server for GBrowse 2.52 and ./build demo

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Query regarding server for GBrowse 2.52 and ./build demo

Rohit23

Hello.

I am a bit confused about the configuration of the server to use for Gbrowse 2.52.

my ./build demo did not work but I carried on with the install. But I am not sure about the server to use, is it Apache2 or httpd.
Httpd is a form of apache but they both have different means to start right.

http starts by
$ service httpd start


apache2 by
/usr/local/apache2/bin/apachectl start


I don't understand the difference between the two, so I made a folder in /usr/local/apache2/ named conf and copied the httpd.conf into it, furthermore I made a soft-link between them.
But I still find problem in using either

$ /usr/local/apache2/bin/apachectl status
ELinks: Connection refused

$ service httpd status
httpd.service - The Apache HTTP Server (prefork MPM)
      Loaded: loaded (/lib/systemd/system/httpd.service; enabled)
      Active: failed since Thu, 06 Dec 2012 18:40:36 +0530; 6s ago
     Process: 13252 ExecStop=/usr/sbin/httpd $OPTIONS -k stop (code=exited, status=0/SUCCESS)
     Process: 13254 ExecStart=/usr/sbin/httpd $OPTIONS -k start (code=exited, status=1/FAILURE)
    Main PID: 1089 (code=exited, status=0/SUCCESS)
      CGroup: name=systemd:/system/httpd.service


What is the solution to it?


--

Regards...
Sree Rohit Raj
. K



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Re: Query regarding server for GBrowse 2.52 and ./build demo

girlwithglasses
Hi Rohit,

Which version of GBrowse are you using? Have you checked the Apache logs? If you can paste some of the errors from the Apache logs, that will help us diagnose the problem.


On Fri, Dec 14, 2012 at 12:05 AM, Sree Rohit Raj <[hidden email]> wrote:

Dear Ameilia,

Thank you so much for the link. I have gone through it and it helped me in understanding Apache a little.
My service starts with httpd and I am not getting failed message while checking httpd status now.

My GBrowse has been reinstalled and the start page opens with no problem.
But when I open the gbrowse example data I face the same problem.

http://localhost/gb2/gbrowse/yeast_advanced
Shows a 500 Internal server error.

http://localhost/cgi-bin/gb2/gbrowse/yeast
Shows 404 Not found error.

The server runs fine but I don't understand why this error shows up even when my local server is not running any other processes.
I did try to remove memory consuming programs and add-ons the last time I found the Internal server error itself.

Is there still problem in my Apache or is my GBrowse not configured properly?

Regards,
Rohit


On 13 December 2012 21:44, Amelia Ireland <[hidden email]> wrote:
Good morning Rohit,

This is an apache problem rather than a GBrowse problem, you're right. Did you try googling around for that error message you got? This looks like a similar problem, from serverfault.com:


There's also an explanation of what apachectl is that will answer your question about the differences between it and httpd. That might be of some help.

On Wed, Dec 12, 2012 at 9:12 PM, Sree Rohit Raj <[hidden email]> wrote:
ELinks: Connection refused



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



--

Regards...
Sree Rohit Raj
. K





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

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Re: Query regarding server for GBrowse 2.52 and ./build demo

Scott Cain
Also, did you install apache at /usr/local/apache, typically by
building it from source?  And if so, is there a reason you did that
(like some functionality that not available in the apache that you get
from your linux distribution)?  If not, you should delete
/usr/local/apache and reinstall; the installer assumes that if you
have a directory called /usr/local/apache (or apache2), that you built
apache from source for some reason and will want to use that over the
one that comes with the operating system.

Scott


On Fri, Dec 14, 2012 at 9:48 AM, Amelia Ireland <[hidden email]> wrote:

> Hi Rohit,
>
> Which version of GBrowse are you using? Have you checked the Apache logs? If
> you can paste some of the errors from the Apache logs, that will help us
> diagnose the problem.
>
>
> On Fri, Dec 14, 2012 at 12:05 AM, Sree Rohit Raj <[hidden email]>
> wrote:
>>
>>
>> Dear Ameilia,
>>
>> Thank you so much for the link. I have gone through it and it helped me in
>> understanding Apache a little.
>> My service starts with httpd and I am not getting failed message while
>> checking httpd status now.
>>
>> My GBrowse has been reinstalled and the start page opens with no problem.
>> But when I open the gbrowse example data I face the same problem.
>>
>> http://localhost/gb2/gbrowse/yeast_advanced
>> Shows a 500 Internal server error.
>>
>> http://localhost/cgi-bin/gb2/gbrowse/yeast
>> Shows 404 Not found error.
>>
>> The server runs fine but I don't understand why this error shows up even
>> when my local server is not running any other processes.
>> I did try to remove memory consuming programs and add-ons the last time I
>> found the Internal server error itself.
>>
>> Is there still problem in my Apache or is my GBrowse not configured
>> properly?
>>
>> Regards,
>> Rohit
>>
>>
>> On 13 December 2012 21:44, Amelia Ireland <[hidden email]> wrote:
>>>
>>> Good morning Rohit,
>>>
>>> This is an apache problem rather than a GBrowse problem, you're right.
>>> Did you try googling around for that error message you got? This looks like
>>> a similar problem, from serverfault.com:
>>>
>>>
>>> http://serverfault.com/questions/174036/trouble-starting-apache-via-apachectl
>>>
>>> There's also an explanation of what apachectl is that will answer your
>>> question about the differences between it and httpd. That might be of some
>>> help.
>>>
>>> On Wed, Dec 12, 2012 at 9:12 PM, Sree Rohit Raj <[hidden email]>
>>> wrote:
>>>>
>>>> ELinks: Connection refused
>>>
>>>
>>>
>>>
>>> --
>>> Amelia Ireland
>>> GMOD Community Support || http://gmod.org
>>
>>
>>
>>
>> --
>>
>> Regards...
>> Sree Rohit Raj. K
>>
>
>
>
> --
> Amelia Ireland
> GMOD Community Support || http://gmod.org
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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

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Re: Query regarding server for GBrowse 2.52 and ./build demo

Rohit23

Hello Scott and Amelia,

I am using the GBrowse 2.52. I will check the error logs now and rectify it.

Apache was installed though 'Yum'. I have done it after removing the apache previously.
But I will give it a go once again by removing the directory and installing again.

Thanks for the help.

Regards,
Rohit

On 14 December 2012 20:32, Scott Cain <[hidden email]> wrote:
Also, did you install apache at /usr/local/apache, typically by
building it from source?  And if so, is there a reason you did that
(like some functionality that not available in the apache that you get
from your linux distribution)?  If not, you should delete
/usr/local/apache and reinstall; the installer assumes that if you
have a directory called /usr/local/apache (or apache2), that you built
apache from source for some reason and will want to use that over the
one that comes with the operating system.

Scott


On Fri, Dec 14, 2012 at 9:48 AM, Amelia Ireland <[hidden email]> wrote:
> Hi Rohit,
>
> Which version of GBrowse are you using? Have you checked the Apache logs? If
> you can paste some of the errors from the Apache logs, that will help us
> diagnose the problem.
>
>
> On Fri, Dec 14, 2012 at 12:05 AM, Sree Rohit Raj <[hidden email]>
> wrote:
>>
>>
>> Dear Ameilia,
>>
>> Thank you so much for the link. I have gone through it and it helped me in
>> understanding Apache a little.
>> My service starts with httpd and I am not getting failed message while
>> checking httpd status now.
>>
>> My GBrowse has been reinstalled and the start page opens with no problem.
>> But when I open the gbrowse example data I face the same problem.
>>
>> http://localhost/gb2/gbrowse/yeast_advanced
>> Shows a 500 Internal server error.
>>
>> http://localhost/cgi-bin/gb2/gbrowse/yeast
>> Shows 404 Not found error.
>>
>> The server runs fine but I don't understand why this error shows up even
>> when my local server is not running any other processes.
>> I did try to remove memory consuming programs and add-ons the last time I
>> found the Internal server error itself.
>>
>> Is there still problem in my Apache or is my GBrowse not configured
>> properly?
>>
>> Regards,
>> Rohit
>>
>>
>> On 13 December 2012 21:44, Amelia Ireland <[hidden email]> wrote:
>>>
>>> Good morning Rohit,
>>>
>>> This is an apache problem rather than a GBrowse problem, you're right.
>>> Did you try googling around for that error message you got? This looks like
>>> a similar problem, from serverfault.com:
>>>
>>>
>>> http://serverfault.com/questions/174036/trouble-starting-apache-via-apachectl
>>>
>>> There's also an explanation of what apachectl is that will answer your
>>> question about the differences between it and httpd. That might be of some
>>> help.
>>>
>>> On Wed, Dec 12, 2012 at 9:12 PM, Sree Rohit Raj <[hidden email]>
>>> wrote:
>>>>
>>>> ELinks: Connection refused
>>>
>>>
>>>
>>>
>>> --
>>> Amelia Ireland
>>> GMOD Community Support || http://gmod.org
>>
>>
>>
>>
>> --
>>
>> Regards...
>> Sree Rohit Raj. K
>>
>
>
>
> --
> Amelia Ireland
> GMOD Community Support || http://gmod.org
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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



--

Regards...
Sree Rohit Raj
. K



------------------------------------------------------------------------------
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Re: Query regarding server for GBrowse 2.52 and ./build demo

Scott Cain
In reply to this post by Scott Cain
Hi Sree,

I believe on with a yum installed apache, your html document root is
/var/www/html, so static html pages you want to see needs to be under
that directory unless you edit the apache config file.  So,
/var/www/GBrowse-2.52/htdocs will be invisible to apache,  Unless you
want to edit the apache config, it might be better to use the default
locations:

Directory for GBrowse's config and support files?
[/root/perl5/etc/gbrowse2] /etc/gbrowse2
Directory for GBrowse's static images & HTML files?
[/root/perl5/htdocs] /var/www/html/gbrowse2
Directory for GBrowse's temporary data [/root/perl5/tmp/gbrowse2]
/var/tmp/gbrowse2
Directory for GBrowse's sessions, uploaded tracks and other persistent
data [/root/perl5/lib/gbrowse2] /var/lib/gbrowse2
Directory for GBrowse's example databases
[/root/perl5/lib/gbrowse2/databases] /var/lib/gbrowse2/databases
Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
Internet port to run demo web site on (for demo)? [8000]
Apache loadable module directory (for demo)? [/etc/httpd/modules]
User account under which Apache daemon runs? [apache] apache

I'm not positive that the apache user name is apache; it might also be
httpd.  If you are installing from a downloaded tar file instead of
from the cpan shell and would like to get the default suggestions
back, you can run "./Build realclean" and it will delete all of the
saved answers from previous installation attempts.

Scott


On Mon, Dec 17, 2012 at 4:26 AM, Sree Rohit Raj <[hidden email]> wrote:

>
> Hi Scott,
>
> I did not install apache from source.
>
> My httpd service was working fine but the Gbrowse example databases page
> were not opening.
> I deleted the /usr/local/apache2 folder to reinstall later.
> So I later installed apache httpd through
> yum install httpd
>
> I tried to rebuild GBrowse by modifying the config as -
> Directory for GBrowse's config and support files? [/root/perl5/etc/gbrowse2]
> /var/www/GBrowse-2.52/conf
> Directory for GBrowse's static images & HTML files? [/root/perl5/htdocs]
> /var/www/GBrowse-2.52/htdocs
> Directory for GBrowse's temporary data [/root/perl5/tmp/gbrowse2]
> /var/www/GBrowse-2.52/tmp
> Directory for GBrowse's sessions, uploaded tracks and other persistent data
> [/root/perl5/lib/gbrowse2] /var/www/GBrowse-2.52/lib
> Directory for GBrowse's example databases
> [/root/perl5/lib/gbrowse2/databases] /var/www/GBrowse-2.52/lib
> Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
> Internet port to run demo web site on (for demo)? [8000]
> Apache loadable module directory (for demo)? [/etc/httpd/modules]
> User account under which Apache daemon runs? [apache] lmg
> Automatically update Apache config files to run GBrowse? [y] y
> Automatically update system config files to run gbrowse-slave? [y] y
>
>
> Then I started the httpd which runs fine. But now not even the GBrowse home
> page that used to open on localhost/gbrowse2 aint working. It gives a Not
> Found on server error.
> Apache2 folder is completely missing now, but httd is present in /etc/httpd
> I did not make a backup of my apache folder before deleting to retest it
> with the previous folder again.
>
> Am I in serious trouble? :(
>
> On 14 December 2012 20:32, Scott Cain <[hidden email]> wrote:
>>
>> Also, did you install apache at /usr/local/apache, typically by
>> building it from source?  And if so, is there a reason you did that
>> (like some functionality that not available in the apache that you get
>> from your linux distribution)?  If not, you should delete
>> /usr/local/apache and reinstall; the installer assumes that if you
>> have a directory called /usr/local/apache (or apache2), that you built
>> apache from source for some reason and will want to use that over the
>> one that comes with the operating system.
>>
>> Scott
>>
>>
>> On Fri, Dec 14, 2012 at 9:48 AM, Amelia Ireland <[hidden email]>
>> wrote:
>> > Hi Rohit,
>> >
>> > Which version of GBrowse are you using? Have you checked the Apache
>> > logs? If
>> > you can paste some of the errors from the Apache logs, that will help us
>> > diagnose the problem.
>> >
>> >
>> > On Fri, Dec 14, 2012 at 12:05 AM, Sree Rohit Raj <[hidden email]>
>> > wrote:
>> >>
>> >>
>> >> Dear Ameilia,
>> >>
>> >> Thank you so much for the link. I have gone through it and it helped me
>> >> in
>> >> understanding Apache a little.
>> >> My service starts with httpd and I am not getting failed message while
>> >> checking httpd status now.
>> >>
>> >> My GBrowse has been reinstalled and the start page opens with no
>> >> problem.
>> >> But when I open the gbrowse example data I face the same problem.
>> >>
>> >> http://localhost/gb2/gbrowse/yeast_advanced
>> >> Shows a 500 Internal server error.
>> >>
>> >> http://localhost/cgi-bin/gb2/gbrowse/yeast
>> >> Shows 404 Not found error.
>> >>
>> >> The server runs fine but I don't understand why this error shows up
>> >> even
>> >> when my local server is not running any other processes.
>> >> I did try to remove memory consuming programs and add-ons the last time
>> >> I
>> >> found the Internal server error itself.
>> >>
>> >> Is there still problem in my Apache or is my GBrowse not configured
>> >> properly?
>> >>
>> >> Regards,
>> >> Rohit
>> >>
>> >>
>> >> On 13 December 2012 21:44, Amelia Ireland <[hidden email]>
>> >> wrote:
>> >>>
>> >>> Good morning Rohit,
>> >>>
>> >>> This is an apache problem rather than a GBrowse problem, you're right.
>> >>> Did you try googling around for that error message you got? This looks
>> >>> like
>> >>> a similar problem, from serverfault.com:
>> >>>
>> >>>
>> >>>
>> >>> http://serverfault.com/questions/174036/trouble-starting-apache-via-apachectl
>> >>>
>> >>> There's also an explanation of what apachectl is that will answer your
>> >>> question about the differences between it and httpd. That might be of
>> >>> some
>> >>> help.
>> >>>
>> >>> On Wed, Dec 12, 2012 at 9:12 PM, Sree Rohit Raj
>> >>> <[hidden email]>
>> >>> wrote:
>> >>>>
>> >>>> ELinks: Connection refused
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Amelia Ireland
>> >>> GMOD Community Support || http://gmod.org
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> Regards...
>> >> Sree Rohit Raj. K
>> >>
>> >
>> >
>> >
>> > --
>> > Amelia Ireland
>> > GMOD Community Support || http://gmod.org
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>> > Remotely access PCs and mobile devices and provide instant support
>> > Improve your efficiency, and focus on delivering more value-add services
>> > Discover what IT Professionals Know. Rescue delivers
>> > http://p.sf.net/sfu/logmein_12329d2d
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
>
> Regards...
> Sree Rohit Raj. K
>



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

------------------------------------------------------------------------------
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Re: Query regarding server for GBrowse 2.52 and ./build demo

Rohit23

Dear Scott,

Thank you for the advice.

I reinstalled the Gbrowse with default configuration. .Build demo showed that the demo might already been running. My apache user was apache itself, which was running fine.
Now my Gbrowse is running like before on http://localhost/gbrowse2.

But the example databases are still not shown. I tried the urls on the homepage but all of them give an Internal server error. This was the problem from the beginning due to which I have been reinstalling apache and GBrowse multiple times.
How do I see the example data?
Directory for GBrowse's example databases is /root/perl5/lib/gbrowse2/databases which I had given as per default.


Regards,
Rohit

On 17 December 2012 20:10, Scott Cain <[hidden email]> wrote:
Hi Sree,

I believe on with a yum installed apache, your html document root is
/var/www/html, so static html pages you want to see needs to be under
that directory unless you edit the apache config file.  So,
/var/www/GBrowse-2.52/htdocs will be invisible to apache,  Unless you
want to edit the apache config, it might be better to use the default
locations:

Directory for GBrowse's config and support files?
[/root/perl5/etc/gbrowse2] /etc/gbrowse2
Directory for GBrowse's static images & HTML files?
[/root/perl5/htdocs] /var/www/html/gbrowse2
Directory for GBrowse's temporary data [/root/perl5/tmp/gbrowse2]
/var/tmp/gbrowse2
Directory for GBrowse's sessions, uploaded tracks and other persistent
data [/root/perl5/lib/gbrowse2] /var/lib/gbrowse2
Directory for GBrowse's example databases
[/root/perl5/lib/gbrowse2/databases] /var/lib/gbrowse2/databases
Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
Internet port to run demo web site on (for demo)? [8000]
Apache loadable module directory (for demo)? [/etc/httpd/modules]
User account under which Apache daemon runs? [apache] apache

I'm not positive that the apache user name is apache; it might also be
httpd.  If you are installing from a downloaded tar file instead of
from the cpan shell and would like to get the default suggestions
back, you can run "./Build realclean" and it will delete all of the
saved answers from previous installation attempts.

Scott


On Mon, Dec 17, 2012 at 4:26 AM, Sree Rohit Raj <[hidden email]> wrote:
>
> Hi Scott,
>
> I did not install apache from source.
>
> My httpd service was working fine but the Gbrowse example databases page
> were not opening.
> I deleted the /usr/local/apache2 folder to reinstall later.
> So I later installed apache httpd through
> yum install httpd
>
> I tried to rebuild GBrowse by modifying the config as -
> Directory for GBrowse's config and support files? [/root/perl5/etc/gbrowse2]
> /var/www/GBrowse-2.52/conf
> Directory for GBrowse's static images & HTML files? [/root/perl5/htdocs]
> /var/www/GBrowse-2.52/htdocs
> Directory for GBrowse's temporary data [/root/perl5/tmp/gbrowse2]
> /var/www/GBrowse-2.52/tmp
> Directory for GBrowse's sessions, uploaded tracks and other persistent data
> [/root/perl5/lib/gbrowse2] /var/www/GBrowse-2.52/lib
> Directory for GBrowse's example databases
> [/root/perl5/lib/gbrowse2/databases] /var/www/GBrowse-2.52/lib
> Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
> Internet port to run demo web site on (for demo)? [8000]
> Apache loadable module directory (for demo)? [/etc/httpd/modules]
> User account under which Apache daemon runs? [apache] lmg
> Automatically update Apache config files to run GBrowse? [y] y
> Automatically update system config files to run gbrowse-slave? [y] y
>
>
> Then I started the httpd which runs fine. But now not even the GBrowse home
> page that used to open on localhost/gbrowse2 aint working. It gives a Not
> Found on server error.
> Apache2 folder is completely missing now, but httd is present in /etc/httpd
> I did not make a backup of my apache folder before deleting to retest it
> with the previous folder again.
>
> Am I in serious trouble? :(
>
> On 14 December 2012 20:32, Scott Cain <[hidden email]> wrote:
>>
>> Also, did you install apache at /usr/local/apache, typically by
>> building it from source?  And if so, is there a reason you did that
>> (like some functionality that not available in the apache that you get
>> from your linux distribution)?  If not, you should delete
>> /usr/local/apache and reinstall; the installer assumes that if you
>> have a directory called /usr/local/apache (or apache2), that you built
>> apache from source for some reason and will want to use that over the
>> one that comes with the operating system.
>>
>> Scott
>>
>>
>> On Fri, Dec 14, 2012 at 9:48 AM, Amelia Ireland <[hidden email]>
>> wrote:
>> > Hi Rohit,
>> >
>> > Which version of GBrowse are you using? Have you checked the Apache
>> > logs? If
>> > you can paste some of the errors from the Apache logs, that will help us
>> > diagnose the problem.
>> >
>> >
>> > On Fri, Dec 14, 2012 at 12:05 AM, Sree Rohit Raj <[hidden email]>
>> > wrote:
>> >>
>> >>
>> >> Dear Ameilia,
>> >>
>> >> Thank you so much for the link. I have gone through it and it helped me
>> >> in
>> >> understanding Apache a little.
>> >> My service starts with httpd and I am not getting failed message while
>> >> checking httpd status now.
>> >>
>> >> My GBrowse has been reinstalled and the start page opens with no
>> >> problem.
>> >> But when I open the gbrowse example data I face the same problem.
>> >>
>> >> http://localhost/gb2/gbrowse/yeast_advanced
>> >> Shows a 500 Internal server error.
>> >>
>> >> http://localhost/cgi-bin/gb2/gbrowse/yeast
>> >> Shows 404 Not found error.
>> >>
>> >> The server runs fine but I don't understand why this error shows up
>> >> even
>> >> when my local server is not running any other processes.
>> >> I did try to remove memory consuming programs and add-ons the last time
>> >> I
>> >> found the Internal server error itself.
>> >>
>> >> Is there still problem in my Apache or is my GBrowse not configured
>> >> properly?
>> >>
>> >> Regards,
>> >> Rohit
>> >>
>> >>
>> >> On 13 December 2012 21:44, Amelia Ireland <[hidden email]>
>> >> wrote:
>> >>>
>> >>> Good morning Rohit,
>> >>>
>> >>> This is an apache problem rather than a GBrowse problem, you're right.
>> >>> Did you try googling around for that error message you got? This looks
>> >>> like
>> >>> a similar problem, from serverfault.com:
>> >>>
>> >>>
>> >>>
>> >>> http://serverfault.com/questions/174036/trouble-starting-apache-via-apachectl
>> >>>
>> >>> There's also an explanation of what apachectl is that will answer your
>> >>> question about the differences between it and httpd. That might be of
>> >>> some
>> >>> help.
>> >>>
>> >>> On Wed, Dec 12, 2012 at 9:12 PM, Sree Rohit Raj
>> >>> <[hidden email]>
>> >>> wrote:
>> >>>>
>> >>>> ELinks: Connection refused
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Amelia Ireland
>> >>> GMOD Community Support || http://gmod.org
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> Regards...
>> >> Sree Rohit Raj. K
>> >>
>> >
>> >
>> >
>> > --
>> > Amelia Ireland
>> > GMOD Community Support || http://gmod.org
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>> > Remotely access PCs and mobile devices and provide instant support
>> > Improve your efficiency, and focus on delivering more value-add services
>> > Discover what IT Professionals Know. Rescue delivers
>> > http://p.sf.net/sfu/logmein_12329d2d
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
>
> Regards...
> Sree Rohit Raj. K
>



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



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Re: Query regarding server for GBrowse 2.52 and ./build demo

Scott Cain
Hi Rohit,

The GBrowse installer would never suggest anywhere in /root to install
anything related to GBrowse; could it be using that from a previous
installation attempt?  The GBrowse installer remembers from one
attempt at installation to the next what was used; that's why I
suggested ./Build realclean, though on thinking about it, I'm not
positive that "realclean" does it.  Certainly, you can try "./Build
reconfig" and when it asks you if you want to use previous values,
answer no.

Scott


On Tue, Dec 18, 2012 at 1:49 AM, Sree Rohit Raj <[hidden email]> wrote:

>
> Dear Scott,
>
> Thank you for the advice.
>
> I reinstalled the Gbrowse with default configuration. .Build demo showed
> that the demo might already been running. My apache user was apache itself,
> which was running fine.
> Now my Gbrowse is running like before on http://localhost/gbrowse2.
>
> But the example databases are still not shown. I tried the urls on the
> homepage but all of them give an Internal server error. This was the problem
> from the beginning due to which I have been reinstalling apache and GBrowse
> multiple times.
> How do I see the example data?
> Directory for GBrowse's example databases is
> /root/perl5/lib/gbrowse2/databases which I had given as per default.
>
>
> Regards,
> Rohit
>
>
> On 17 December 2012 20:10, Scott Cain <[hidden email]> wrote:
>>
>> Hi Sree,
>>
>> I believe on with a yum installed apache, your html document root is
>> /var/www/html, so static html pages you want to see needs to be under
>> that directory unless you edit the apache config file.  So,
>> /var/www/GBrowse-2.52/htdocs will be invisible to apache,  Unless you
>> want to edit the apache config, it might be better to use the default
>> locations:
>>
>> Directory for GBrowse's config and support files?
>> [/root/perl5/etc/gbrowse2] /etc/gbrowse2
>> Directory for GBrowse's static images & HTML files?
>> [/root/perl5/htdocs] /var/www/html/gbrowse2
>> Directory for GBrowse's temporary data [/root/perl5/tmp/gbrowse2]
>> /var/tmp/gbrowse2
>> Directory for GBrowse's sessions, uploaded tracks and other persistent
>> data [/root/perl5/lib/gbrowse2] /var/lib/gbrowse2
>> Directory for GBrowse's example databases
>> [/root/perl5/lib/gbrowse2/databases] /var/lib/gbrowse2/databases
>> Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
>> Internet port to run demo web site on (for demo)? [8000]
>> Apache loadable module directory (for demo)? [/etc/httpd/modules]
>> User account under which Apache daemon runs? [apache] apache
>>
>> I'm not positive that the apache user name is apache; it might also be
>> httpd.  If you are installing from a downloaded tar file instead of
>> from the cpan shell and would like to get the default suggestions
>> back, you can run "./Build realclean" and it will delete all of the
>> saved answers from previous installation attempts.
>>
>> Scott
>>
>>
>> On Mon, Dec 17, 2012 at 4:26 AM, Sree Rohit Raj <[hidden email]>
>> wrote:
>> >
>> > Hi Scott,
>> >
>> > I did not install apache from source.
>> >
>> > My httpd service was working fine but the Gbrowse example databases page
>> > were not opening.
>> > I deleted the /usr/local/apache2 folder to reinstall later.
>> > So I later installed apache httpd through
>> > yum install httpd
>> >
>> > I tried to rebuild GBrowse by modifying the config as -
>> > Directory for GBrowse's config and support files?
>> > [/root/perl5/etc/gbrowse2]
>> > /var/www/GBrowse-2.52/conf
>> > Directory for GBrowse's static images & HTML files? [/root/perl5/htdocs]
>> > /var/www/GBrowse-2.52/htdocs
>> > Directory for GBrowse's temporary data [/root/perl5/tmp/gbrowse2]
>> > /var/www/GBrowse-2.52/tmp
>> > Directory for GBrowse's sessions, uploaded tracks and other persistent
>> > data
>> > [/root/perl5/lib/gbrowse2] /var/www/GBrowse-2.52/lib
>> > Directory for GBrowse's example databases
>> > [/root/perl5/lib/gbrowse2/databases] /var/www/GBrowse-2.52/lib
>> > Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2]
>> > Internet port to run demo web site on (for demo)? [8000]
>> > Apache loadable module directory (for demo)? [/etc/httpd/modules]
>> > User account under which Apache daemon runs? [apache] lmg
>> > Automatically update Apache config files to run GBrowse? [y] y
>> > Automatically update system config files to run gbrowse-slave? [y] y
>> >
>> >
>> > Then I started the httpd which runs fine. But now not even the GBrowse
>> > home
>> > page that used to open on localhost/gbrowse2 aint working. It gives a
>> > Not
>> > Found on server error.
>> > Apache2 folder is completely missing now, but httd is present in
>> > /etc/httpd
>> > I did not make a backup of my apache folder before deleting to retest it
>> > with the previous folder again.
>> >
>> > Am I in serious trouble? :(
>> >
>> > On 14 December 2012 20:32, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Also, did you install apache at /usr/local/apache, typically by
>> >> building it from source?  And if so, is there a reason you did that
>> >> (like some functionality that not available in the apache that you get
>> >> from your linux distribution)?  If not, you should delete
>> >> /usr/local/apache and reinstall; the installer assumes that if you
>> >> have a directory called /usr/local/apache (or apache2), that you built
>> >> apache from source for some reason and will want to use that over the
>> >> one that comes with the operating system.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Fri, Dec 14, 2012 at 9:48 AM, Amelia Ireland
>> >> <[hidden email]>
>> >> wrote:
>> >> > Hi Rohit,
>> >> >
>> >> > Which version of GBrowse are you using? Have you checked the Apache
>> >> > logs? If
>> >> > you can paste some of the errors from the Apache logs, that will help
>> >> > us
>> >> > diagnose the problem.
>> >> >
>> >> >
>> >> > On Fri, Dec 14, 2012 at 12:05 AM, Sree Rohit Raj
>> >> > <[hidden email]>
>> >> > wrote:
>> >> >>
>> >> >>
>> >> >> Dear Ameilia,
>> >> >>
>> >> >> Thank you so much for the link. I have gone through it and it helped
>> >> >> me
>> >> >> in
>> >> >> understanding Apache a little.
>> >> >> My service starts with httpd and I am not getting failed message
>> >> >> while
>> >> >> checking httpd status now.
>> >> >>
>> >> >> My GBrowse has been reinstalled and the start page opens with no
>> >> >> problem.
>> >> >> But when I open the gbrowse example data I face the same problem.
>> >> >>
>> >> >> http://localhost/gb2/gbrowse/yeast_advanced
>> >> >> Shows a 500 Internal server error.
>> >> >>
>> >> >> http://localhost/cgi-bin/gb2/gbrowse/yeast
>> >> >> Shows 404 Not found error.
>> >> >>
>> >> >> The server runs fine but I don't understand why this error shows up
>> >> >> even
>> >> >> when my local server is not running any other processes.
>> >> >> I did try to remove memory consuming programs and add-ons the last
>> >> >> time
>> >> >> I
>> >> >> found the Internal server error itself.
>> >> >>
>> >> >> Is there still problem in my Apache or is my GBrowse not configured
>> >> >> properly?
>> >> >>
>> >> >> Regards,
>> >> >> Rohit
>> >> >>
>> >> >>
>> >> >> On 13 December 2012 21:44, Amelia Ireland <[hidden email]>
>> >> >> wrote:
>> >> >>>
>> >> >>> Good morning Rohit,
>> >> >>>
>> >> >>> This is an apache problem rather than a GBrowse problem, you're
>> >> >>> right.
>> >> >>> Did you try googling around for that error message you got? This
>> >> >>> looks
>> >> >>> like
>> >> >>> a similar problem, from serverfault.com:
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> http://serverfault.com/questions/174036/trouble-starting-apache-via-apachectl
>> >> >>>
>> >> >>> There's also an explanation of what apachectl is that will answer
>> >> >>> your
>> >> >>> question about the differences between it and httpd. That might be
>> >> >>> of
>> >> >>> some
>> >> >>> help.
>> >> >>>
>> >> >>> On Wed, Dec 12, 2012 at 9:12 PM, Sree Rohit Raj
>> >> >>> <[hidden email]>
>> >> >>> wrote:
>> >> >>>>
>> >> >>>> ELinks: Connection refused
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> --
>> >> >>> Amelia Ireland
>> >> >>> GMOD Community Support || http://gmod.org
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >> Regards...
>> >> >> Sree Rohit Raj. K
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Amelia Ireland
>> >> > GMOD Community Support || http://gmod.org
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>> >> > Remotely access PCs and mobile devices and provide instant support
>> >> > Improve your efficiency, and focus on delivering more value-add
>> >> > services
>> >> > Discover what IT Professionals Know. Rescue delivers
>> >> > http://p.sf.net/sfu/logmein_12329d2d
>> >> > _______________________________________________
>> >> > Gmod-gbrowse mailing list
>> >> > [hidden email]
>> >> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> >
>> >
>> > --
>> >
>> > Regards...
>> > Sree Rohit Raj. K
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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

------------------------------------------------------------------------------
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Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
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