Local Installation of Webgbrowse: Error with configureTracks: Permission Denied

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Local Installation of Webgbrowse: Error with configureTracks: Permission Denied

Prakhar Gaur
Hello,

I have a local installation of WebGbrowse.

The upload data page is working, but when I select the test gff3 file
and click submit button, this msg is displayed.
"
Not Found

The requested URL /cgi-bin/errorpage was not found on this server.

Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80
"
See the attached screenshot.

Also the url bar has unusual content.
"<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
20denied"

Is this the problem? Permission denied for what?

Thanking you,
--
Prakhar Gaur

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Re: Local Installation of Webgbrowse: Error with configureTracks: Permission Denied

Ram Podicheti-2
Hi Prakhar,
There are two things that might be going wrong.

1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
                Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
                Ensure that this folder exists and it has write permissions for Apache.
                Fixing this should let your program run without any issues.

2. The file errorpage is not in the location specified.
                This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.

Thanks,

Ram

-----Original Message-----
From: Prakhar Gaur [mailto:[hidden email]]
Sent: Monday, June 04, 2012 5:18 AM
To: [hidden email]
Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied

Hello,

I have a local installation of WebGbrowse.

The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
"
Not Found

The requested URL /cgi-bin/errorpage was not found on this server.

Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
See the attached screenshot.

Also the url bar has unusual content.
"<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
20denied"

Is this the problem? Permission denied for what?

Thanking you,
--
Prakhar Gaur
------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Local Installation of Webgbrowse: Error with configureTracks: Permission Denied

Ram Podicheti-2
Hi Prakhar,
It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.

Go to line number 167 in the file WebGB.pm. Change the line:

return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");

to

return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");

That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.

Thanks,

Ram



-----Original Message-----
From: Podicheti, Ram [mailto:[hidden email]]
Sent: Monday, June 04, 2012 8:39 AM
To: Prakhar Gaur; [hidden email]
Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied

Hi Prakhar,
There are two things that might be going wrong.

1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
                Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
                Ensure that this folder exists and it has write permissions for Apache.
                Fixing this should let your program run without any issues.

2. The file errorpage is not in the location specified.
                This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.

Thanks,

Ram

-----Original Message-----
From: Prakhar Gaur [mailto:[hidden email]]
Sent: Monday, June 04, 2012 5:18 AM
To: [hidden email]
Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied

Hello,

I have a local installation of WebGbrowse.

The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
"
Not Found

The requested URL /cgi-bin/errorpage was not found on this server.

Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
See the attached screenshot.

Also the url bar has unusual content.
"<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
20denied"

Is this the problem? Permission denied for what?

Thanking you,
--
Prakhar Gaur
------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse

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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
Hello Ram,

Thank you for the help.
We have another issue now,
Now I am getting the Configure Track web-page and am able to configure
tracks.

But when I click "Display In Gbrowse2.0", I get an "internal server
error" page.
Please find the screen shot attached.


The previous issue was due to the permissions on the tmp folder.
I changed folder owner to "apache" and group to "root".
The tarball was downloaded from the Webgbrowse website, last week.


Thanking you,
--
Prakhar Gaur








On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:

> Hi Prakhar,
> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>
> Go to line number 167 in the file WebGB.pm. Change the line:
>
> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>
> to
>
> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>
> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>
> Thanks,
>
> Ram
>
>
>
> -----Original Message-----
> From: Podicheti, Ram [mailto:[hidden email]]
> Sent: Monday, June 04, 2012 8:39 AM
> To: Prakhar Gaur; [hidden email]
> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>
> Hi Prakhar,
> There are two things that might be going wrong.
>
> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
> Ensure that this folder exists and it has write permissions for Apache.
> Fixing this should let your program run without any issues.
>
> 2. The file errorpage is not in the location specified.
> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>
> Thanks,
>
> Ram
>
> -----Original Message-----
> From: Prakhar Gaur [mailto:[hidden email]]
> Sent: Monday, June 04, 2012 5:18 AM
> To: [hidden email]
> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>
> Hello,
>
> I have a local installation of WebGbrowse.
>
> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
> "
> Not Found
>
> The requested URL /cgi-bin/errorpage was not found on this server.
>
> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
> See the attached screenshot.
>
> Also the url bar has unusual content.
> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
> 20denied"
>
> Is this the problem? Permission denied for what?
>
> Thanking you,
> --
> Prakhar Gaur
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-webgbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse


------------------------------------------------------------------------------
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will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Ram Podicheti-2
Hi Prakhar,
I am not sure why you are getting the internal server error. There must
be a more useful error message apache must be spitting in the error.log
file. Can you verify that?
Thanks,

Ram

Prakhar Gaur wrote:

> Hello Ram,
>
> Thank you for the help.
> We have another issue now,
> Now I am getting the Configure Track web-page and am able to configure
> tracks.
>
> But when I click "Display In Gbrowse2.0", I get an "internal server
> error" page.
> Please find the screen shot attached.
>
>
> The previous issue was due to the permissions on the tmp folder.
> I changed folder owner to "apache" and group to "root".
> The tarball was downloaded from the Webgbrowse website, last week.
>
>
> Thanking you,
> --
> Prakhar Gaur
>
>
>
>
>
>
>
>
> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>  
>> Hi Prakhar,
>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>
>> Go to line number 167 in the file WebGB.pm. Change the line:
>>
>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>
>> to
>>
>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>
>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>
>> Thanks,
>>
>> Ram
>>
>>
>>
>> -----Original Message-----
>> From: Podicheti, Ram [mailto:[hidden email]]
>> Sent: Monday, June 04, 2012 8:39 AM
>> To: Prakhar Gaur; [hidden email]
>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>
>> Hi Prakhar,
>> There are two things that might be going wrong.
>>
>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>> Ensure that this folder exists and it has write permissions for Apache.
>> Fixing this should let your program run without any issues.
>>
>> 2. The file errorpage is not in the location specified.
>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>
>> Thanks,
>>
>> Ram
>>
>> -----Original Message-----
>> From: Prakhar Gaur [mailto:[hidden email]]
>> Sent: Monday, June 04, 2012 5:18 AM
>> To: [hidden email]
>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>
>> Hello,
>>
>> I have a local installation of WebGbrowse.
>>
>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>> "
>> Not Found
>>
>> The requested URL /cgi-bin/errorpage was not found on this server.
>>
>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>> See the attached screenshot.
>>
>> Also the url bar has unusual content.
>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>> 20denied"
>>
>> Is this the problem? Permission denied for what?
>>
>> Thanking you,
>> --
>> Prakhar Gaur
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Gmod-webgbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>    
>
>
>  
>
> ------------------------------------------------------------------------
>


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will include endpoint security, mobile security and the latest in malware
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
Hello Ram,

I just repeated the steps and then shecked the apache error and access
log file.
The error log file has 3 lines, pertaining to that period of time,

[Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
exist: /var/www/html/favicon.ico
[Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
line 160., referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
[Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
of script headers: generateConfigurationData2.0, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b


Thanking you,
--
Prakhar Gaur



On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:

> Hi Prakhar,
> I am not sure why you are getting the internal server error. There must
> be a more useful error message apache must be spitting in the error.log
> file. Can you verify that?
> Thanks,
>
> Ram
>
> Prakhar Gaur wrote:
> > Hello Ram,
> >
> > Thank you for the help.
> > We have another issue now,
> > Now I am getting the Configure Track web-page and am able to configure
> > tracks.
> >
> > But when I click "Display In Gbrowse2.0", I get an "internal server
> > error" page.
> > Please find the screen shot attached.
> >
> >
> > The previous issue was due to the permissions on the tmp folder.
> > I changed folder owner to "apache" and group to "root".
> > The tarball was downloaded from the Webgbrowse website, last week.
> >
> >
> > Thanking you,
> > --
> > Prakhar Gaur
> >
> >
> >
> >
> >
> >
> >
> >
> > On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
> >  
> >> Hi Prakhar,
> >> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
> >>
> >> Go to line number 167 in the file WebGB.pm. Change the line:
> >>
> >> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
> >>
> >> to
> >>
> >> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
> >>
> >> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
> >>
> >> Thanks,
> >>
> >> Ram
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: Podicheti, Ram [mailto:[hidden email]]
> >> Sent: Monday, June 04, 2012 8:39 AM
> >> To: Prakhar Gaur; [hidden email]
> >> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
> >>
> >> Hi Prakhar,
> >> There are two things that might be going wrong.
> >>
> >> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
> >> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
> >> Ensure that this folder exists and it has write permissions for Apache.
> >> Fixing this should let your program run without any issues.
> >>
> >> 2. The file errorpage is not in the location specified.
> >> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
> >>
> >> Thanks,
> >>
> >> Ram
> >>
> >> -----Original Message-----
> >> From: Prakhar Gaur [mailto:[hidden email]]
> >> Sent: Monday, June 04, 2012 5:18 AM
> >> To: [hidden email]
> >> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
> >>
> >> Hello,
> >>
> >> I have a local installation of WebGbrowse.
> >>
> >> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
> >> "
> >> Not Found
> >>
> >> The requested URL /cgi-bin/errorpage was not found on this server.
> >>
> >> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
> >> See the attached screenshot.
> >>
> >> Also the url bar has unusual content.
> >> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
> >> 20denied"
> >>
> >> Is this the problem? Permission denied for what?
> >>
> >> Thanking you,
> >> --
> >> Prakhar Gaur
> >> ------------------------------------------------------------------------------
> >> Live Security Virtual Conference
> >> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >> _______________________________________________
> >> Gmod-webgbrowse mailing list
> >> [hidden email]
> >> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
> >>    
> >
> >
> >  
> >
> > ------------------------------------------------------------------------
> >
>



------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Ram Podicheti-2
Prakhar,
I am sorry for all these errors. Can you open your script

/var/www/cgi-bin/webgbrowse/generateConfigurationData2.0

and go to line 160 and change it from

-location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
$timeStampDigest

to

-location =>
"http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"

I don't know how it is working on our server in the first place, but
using single quotes was obviously a bug. I will be fixing it in the
repository. Thanks for reporting these issues, they shouldn't have been
there but at least I am fixing them now. Do let me know if you run into
more issues.

Thanks,

Ram

Prakhar Gaur wrote:

> Hello Ram,
>
> I just repeated the steps and then shecked the apache error and access
> log file.
> The error log file has 3 lines, pertaining to that period of time,
>
> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
> exist: /var/www/html/favicon.ico
> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
> line 160., referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
> of script headers: generateConfigurationData2.0, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>
>
> Thanking you,
> --
> Prakhar Gaur
>
>
>
> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>  
>> Hi Prakhar,
>> I am not sure why you are getting the internal server error. There must
>> be a more useful error message apache must be spitting in the error.log
>> file. Can you verify that?
>> Thanks,
>>
>> Ram
>>
>> Prakhar Gaur wrote:
>>    
>>> Hello Ram,
>>>
>>> Thank you for the help.
>>> We have another issue now,
>>> Now I am getting the Configure Track web-page and am able to configure
>>> tracks.
>>>
>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>> error" page.
>>> Please find the screen shot attached.
>>>
>>>
>>> The previous issue was due to the permissions on the tmp folder.
>>> I changed folder owner to "apache" and group to "root".
>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>  
>>>      
>>>> Hi Prakhar,
>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>
>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>
>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>
>>>> to
>>>>
>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>
>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Podicheti, Ram [mailto:[hidden email]]
>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>> To: Prakhar Gaur; [hidden email]
>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>
>>>> Hi Prakhar,
>>>> There are two things that might be going wrong.
>>>>
>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>> Fixing this should let your program run without any issues.
>>>>
>>>> 2. The file errorpage is not in the location specified.
>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> -----Original Message-----
>>>> From: Prakhar Gaur [mailto:[hidden email]]
>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>> To: [hidden email]
>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>
>>>> Hello,
>>>>
>>>> I have a local installation of WebGbrowse.
>>>>
>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>> "
>>>> Not Found
>>>>
>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>
>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>> See the attached screenshot.
>>>>
>>>> Also the url bar has unusual content.
>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>> 20denied"
>>>>
>>>> Is this the problem? Permission denied for what?
>>>>
>>>> Thanking you,
>>>> --
>>>> Prakhar Gaur
>>>> ------------------------------------------------------------------------------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Gmod-webgbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>    
>>>>        
>>>  
>>>
>>> ------------------------------------------------------------------------
>>>
>>>      
>
>
>  


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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
Hello,

On repeating the process, its still not working, getting the same
Internal Server Error.
The relevant line from the error log is below.

[Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
exist: /var/www/html/favicon.ico
[Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
conf
file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
[Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
of script headers: generateConfigurationData2.0, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0



Thanking you,
--
Prakhar Gaur



On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:

> Prakhar,
> I am sorry for all these errors. Can you open your script
>
> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>
> and go to line 160 and change it from
>
> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
> $timeStampDigest
>
> to
>
> -location =>
> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>
> I don't know how it is working on our server in the first place, but
> using single quotes was obviously a bug. I will be fixing it in the
> repository. Thanks for reporting these issues, they shouldn't have been
> there but at least I am fixing them now. Do let me know if you run into
> more issues.
>
> Thanks,
>
> Ram
>
> Prakhar Gaur wrote:
> > Hello Ram,
> >
> > I just repeated the steps and then shecked the apache error and access
> > log file.
> > The error log file has 3 lines, pertaining to that period of time,
> >
> > [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
> > exist: /var/www/html/favicon.ico
> > [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
> > SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
> > line 160., referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
> > [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
> > of script headers: generateConfigurationData2.0, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
> >
> >
> > Thanking you,
> > --
> > Prakhar Gaur
> >
> >
> >
> > On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
> >  
> >> Hi Prakhar,
> >> I am not sure why you are getting the internal server error. There must
> >> be a more useful error message apache must be spitting in the error.log
> >> file. Can you verify that?
> >> Thanks,
> >>
> >> Ram
> >>
> >> Prakhar Gaur wrote:
> >>    
> >>> Hello Ram,
> >>>
> >>> Thank you for the help.
> >>> We have another issue now,
> >>> Now I am getting the Configure Track web-page and am able to configure
> >>> tracks.
> >>>
> >>> But when I click "Display In Gbrowse2.0", I get an "internal server
> >>> error" page.
> >>> Please find the screen shot attached.
> >>>
> >>>
> >>> The previous issue was due to the permissions on the tmp folder.
> >>> I changed folder owner to "apache" and group to "root".
> >>> The tarball was downloaded from the Webgbrowse website, last week.
> >>>
> >>>
> >>> Thanking you,
> >>> --
> >>> Prakhar Gaur
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
> >>>  
> >>>      
> >>>> Hi Prakhar,
> >>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
> >>>>
> >>>> Go to line number 167 in the file WebGB.pm. Change the line:
> >>>>
> >>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
> >>>>
> >>>> to
> >>>>
> >>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
> >>>>
> >>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Ram
> >>>>
> >>>>
> >>>>
> >>>> -----Original Message-----
> >>>> From: Podicheti, Ram [mailto:[hidden email]]
> >>>> Sent: Monday, June 04, 2012 8:39 AM
> >>>> To: Prakhar Gaur; [hidden email]
> >>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
> >>>>
> >>>> Hi Prakhar,
> >>>> There are two things that might be going wrong.
> >>>>
> >>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
> >>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
> >>>> Ensure that this folder exists and it has write permissions for Apache.
> >>>> Fixing this should let your program run without any issues.
> >>>>
> >>>> 2. The file errorpage is not in the location specified.
> >>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Ram
> >>>>
> >>>> -----Original Message-----
> >>>> From: Prakhar Gaur [mailto:[hidden email]]
> >>>> Sent: Monday, June 04, 2012 5:18 AM
> >>>> To: [hidden email]
> >>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
> >>>>
> >>>> Hello,
> >>>>
> >>>> I have a local installation of WebGbrowse.
> >>>>
> >>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
> >>>> "
> >>>> Not Found
> >>>>
> >>>> The requested URL /cgi-bin/errorpage was not found on this server.
> >>>>
> >>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
> >>>> See the attached screenshot.
> >>>>
> >>>> Also the url bar has unusual content.
> >>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
> >>>> 20denied"
> >>>>
> >>>> Is this the problem? Permission denied for what?
> >>>>
> >>>> Thanking you,
> >>>> --
> >>>> Prakhar Gaur
> >>>> ------------------------------------------------------------------------------
> >>>> Live Security Virtual Conference
> >>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >>>> _______________________________________________
> >>>> Gmod-webgbrowse mailing list
> >>>> [hidden email]
> >>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
> >>>>    
> >>>>        
> >>>  
> >>>
> >>> ------------------------------------------------------------------------
> >>>
> >>>      
> >
> >
> >  
>



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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Ram Podicheti-2
This looks to me like another permission issue. Can you please check if
apache has permissions to write to the folder

/etc/gbrowse2/GBrowse.conf/


The program is trying to create a file
/etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
not able to do so.

Ram


Prakhar Gaur wrote:

> Hello,
>
> On repeating the process, its still not working, getting the same
> Internal Server Error.
> The relevant line from the error log is below.
>
> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
> exist: /var/www/html/favicon.ico
> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
> conf
> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
> referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
> of script headers: generateConfigurationData2.0, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>
>
>
> Thanking you,
> --
> Prakhar Gaur
>
>
>
> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>  
>> Prakhar,
>> I am sorry for all these errors. Can you open your script
>>
>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>
>> and go to line 160 and change it from
>>
>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>> $timeStampDigest
>>
>> to
>>
>> -location =>
>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>
>> I don't know how it is working on our server in the first place, but
>> using single quotes was obviously a bug. I will be fixing it in the
>> repository. Thanks for reporting these issues, they shouldn't have been
>> there but at least I am fixing them now. Do let me know if you run into
>> more issues.
>>
>> Thanks,
>>
>> Ram
>>
>> Prakhar Gaur wrote:
>>    
>>> Hello Ram,
>>>
>>> I just repeated the steps and then shecked the apache error and access
>>> log file.
>>> The error log file has 3 lines, pertaining to that period of time,
>>>
>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>> line 160., referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>  
>>>      
>>>> Hi Prakhar,
>>>> I am not sure why you are getting the internal server error. There must
>>>> be a more useful error message apache must be spitting in the error.log
>>>> file. Can you verify that?
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>    
>>>>        
>>>>> Hello Ram,
>>>>>
>>>>> Thank you for the help.
>>>>> We have another issue now,
>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>> tracks.
>>>>>
>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>> error" page.
>>>>> Please find the screen shot attached.
>>>>>
>>>>>
>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>> I changed folder owner to "apache" and group to "root".
>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>  
>>>>>      
>>>>>          
>>>>>> Hi Prakhar,
>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>
>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>
>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>
>>>>>> to
>>>>>>
>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>
>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Podicheti, Ram [mailto:[hidden email]]
>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>> To: Prakhar Gaur; [hidden email]
>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>
>>>>>> Hi Prakhar,
>>>>>> There are two things that might be going wrong.
>>>>>>
>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>> Fixing this should let your program run without any issues.
>>>>>>
>>>>>> 2. The file errorpage is not in the location specified.
>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Prakhar Gaur [mailto:[hidden email]]
>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>> To: [hidden email]
>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I have a local installation of WebGbrowse.
>>>>>>
>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>> "
>>>>>> Not Found
>>>>>>
>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>
>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>> See the attached screenshot.
>>>>>>
>>>>>> Also the url bar has unusual content.
>>>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>> 20denied"
>>>>>>
>>>>>> Is this the problem? Permission denied for what?
>>>>>>
>>>>>> Thanking you,
>>>>>> --
>>>>>> Prakhar Gaur
>>>>>> ------------------------------------------------------------------------------
>>>>>> Live Security Virtual Conference
>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>> _______________________________________________
>>>>>> Gmod-webgbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>  
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>>      
>>>>>          
>>>  
>>>      
>
>
>
>  


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will include endpoint security, mobile security and the latest in malware
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
Hello,

I checked and double checked.
The folder group is set to 'root' and I have set all permissions to full
access.
$ls -lh
   drwxrwxrwx.  7 ganit root   4.0K Jun  4 22:08 gbrowse2

I have also added user "apache" to group "root".
If this is not the way, then how to give apache access ?

--
Prakhar Gaur


On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:

> This looks to me like another permission issue. Can you please check if
> apache has permissions to write to the folder
>
> /etc/gbrowse2/GBrowse.conf/
>
>
> The program is trying to create a file
> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
> not able to do so.
>
> Ram
>
>
> Prakhar Gaur wrote:
> > Hello,
> >
> > On repeating the process, its still not working, getting the same
> > Internal Server Error.
> > The relevant line from the error log is below.
> >
> > [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
> > exist: /var/www/html/favicon.ico
> > [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
> > conf
> > file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
> > at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
> > referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
> > [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
> > of script headers: generateConfigurationData2.0, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
> >
> >
> >
> > Thanking you,
> > --
> > Prakhar Gaur
> >
> >
> >
> > On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
> >  
> >> Prakhar,
> >> I am sorry for all these errors. Can you open your script
> >>
> >> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
> >>
> >> and go to line 160 and change it from
> >>
> >> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
> >> $timeStampDigest
> >>
> >> to
> >>
> >> -location =>
> >> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
> >>
> >> I don't know how it is working on our server in the first place, but
> >> using single quotes was obviously a bug. I will be fixing it in the
> >> repository. Thanks for reporting these issues, they shouldn't have been
> >> there but at least I am fixing them now. Do let me know if you run into
> >> more issues.
> >>
> >> Thanks,
> >>
> >> Ram
> >>
> >> Prakhar Gaur wrote:
> >>    
> >>> Hello Ram,
> >>>
> >>> I just repeated the steps and then shecked the apache error and access
> >>> log file.
> >>> The error log file has 3 lines, pertaining to that period of time,
> >>>
> >>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
> >>> exist: /var/www/html/favicon.ico
> >>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
> >>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
> >>> line 160., referer:
> >>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
> >>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
> >>> of script headers: generateConfigurationData2.0, referer:
> >>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
> >>>
> >>>
> >>> Thanking you,
> >>> --
> >>> Prakhar Gaur
> >>>
> >>>
> >>>
> >>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
> >>>  
> >>>      
> >>>> Hi Prakhar,
> >>>> I am not sure why you are getting the internal server error. There must
> >>>> be a more useful error message apache must be spitting in the error.log
> >>>> file. Can you verify that?
> >>>> Thanks,
> >>>>
> >>>> Ram
> >>>>
> >>>> Prakhar Gaur wrote:
> >>>>    
> >>>>        
> >>>>> Hello Ram,
> >>>>>
> >>>>> Thank you for the help.
> >>>>> We have another issue now,
> >>>>> Now I am getting the Configure Track web-page and am able to configure
> >>>>> tracks.
> >>>>>
> >>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
> >>>>> error" page.
> >>>>> Please find the screen shot attached.
> >>>>>
> >>>>>
> >>>>> The previous issue was due to the permissions on the tmp folder.
> >>>>> I changed folder owner to "apache" and group to "root".
> >>>>> The tarball was downloaded from the Webgbrowse website, last week.
> >>>>>
> >>>>>
> >>>>> Thanking you,
> >>>>> --
> >>>>> Prakhar Gaur
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
> >>>>>  
> >>>>>      
> >>>>>          
> >>>>>> Hi Prakhar,
> >>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
> >>>>>>
> >>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
> >>>>>>
> >>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
> >>>>>>
> >>>>>> to
> >>>>>>
> >>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
> >>>>>>
> >>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
> >>>>>>
> >>>>>> Thanks,
> >>>>>>
> >>>>>> Ram
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: Podicheti, Ram [mailto:[hidden email]]
> >>>>>> Sent: Monday, June 04, 2012 8:39 AM
> >>>>>> To: Prakhar Gaur; [hidden email]
> >>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
> >>>>>>
> >>>>>> Hi Prakhar,
> >>>>>> There are two things that might be going wrong.
> >>>>>>
> >>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
> >>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
> >>>>>> Ensure that this folder exists and it has write permissions for Apache.
> >>>>>> Fixing this should let your program run without any issues.
> >>>>>>
> >>>>>> 2. The file errorpage is not in the location specified.
> >>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
> >>>>>>
> >>>>>> Thanks,
> >>>>>>
> >>>>>> Ram
> >>>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: Prakhar Gaur [mailto:[hidden email]]
> >>>>>> Sent: Monday, June 04, 2012 5:18 AM
> >>>>>> To: [hidden email]
> >>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
> >>>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> I have a local installation of WebGbrowse.
> >>>>>>
> >>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
> >>>>>> "
> >>>>>> Not Found
> >>>>>>
> >>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
> >>>>>>
> >>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
> >>>>>> See the attached screenshot.
> >>>>>>
> >>>>>> Also the url bar has unusual content.
> >>>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
> >>>>>> 20denied"
> >>>>>>
> >>>>>> Is this the problem? Permission denied for what?
> >>>>>>
> >>>>>> Thanking you,
> >>>>>> --
> >>>>>> Prakhar Gaur
> >>>>>> ------------------------------------------------------------------------------
> >>>>>> Live Security Virtual Conference
> >>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >>>>>> _______________________________________________
> >>>>>> Gmod-webgbrowse mailing list
> >>>>>> [hidden email]
> >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
> >>>>>>    
> >>>>>>        
> >>>>>>            
> >>>>>  
> >>>>>
> >>>>> ------------------------------------------------------------------------
> >>>>>
> >>>>>      
> >>>>>          
> >>>  
> >>>      
> >
> >
> >
> >  
>



------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Ram Podicheti-2
I think you set the value for $CONF2 to "/etc/gbrowse2/GBrowse.conf".
Try setting it to "/etc/gbrowse2"

Starting from GBrowse 2.0, GBrowse.conf is no longer a folder, but is a
file that has all the conf file mappings. Your conf folder needs to be
the gbrowse2 folder.


Prakhar Gaur wrote:

> Hello,
>
> I checked and double checked.
> The folder group is set to 'root' and I have set all permissions to full
> access.
> $ls -lh
>    drwxrwxrwx.  7 ganit root   4.0K Jun  4 22:08 gbrowse2
>
> I have also added user "apache" to group "root".
> If this is not the way, then how to give apache access ?
>
> --
> Prakhar Gaur
>
>
> On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:
>  
>> This looks to me like another permission issue. Can you please check if
>> apache has permissions to write to the folder
>>
>> /etc/gbrowse2/GBrowse.conf/
>>
>>
>> The program is trying to create a file
>> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
>> not able to do so.
>>
>> Ram
>>
>>
>> Prakhar Gaur wrote:
>>    
>>> Hello,
>>>
>>> On repeating the process, its still not working, getting the same
>>> Internal Server Error.
>>> The relevant line from the error log is below.
>>>
>>> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
>>> conf
>>> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
>>> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
>>> referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>>
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>>>  
>>>      
>>>> Prakhar,
>>>> I am sorry for all these errors. Can you open your script
>>>>
>>>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>
>>>> and go to line 160 and change it from
>>>>
>>>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>>>> $timeStampDigest
>>>>
>>>> to
>>>>
>>>> -location =>
>>>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>>>
>>>> I don't know how it is working on our server in the first place, but
>>>> using single quotes was obviously a bug. I will be fixing it in the
>>>> repository. Thanks for reporting these issues, they shouldn't have been
>>>> there but at least I am fixing them now. Do let me know if you run into
>>>> more issues.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>    
>>>>        
>>>>> Hello Ram,
>>>>>
>>>>> I just repeated the steps and then shecked the apache error and access
>>>>> log file.
>>>>> The error log file has 3 lines, pertaining to that period of time,
>>>>>
>>>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>>>> exist: /var/www/html/favicon.ico
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>> line 160., referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>>>> of script headers: generateConfigurationData2.0, referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>>>  
>>>>>      
>>>>>          
>>>>>> Hi Prakhar,
>>>>>> I am not sure why you are getting the internal server error. There must
>>>>>> be a more useful error message apache must be spitting in the error.log
>>>>>> file. Can you verify that?
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> Prakhar Gaur wrote:
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>>> Hello Ram,
>>>>>>>
>>>>>>> Thank you for the help.
>>>>>>> We have another issue now,
>>>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>>>> tracks.
>>>>>>>
>>>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>>>> error" page.
>>>>>>> Please find the screen shot attached.
>>>>>>>
>>>>>>>
>>>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>>>> I changed folder owner to "apache" and group to "root".
>>>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>>>
>>>>>>>
>>>>>>> Thanking you,
>>>>>>> --
>>>>>>> Prakhar Gaur
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>>>  
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>>>> Hi Prakhar,
>>>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>>>
>>>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Podicheti, Ram [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>>>> To: Prakhar Gaur; [hidden email]
>>>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> There are two things that might be going wrong.
>>>>>>>>
>>>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>>>> Fixing this should let your program run without any issues.
>>>>>>>>
>>>>>>>> 2. The file errorpage is not in the location specified.
>>>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Prakhar Gaur [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>>>> To: [hidden email]
>>>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have a local installation of WebGbrowse.
>>>>>>>>
>>>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>>>> "
>>>>>>>> Not Found
>>>>>>>>
>>>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>>>
>>>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>>>> See the attached screenshot.
>>>>>>>>
>>>>>>>> Also the url bar has unusual content.
>>>>>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>>>> 20denied"
>>>>>>>>
>>>>>>>> Is this the problem? Permission denied for what?
>>>>>>>>
>>>>>>>> Thanking you,
>>>>>>>> --
>>>>>>>> Prakhar Gaur
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Live Security Virtual Conference
>>>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-webgbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>>>    
>>>>>>>>        
>>>>>>>>            
>>>>>>>>                
>>>>>>>  
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>  
>>>>>      
>>>>>          
>>>
>>>  
>>>      
>
>
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> Subject: Re: Local Installation of Webgbrowse: Internal Server Error on
>  "Display in Gbrowse 2.0"
> From: Prakhar Gaur <[hidden email]>
> To: Ram Podicheti <[hidden email]>
> CC: <[hidden email]>
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> Hello,
>
> I checked and double checked.
> The folder group is set to 'root' and I have set all permissions to full
> access.
> $ls -lh
>    drwxrwxrwx.  7 ganit root   4.0K Jun  4 22:08 gbrowse2
>
> I have also added user "apache" to group "root".
> If this is not the way, then how to give apache access ?
>
> --
> Prakhar Gaur
>
>
> On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:
>  
>> This looks to me like another permission issue. Can you please check if
>> apache has permissions to write to the folder
>>
>> /etc/gbrowse2/GBrowse.conf/
>>
>>
>> The program is trying to create a file
>> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
>> not able to do so.
>>
>> Ram
>>
>>
>> Prakhar Gaur wrote:
>>    
>>> Hello,
>>>
>>> On repeating the process, its still not working, getting the same
>>> Internal Server Error.
>>> The relevant line from the error log is below.
>>>
>>> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
>>> conf
>>> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
>>> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
>>> referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>>
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>>>  
>>>      
>>>> Prakhar,
>>>> I am sorry for all these errors. Can you open your script
>>>>
>>>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>
>>>> and go to line 160 and change it from
>>>>
>>>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>>>> $timeStampDigest
>>>>
>>>> to
>>>>
>>>> -location =>
>>>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>>>
>>>> I don't know how it is working on our server in the first place, but
>>>> using single quotes was obviously a bug. I will be fixing it in the
>>>> repository. Thanks for reporting these issues, they shouldn't have been
>>>> there but at least I am fixing them now. Do let me know if you run into
>>>> more issues.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>    
>>>>        
>>>>> Hello Ram,
>>>>>
>>>>> I just repeated the steps and then shecked the apache error and access
>>>>> log file.
>>>>> The error log file has 3 lines, pertaining to that period of time,
>>>>>
>>>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>>>> exist: /var/www/html/favicon.ico
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>> line 160., referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>>>> of script headers: generateConfigurationData2.0, referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>>>  
>>>>>      
>>>>>          
>>>>>> Hi Prakhar,
>>>>>> I am not sure why you are getting the internal server error. There must
>>>>>> be a more useful error message apache must be spitting in the error.log
>>>>>> file. Can you verify that?
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> Prakhar Gaur wrote:
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>>> Hello Ram,
>>>>>>>
>>>>>>> Thank you for the help.
>>>>>>> We have another issue now,
>>>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>>>> tracks.
>>>>>>>
>>>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>>>> error" page.
>>>>>>> Please find the screen shot attached.
>>>>>>>
>>>>>>>
>>>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>>>> I changed folder owner to "apache" and group to "root".
>>>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>>>
>>>>>>>
>>>>>>> Thanking you,
>>>>>>> --
>>>>>>> Prakhar Gaur
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>>>  
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>>>> Hi Prakhar,
>>>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>>>
>>>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Podicheti, Ram [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>>>> To: Prakhar Gaur; [hidden email]
>>>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> There are two things that might be going wrong.
>>>>>>>>
>>>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>>>> Fixing this should let your program run without any issues.
>>>>>>>>
>>>>>>>> 2. The file errorpage is not in the location specified.
>>>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Prakhar Gaur [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>>>> To: [hidden email]
>>>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have a local installation of WebGbrowse.
>>>>>>>>
>>>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>>>> "
>>>>>>>> Not Found
>>>>>>>>
>>>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>>>
>>>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>>>> See the attached screenshot.
>>>>>>>>
>>>>>>>> Also the url bar has unusual content.
>>>>>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>>>> 20denied"
>>>>>>>>
>>>>>>>> Is this the problem? Permission denied for what?
>>>>>>>>
>>>>>>>> Thanking you,
>>>>>>>> --
>>>>>>>> Prakhar Gaur
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Live Security Virtual Conference
>>>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-webgbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>>>    
>>>>>>>>        
>>>>>>>>            
>>>>>>>>                
>>>>>>>  
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>  
>>>>>      
>>>>>          
>>>
>>>  
>>>      
>
>
>  


------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
Dear Ram,

Thanks that worked, but still some more errors.
That Internal Server error is still there.

But the error log shows, these new errors,
-----
[Mon Jun 04 23:29:35 2012] [error] [client 127.0.0.1] Could not open database: , referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=30e3662bc0feae4a46b362acc815ee95
[Mon Jun 04 23:29:35 2012] [error] [client 127.0.0.1] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=30e3662bc0feae4a46b362acc815ee95
[Mon Jun 04 23:29:35 2012] [error] [client 127.0.0.1] MSG: Couldn't open /var/www/html/webgbrowse/gbrowse2/databases/30e3662bc0feae4a46b362acc815ee95: No such file or directory, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=30e3662bc0feae4a46b362acc815ee95
[Mon Jun 04 23:29:35 2012] [error] [client 127.0.0.1] STACK: Error::throw, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=30e3662bc0feae4a46b362acc815ee95

Thanking you,
--
Prakhar Gaur


Sent on my BlackBerry® from Vodafone

-----Original Message-----
From: Ram Podicheti <[hidden email]>
Date: Mon, 4 Jun 2012 14:01:24
To: Prakhar Gaur<[hidden email]>
Cc: <[hidden email]>
Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

I think you set the value for $CONF2 to "/etc/gbrowse2/GBrowse.conf".
Try setting it to "/etc/gbrowse2"

Starting from GBrowse 2.0, GBrowse.conf is no longer a folder, but is a
file that has all the conf file mappings. Your conf folder needs to be
the gbrowse2 folder.


Prakhar Gaur wrote:

> Hello,
>
> I checked and double checked.
> The folder group is set to 'root' and I have set all permissions to full
> access.
> $ls -lh
>    drwxrwxrwx.  7 ganit root   4.0K Jun  4 22:08 gbrowse2
>
> I have also added user "apache" to group "root".
> If this is not the way, then how to give apache access ?
>
> --
> Prakhar Gaur
>
>
> On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:
>  
>> This looks to me like another permission issue. Can you please check if
>> apache has permissions to write to the folder
>>
>> /etc/gbrowse2/GBrowse.conf/
>>
>>
>> The program is trying to create a file
>> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
>> not able to do so.
>>
>> Ram
>>
>>
>> Prakhar Gaur wrote:
>>    
>>> Hello,
>>>
>>> On repeating the process, its still not working, getting the same
>>> Internal Server Error.
>>> The relevant line from the error log is below.
>>>
>>> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
>>> conf
>>> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
>>> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
>>> referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>>
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>>>  
>>>      
>>>> Prakhar,
>>>> I am sorry for all these errors. Can you open your script
>>>>
>>>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>
>>>> and go to line 160 and change it from
>>>>
>>>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>>>> $timeStampDigest
>>>>
>>>> to
>>>>
>>>> -location =>
>>>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>>>
>>>> I don't know how it is working on our server in the first place, but
>>>> using single quotes was obviously a bug. I will be fixing it in the
>>>> repository. Thanks for reporting these issues, they shouldn't have been
>>>> there but at least I am fixing them now. Do let me know if you run into
>>>> more issues.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>    
>>>>        
>>>>> Hello Ram,
>>>>>
>>>>> I just repeated the steps and then shecked the apache error and access
>>>>> log file.
>>>>> The error log file has 3 lines, pertaining to that period of time,
>>>>>
>>>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>>>> exist: /var/www/html/favicon.ico
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>> line 160., referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>>>> of script headers: generateConfigurationData2.0, referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>>>  
>>>>>      
>>>>>          
>>>>>> Hi Prakhar,
>>>>>> I am not sure why you are getting the internal server error. There must
>>>>>> be a more useful error message apache must be spitting in the error.log
>>>>>> file. Can you verify that?
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> Prakhar Gaur wrote:
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>>> Hello Ram,
>>>>>>>
>>>>>>> Thank you for the help.
>>>>>>> We have another issue now,
>>>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>>>> tracks.
>>>>>>>
>>>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>>>> error" page.
>>>>>>> Please find the screen shot attached.
>>>>>>>
>>>>>>>
>>>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>>>> I changed folder owner to "apache" and group to "root".
>>>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>>>
>>>>>>>
>>>>>>> Thanking you,
>>>>>>> --
>>>>>>> Prakhar Gaur
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>>>  
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>>>> Hi Prakhar,
>>>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>>>
>>>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Podicheti, Ram [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>>>> To: Prakhar Gaur; [hidden email]
>>>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> There are two things that might be going wrong.
>>>>>>>>
>>>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>>>> Fixing this should let your program run without any issues.
>>>>>>>>
>>>>>>>> 2. The file errorpage is not in the location specified.
>>>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Prakhar Gaur [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>>>> To: [hidden email]
>>>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have a local installation of WebGbrowse.
>>>>>>>>
>>>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>>>> "
>>>>>>>> Not Found
>>>>>>>>
>>>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>>>
>>>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>>>> See the attached screenshot.
>>>>>>>>
>>>>>>>> Also the url bar has unusual content.
>>>>>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>>>> 20denied"
>>>>>>>>
>>>>>>>> Is this the problem? Permission denied for what?
>>>>>>>>
>>>>>>>> Thanking you,
>>>>>>>> --
>>>>>>>> Prakhar Gaur
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Live Security Virtual Conference
>>>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-webgbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>>>    
>>>>>>>>        
>>>>>>>>            
>>>>>>>>                
>>>>>>>  
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>  
>>>>>      
>>>>>          
>>>
>>>  
>>>      
>
>
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> Message-ID: <[hidden email]>
> Subject: Re: Local Installation of Webgbrowse: Internal Server Error on
>  "Display in Gbrowse 2.0"
> From: Prakhar Gaur <[hidden email]>
> To: Ram Podicheti <[hidden email]>
> CC: <[hidden email]>
> Date: Mon, 4 Jun 2012 22:22:28 +0530
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>
> Hello,
>
> I checked and double checked.
> The folder group is set to 'root' and I have set all permissions to full
> access.
> $ls -lh
>    drwxrwxrwx.  7 ganit root   4.0K Jun  4 22:08 gbrowse2
>
> I have also added user "apache" to group "root".
> If this is not the way, then how to give apache access ?
>
> --
> Prakhar Gaur
>
>
> On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:
>  
>> This looks to me like another permission issue. Can you please check if
>> apache has permissions to write to the folder
>>
>> /etc/gbrowse2/GBrowse.conf/
>>
>>
>> The program is trying to create a file
>> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
>> not able to do so.
>>
>> Ram
>>
>>
>> Prakhar Gaur wrote:
>>    
>>> Hello,
>>>
>>> On repeating the process, its still not working, getting the same
>>> Internal Server Error.
>>> The relevant line from the error log is below.
>>>
>>> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
>>> conf
>>> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
>>> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
>>> referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>>
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>>>  
>>>      
>>>> Prakhar,
>>>> I am sorry for all these errors. Can you open your script
>>>>
>>>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>
>>>> and go to line 160 and change it from
>>>>
>>>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>>>> $timeStampDigest
>>>>
>>>> to
>>>>
>>>> -location =>
>>>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>>>
>>>> I don't know how it is working on our server in the first place, but
>>>> using single quotes was obviously a bug. I will be fixing it in the
>>>> repository. Thanks for reporting these issues, they shouldn't have been
>>>> there but at least I am fixing them now. Do let me know if you run into
>>>> more issues.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>    
>>>>        
>>>>> Hello Ram,
>>>>>
>>>>> I just repeated the steps and then shecked the apache error and access
>>>>> log file.
>>>>> The error log file has 3 lines, pertaining to that period of time,
>>>>>
>>>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>>>> exist: /var/www/html/favicon.ico
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>> line 160., referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>>>> of script headers: generateConfigurationData2.0, referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>>>  
>>>>>      
>>>>>          
>>>>>> Hi Prakhar,
>>>>>> I am not sure why you are getting the internal server error. There must
>>>>>> be a more useful error message apache must be spitting in the error.log
>>>>>> file. Can you verify that?
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> Prakhar Gaur wrote:
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>>> Hello Ram,
>>>>>>>
>>>>>>> Thank you for the help.
>>>>>>> We have another issue now,
>>>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>>>> tracks.
>>>>>>>
>>>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>>>> error" page.
>>>>>>> Please find the screen shot attached.
>>>>>>>
>>>>>>>
>>>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>>>> I changed folder owner to "apache" and group to "root".
>>>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>>>
>>>>>>>
>>>>>>> Thanking you,
>>>>>>> --
>>>>>>> Prakhar Gaur
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>>>  
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>>>> Hi Prakhar,
>>>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>>>
>>>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Podicheti, Ram [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>>>> To: Prakhar Gaur; [hidden email]
>>>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> There are two things that might be going wrong.
>>>>>>>>
>>>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>>>> Fixing this should let your program run without any issues.
>>>>>>>>
>>>>>>>> 2. The file errorpage is not in the location specified.
>>>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Prakhar Gaur [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>>>> To: [hidden email]
>>>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have a local installation of WebGbrowse.
>>>>>>>>
>>>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>>>> "
>>>>>>>> Not Found
>>>>>>>>
>>>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>>>
>>>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>>>> See the attached screenshot.
>>>>>>>>
>>>>>>>> Also the url bar has unusual content.
>>>>>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>>>> 20denied"
>>>>>>>>
>>>>>>>> Is this the problem? Permission denied for what?
>>>>>>>>
>>>>>>>> Thanking you,
>>>>>>>> --
>>>>>>>> Prakhar Gaur
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Live Security Virtual Conference
>>>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-webgbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>>>    
>>>>>>>>        
>>>>>>>>            
>>>>>>>>                
>>>>>>>  
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>  
>>>>>      
>>>>>          
>>>
>>>  
>>>      
>
>
>  

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
In reply to this post by Ram Podicheti-2
Dear Ram,

Thanks that worked, but still some more errors.
That Internal Server error is still there.

But the error log shows new errors.
Please check the file attached herewith.

-----
Thanking you,
--
Prakhar Gaur


Sent on my BlackBerry® from Vodafone

-----Original Message-----
From: Ram Podicheti <[hidden email]>
Date: Mon, 4 Jun 2012 14:01:24
To: Prakhar Gaur<[hidden email]>
Cc: <[hidden email]>
Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

I think you set the value for $CONF2 to "/etc/gbrowse2/GBrowse.conf".
Try setting it to "/etc/gbrowse2"

Starting from GBrowse 2.0, GBrowse.conf is no longer a folder, but is a
file that has all the conf file mappings. Your conf folder needs to be
the gbrowse2 folder.


Prakhar Gaur wrote:

> Hello,
>
> I checked and double checked.
> The folder group is set to 'root' and I have set all permissions to full
> access.
> $ls -lh
>    drwxrwxrwx.  7 ganit root   4.0K Jun  4 22:08 gbrowse2
>
> I have also added user "apache" to group "root".
> If this is not the way, then how to give apache access ?
>
> --
> Prakhar Gaur
>
>
> On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:
>  
>> This looks to me like another permission issue. Can you please check if
>> apache has permissions to write to the folder
>>
>> /etc/gbrowse2/GBrowse.conf/
>>
>>
>> The program is trying to create a file
>> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
>> not able to do so.
>>
>> Ram
>>
>>
>> Prakhar Gaur wrote:
>>    
>>> Hello,
>>>
>>> On repeating the process, its still not working, getting the same
>>> Internal Server Error.
>>> The relevant line from the error log is below.
>>>
>>> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
>>> conf
>>> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
>>> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
>>> referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>>
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>>>  
>>>      
>>>> Prakhar,
>>>> I am sorry for all these errors. Can you open your script
>>>>
>>>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>
>>>> and go to line 160 and change it from
>>>>
>>>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>>>> $timeStampDigest
>>>>
>>>> to
>>>>
>>>> -location =>
>>>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>>>
>>>> I don't know how it is working on our server in the first place, but
>>>> using single quotes was obviously a bug. I will be fixing it in the
>>>> repository. Thanks for reporting these issues, they shouldn't have been
>>>> there but at least I am fixing them now. Do let me know if you run into
>>>> more issues.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>    
>>>>        
>>>>> Hello Ram,
>>>>>
>>>>> I just repeated the steps and then shecked the apache error and access
>>>>> log file.
>>>>> The error log file has 3 lines, pertaining to that period of time,
>>>>>
>>>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>>>> exist: /var/www/html/favicon.ico
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>> line 160., referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>>>> of script headers: generateConfigurationData2.0, referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>>>  
>>>>>      
>>>>>          
>>>>>> Hi Prakhar,
>>>>>> I am not sure why you are getting the internal server error. There must
>>>>>> be a more useful error message apache must be spitting in the error.log
>>>>>> file. Can you verify that?
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> Prakhar Gaur wrote:
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>>> Hello Ram,
>>>>>>>
>>>>>>> Thank you for the help.
>>>>>>> We have another issue now,
>>>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>>>> tracks.
>>>>>>>
>>>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>>>> error" page.
>>>>>>> Please find the screen shot attached.
>>>>>>>
>>>>>>>
>>>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>>>> I changed folder owner to "apache" and group to "root".
>>>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>>>
>>>>>>>
>>>>>>> Thanking you,
>>>>>>> --
>>>>>>> Prakhar Gaur
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>>>  
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>>>> Hi Prakhar,
>>>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>>>
>>>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Podicheti, Ram [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>>>> To: Prakhar Gaur; [hidden email]
>>>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> There are two things that might be going wrong.
>>>>>>>>
>>>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>>>> Fixing this should let your program run without any issues.
>>>>>>>>
>>>>>>>> 2. The file errorpage is not in the location specified.
>>>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Prakhar Gaur [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>>>> To: [hidden email]
>>>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have a local installation of WebGbrowse.
>>>>>>>>
>>>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>>>> "
>>>>>>>> Not Found
>>>>>>>>
>>>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>>>
>>>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>>>> See the attached screenshot.
>>>>>>>>
>>>>>>>> Also the url bar has unusual content.
>>>>>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>>>> 20denied"
>>>>>>>>
>>>>>>>> Is this the problem? Permission denied for what?
>>>>>>>>
>>>>>>>> Thanking you,
>>>>>>>> --
>>>>>>>> Prakhar Gaur
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Live Security Virtual Conference
>>>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-webgbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>>>    
>>>>>>>>        
>>>>>>>>            
>>>>>>>>                
>>>>>>>  
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>  
>>>>>      
>>>>>          
>>>
>>>  
>>>      
>
>
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> Message-ID: <[hidden email]>
> Subject: Re: Local Installation of Webgbrowse: Internal Server Error on
>  "Display in Gbrowse 2.0"
> From: Prakhar Gaur <[hidden email]>
> To: Ram Podicheti <[hidden email]>
> CC: <[hidden email]>
> Date: Mon, 4 Jun 2012 22:22:28 +0530
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>
> Hello,
>
> I checked and double checked.
> The folder group is set to 'root' and I have set all permissions to full
> access.
> $ls -lh
>    drwxrwxrwx.  7 ganit root   4.0K Jun  4 22:08 gbrowse2
>
> I have also added user "apache" to group "root".
> If this is not the way, then how to give apache access ?
>
> --
> Prakhar Gaur
>
>
> On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:
>  
>> This looks to me like another permission issue. Can you please check if
>> apache has permissions to write to the folder
>>
>> /etc/gbrowse2/GBrowse.conf/
>>
>>
>> The program is trying to create a file
>> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
>> not able to do so.
>>
>> Ram
>>
>>
>> Prakhar Gaur wrote:
>>    
>>> Hello,
>>>
>>> On repeating the process, its still not working, getting the same
>>> Internal Server Error.
>>> The relevant line from the error log is below.
>>>
>>> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
>>> conf
>>> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
>>> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
>>> referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>>
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>>>  
>>>      
>>>> Prakhar,
>>>> I am sorry for all these errors. Can you open your script
>>>>
>>>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>
>>>> and go to line 160 and change it from
>>>>
>>>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>>>> $timeStampDigest
>>>>
>>>> to
>>>>
>>>> -location =>
>>>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>>>
>>>> I don't know how it is working on our server in the first place, but
>>>> using single quotes was obviously a bug. I will be fixing it in the
>>>> repository. Thanks for reporting these issues, they shouldn't have been
>>>> there but at least I am fixing them now. Do let me know if you run into
>>>> more issues.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>    
>>>>        
>>>>> Hello Ram,
>>>>>
>>>>> I just repeated the steps and then shecked the apache error and access
>>>>> log file.
>>>>> The error log file has 3 lines, pertaining to that period of time,
>>>>>
>>>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>>>> exist: /var/www/html/favicon.ico
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>> line 160., referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>>>> of script headers: generateConfigurationData2.0, referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>>>  
>>>>>      
>>>>>          
>>>>>> Hi Prakhar,
>>>>>> I am not sure why you are getting the internal server error. There must
>>>>>> be a more useful error message apache must be spitting in the error.log
>>>>>> file. Can you verify that?
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> Prakhar Gaur wrote:
>>>>>>    
>>>>>>        
>>>>>>            
>>>>>>> Hello Ram,
>>>>>>>
>>>>>>> Thank you for the help.
>>>>>>> We have another issue now,
>>>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>>>> tracks.
>>>>>>>
>>>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>>>> error" page.
>>>>>>> Please find the screen shot attached.
>>>>>>>
>>>>>>>
>>>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>>>> I changed folder owner to "apache" and group to "root".
>>>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>>>
>>>>>>>
>>>>>>> Thanking you,
>>>>>>> --
>>>>>>> Prakhar Gaur
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>>>  
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>>>> Hi Prakhar,
>>>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>>>
>>>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Podicheti, Ram [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>>>> To: Prakhar Gaur; [hidden email]
>>>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> There are two things that might be going wrong.
>>>>>>>>
>>>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>>>> Fixing this should let your program run without any issues.
>>>>>>>>
>>>>>>>> 2. The file errorpage is not in the location specified.
>>>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Prakhar Gaur [mailto:[hidden email]]
>>>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>>>> To: [hidden email]
>>>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have a local installation of WebGbrowse.
>>>>>>>>
>>>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>>>> "
>>>>>>>> Not Found
>>>>>>>>
>>>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>>>
>>>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>>>> See the attached screenshot.
>>>>>>>>
>>>>>>>> Also the url bar has unusual content.
>>>>>>>> "<a href="http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%">http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>>>> 20denied"
>>>>>>>>
>>>>>>>> Is this the problem? Permission denied for what?
>>>>>>>>
>>>>>>>> Thanking you,
>>>>>>>> --
>>>>>>>> Prakhar Gaur
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Live Security Virtual Conference
>>>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-webgbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>>>    
>>>>>>>>        
>>>>>>>>            
>>>>>>>>                
>>>>>>>  
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>      
>>>>>>>          
>>>>>>>              
>>>>>  
>>>>>      
>>>>>          
>>>
>>>  
>>>      
>
>
>  

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
In reply to this post by Prakhar Gaur
Hello,

I have made sure that none of the errors are due to permission issues.
Also I checked the installation of Gbrowse2 on that system, that is also
working fine.

The apache error-log is,
1st line, Which database is Apache talking about here?
The 3rd line, the folder "/var/www/html/webgbrowse/gbrowse2/" does not
even exist.
------------------------------------------------------------------------------
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] Could not open
database: , referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] -------------
EXCEPTION: Bio::Root::Exception -------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] MSG: Couldn't
open /var/www/html/webgbrowse/gbrowse2/databases/aeccf6885062436a020e840b33fb834a: No such file or directory, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Error::throw, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
-----------------------------------------------------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] Premature end
of script headers: gbrowse, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 12:14:25 2012] [error] [client 192.168.1.18] File does not
exist: /var/www/html/favicon.ico
-----------------------------------------

The error log is also attached here.

Thanking you,
--
Prakhar Gaur

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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Ram Podicheti-2
Prakhar,
Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse/gbrowse2/databases/". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html/gbrowse2/databases/". Also, make sure this new path exists. Let me know if anything I surmised is wrong.

Ram

-----Original Message-----
From: Prakhar Gaur [mailto:[hidden email]]
Sent: Tuesday, June 05, 2012 3:26 AM
To: [hidden email]
Cc: Podicheti, Ram
Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Hello,

I have made sure that none of the errors are due to permission issues.
Also I checked the installation of Gbrowse2 on that system, that is also working fine.

The apache error-log is,
1st line, Which database is Apache talking about here?
The 3rd line, the folder "/var/www/html/webgbrowse/gbrowse2/" does not even exist.
------------------------------------------------------------------------------
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] Could not open
database: , referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] -------------
EXCEPTION: Bio::Root::Exception -------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] MSG: Couldn't open /var/www/html/webgbrowse/gbrowse2/databases/aeccf6885062436a020e840b33fb834a: No such file or directory, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Error::throw, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] -----------------------------------------------------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] Premature end of script headers: gbrowse, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 12:14:25 2012] [error] [client 192.168.1.18] File does not
exist: /var/www/html/favicon.ico
-----------------------------------------

The error log is also attached here.

Thanking you,
--
Prakhar Gaur
------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Ram Podicheti-2
In reply to this post by Prakhar Gaur
My apologies. Strike that previous email and read it this way.

Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse ". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html". Also, make sure this new path exists. Let me know if anything I surmised is wrong.


-----Original Message-----
From: Podicheti, Ram
Sent: Tuesday, June 05, 2012 9:12 AM
To: 'Prakhar Gaur'; [hidden email]
Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar,
Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse/gbrowse2/databases/". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html/gbrowse2/databases/". Also, make sure this new path exists. Let me know if anything I surmised is wrong.

Ram

-----Original Message-----
From: Prakhar Gaur [mailto:[hidden email]]
Sent: Tuesday, June 05, 2012 3:26 AM
To: [hidden email]
Cc: Podicheti, Ram
Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Hello,

I have made sure that none of the errors are due to permission issues.
Also I checked the installation of Gbrowse2 on that system, that is also working fine.

The apache error-log is,
1st line, Which database is Apache talking about here?
The 3rd line, the folder "/var/www/html/webgbrowse/gbrowse2/" does not even exist.
------------------------------------------------------------------------------
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] Could not open
database: , referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] -------------
EXCEPTION: Bio::Root::Exception -------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] MSG: Couldn't open /var/www/html/webgbrowse/gbrowse2/databases/aeccf6885062436a020e840b33fb834a: No such file or directory, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Error::throw, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] -----------------------------------------------------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] Premature end of script headers: gbrowse, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
[Tue Jun 05 12:14:25 2012] [error] [client 192.168.1.18] File does not
exist: /var/www/html/favicon.ico
-----------------------------------------

The error log is also attached here.

Thanking you,
--
Prakhar Gaur
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
Hello,

I checked the folders,
/var/www/html/webgbrowse exist as well as,
/var/www/html/gbrowse2/
But,
/var/www/html/webgbrowse/gbrowse2/databases
or
/var/www/html/gbrowse2/databases/
Do not exist.

Now after making the changes, to WWW2 the errors are still there.
But the path for error changes from
"/var/www/html/webgbrowse/gbrowse2/databases/" to
"/var/www/html/gbrowse2/databases/"
Which basically reflects the changes I just made to the variable WWW2.
The new errors are these,

-------------------------------------------------------------------------------------------------------------------------------------------
[Tue Jun 05 18:39:37 2012] [error] [client 192.168.1.18] File does not
exist: /var/www/html/favicon.ico
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] Could not open
database: , referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] -------------
EXCEPTION: Bio::Root::Exception -------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] MSG: Couldn't
open /var/www/html/gbrowse2/databases/af06240c04f255392f5ccd56f4742bb7:
No such file or directory, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Error::throw, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18]
STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18]
-----------------------------------------------------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] Premature end
of script headers: gbrowse, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
----------------------------------------------------------------------------------------------------------------------------------------

Thanking you,
--
Prakhar Gaur


On Tue, 2012-06-05 at 13:15 +0000, Podicheti, Ram wrote:

> My apologies. Strike that previous email and read it this way.
>
> Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse ". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
>
>
> -----Original Message-----
> From: Podicheti, Ram
> Sent: Tuesday, June 05, 2012 9:12 AM
> To: 'Prakhar Gaur'; [hidden email]
> Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
>
> Prakhar,
> Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse/gbrowse2/databases/". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html/gbrowse2/databases/". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
>
> Ram
>
> -----Original Message-----
> From: Prakhar Gaur [mailto:[hidden email]]
> Sent: Tuesday, June 05, 2012 3:26 AM
> To: [hidden email]
> Cc: Podicheti, Ram
> Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
>
> Hello,
>
> I have made sure that none of the errors are due to permission issues.
> Also I checked the installation of Gbrowse2 on that system, that is also working fine.
>
> The apache error-log is,
> 1st line, Which database is Apache talking about here?
> The 3rd line, the folder "/var/www/html/webgbrowse/gbrowse2/" does not even exist.
> ------------------------------------------------------------------------------
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] Could not open
> database: , referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] -------------
> EXCEPTION: Bio::Root::Exception -------------, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] MSG: Couldn't open /var/www/html/webgbrowse/gbrowse2/databases/aeccf6885062436a020e840b33fb834a: No such file or directory, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Error::throw, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
> referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::init_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::init /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
> STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] -----------------------------------------------------------, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18] Premature end of script headers: gbrowse, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf6885062436a020e840b33fb834a
> [Tue Jun 05 12:14:25 2012] [error] [client 192.168.1.18] File does not
> exist: /var/www/html/favicon.ico
> -----------------------------------------
>
> The error log is also attached here.
>
> Thanking you,
> --
> Prakhar Gaur



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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Ram Podicheti-2
Prakhar,
I am bemused. The WWW2 should be set to the location you provided as "root" at the time of installing GBrowse 2.0. The folder "gbrowse2/databases" will be created in the specified root when you install GBrowse. When you said /var/www/html/gbrowse2/databases/ does not exist, either GBrowse is not installed, or it is installed in a different location. I remember you mentioning GBrowse being already installed and it works.  So, it must be location then. Can you check the location for the GBrowse databases folder? It will also be listed on the GBrowse welcome page. Let me know if you are having issues.
Thanks,

Ram

-----Original Message-----
From: Prakhar Gaur [mailto:[hidden email]]
Sent: Tuesday, June 05, 2012 9:39 AM
To: Podicheti, Ram
Cc: [hidden email]
Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Hello,

I checked the folders,
/var/www/html/webgbrowse exist as well as, /var/www/html/gbrowse2/ But, /var/www/html/webgbrowse/gbrowse2/databases
or
/var/www/html/gbrowse2/databases/
Do not exist.

Now after making the changes, to WWW2 the errors are still there.
But the path for error changes from
"/var/www/html/webgbrowse/gbrowse2/databases/" to "/var/www/html/gbrowse2/databases/"
Which basically reflects the changes I just made to the variable WWW2.
The new errors are these,

-------------------------------------------------------------------------------------------------------------------------------------------
[Tue Jun 05 18:39:37 2012] [error] [client 192.168.1.18] File does not
exist: /var/www/html/favicon.ico
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] Could not open
database: , referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] -------------
EXCEPTION: Bio::Root::Exception -------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] MSG: Couldn't open /var/www/html/gbrowse2/databases/af06240c04f255392f5ccd56f4742bb7:
No such file or directory, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Error::throw, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::init /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18]
STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] -----------------------------------------------------------, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
[Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] Premature end of script headers: gbrowse, referer:
http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
----------------------------------------------------------------------------------------------------------------------------------------

Thanking you,
--
Prakhar Gaur


On Tue, 2012-06-05 at 13:15 +0000, Podicheti, Ram wrote:

> My apologies. Strike that previous email and read it this way.
>
> Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse ". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
>
>
> -----Original Message-----
> From: Podicheti, Ram
> Sent: Tuesday, June 05, 2012 9:12 AM
> To: 'Prakhar Gaur'; [hidden email]
> Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
>
> Prakhar,
> Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse/gbrowse2/databases/". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html/gbrowse2/databases/". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
>
> Ram
>
> -----Original Message-----
> From: Prakhar Gaur [mailto:[hidden email]]
> Sent: Tuesday, June 05, 2012 3:26 AM
> To: [hidden email]
> Cc: Podicheti, Ram
> Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
>
> Hello,
>
> I have made sure that none of the errors are due to permission issues.
> Also I checked the installation of Gbrowse2 on that system, that is also working fine.
>
> The apache error-log is,
> 1st line, Which database is Apache talking about here?
> The 3rd line, the folder "/var/www/html/webgbrowse/gbrowse2/" does not even exist.
> ----------------------------------------------------------------------
> -------- [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
> Could not open
> database: , referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] -------------
> EXCEPTION: Bio::Root::Exception -------------, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] MSG: Couldn't open
> /var/www/html/webgbrowse/gbrowse2/databases/aeccf6885062436a020e840b33
> fb834a: No such file or directory, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Error::throw, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
> referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::Loader::load
> /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::memory::post_init
> /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::new
> /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::DataBase::open_database
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::DataSource::open_database
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980,
> referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::init_database
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::init
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::run
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18]
> STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] -----------------------------------------------------------, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> 192.168.1.18] Premature end of script headers: gbrowse, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> 62436a020e840b33fb834a [Tue Jun 05 12:14:25 2012] [error] [client
> 192.168.1.18] File does not
> exist: /var/www/html/favicon.ico
> -----------------------------------------
>
> The error log is also attached here.
>
> Thanking you,
> --
> Prakhar Gaur


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will include endpoint security, mobile security and the latest in malware
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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Prakhar Gaur
Hello,

I checked the path where the Gbrowse2 databases are,
"/var/lib/gbrowse2/databases"
Should I change WWW2 = /var/lib/webgbrowse
Though this folder will have to be created first.

Thanking you,
--
Prakhar Gaur


On Tue, 2012-06-05 at 13:52 +0000, Podicheti, Ram wrote:

> Prakhar,
> I am bemused. The WWW2 should be set to the location you provided as "root" at the time of installing GBrowse 2.0. The folder "gbrowse2/databases" will be created in the specified root when you install GBrowse. When you said /var/www/html/gbrowse2/databases/ does not exist, either GBrowse is not installed, or it is installed in a different location. I remember you mentioning GBrowse being already installed and it works.  So, it must be location then. Can you check the location for the GBrowse databases folder? It will also be listed on the GBrowse welcome page. Let me know if you are having issues.
> Thanks,
>
> Ram
>
> -----Original Message-----
> From: Prakhar Gaur [mailto:[hidden email]]
> Sent: Tuesday, June 05, 2012 9:39 AM
> To: Podicheti, Ram
> Cc: [hidden email]
> Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
>
> Hello,
>
> I checked the folders,
> /var/www/html/webgbrowse exist as well as, /var/www/html/gbrowse2/ But, /var/www/html/webgbrowse/gbrowse2/databases
> or
> /var/www/html/gbrowse2/databases/
> Do not exist.
>
> Now after making the changes, to WWW2 the errors are still there.
> But the path for error changes from
> "/var/www/html/webgbrowse/gbrowse2/databases/" to "/var/www/html/gbrowse2/databases/"
> Which basically reflects the changes I just made to the variable WWW2.
> The new errors are these,
>
> -------------------------------------------------------------------------------------------------------------------------------------------
> [Tue Jun 05 18:39:37 2012] [error] [client 192.168.1.18] File does not
> exist: /var/www/html/favicon.ico
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] Could not open
> database: , referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] -------------
> EXCEPTION: Bio::Root::Exception -------------, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] MSG: Couldn't open /var/www/html/gbrowse2/databases/af06240c04f255392f5ccd56f4742bb7:
> No such file or directory, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Error::throw, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
> referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::init_database /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::init /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer: http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18]
> STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] -----------------------------------------------------------, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] Premature end of script headers: gbrowse, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04f255392f5ccd56f4742bb7
> ----------------------------------------------------------------------------------------------------------------------------------------
>
> Thanking you,
> --
> Prakhar Gaur
>
>
> On Tue, 2012-06-05 at 13:15 +0000, Podicheti, Ram wrote:
> > My apologies. Strike that previous email and read it this way.
> >
> > Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse ". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
> >
> >
> > -----Original Message-----
> > From: Podicheti, Ram
> > Sent: Tuesday, June 05, 2012 9:12 AM
> > To: 'Prakhar Gaur'; [hidden email]
> > Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
> >
> > Prakhar,
> > Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse/gbrowse2/databases/". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html/gbrowse2/databases/". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
> >
> > Ram
> >
> > -----Original Message-----
> > From: Prakhar Gaur [mailto:[hidden email]]
> > Sent: Tuesday, June 05, 2012 3:26 AM
> > To: [hidden email]
> > Cc: Podicheti, Ram
> > Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
> >
> > Hello,
> >
> > I have made sure that none of the errors are due to permission issues.
> > Also I checked the installation of Gbrowse2 on that system, that is also working fine.
> >
> > The apache error-log is,
> > 1st line, Which database is Apache talking about here?
> > The 3rd line, the folder "/var/www/html/webgbrowse/gbrowse2/" does not even exist.
> > ----------------------------------------------------------------------
> > -------- [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
> > Could not open
> > database: , referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] -------------
> > EXCEPTION: Bio::Root::Exception -------------, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] MSG: Couldn't open
> > /var/www/html/webgbrowse/gbrowse2/databases/aeccf6885062436a020e840b33
> > fb834a: No such file or directory, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Error::throw, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
> > referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::Loader::load
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::memory::post_init
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::new
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::DataBase::open_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::DataSource::open_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980,
> > referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::init_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::init
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::run
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18]
> > STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] -----------------------------------------------------------, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] Premature end of script headers: gbrowse, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf68850
> > 62436a020e840b33fb834a [Tue Jun 05 12:14:25 2012] [error] [client
> > 192.168.1.18] File does not
> > exist: /var/www/html/favicon.ico
> > -----------------------------------------
> >
> > The error log is also attached here.
> >
> > Thanking you,
> > --
> > Prakhar Gaur
>
>



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Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Ram Podicheti-2
No, just set WWW2 to "/var/lib/". Also ensure,  "/var/lib/gbrowse2/databases" is writable for apache. I am sure, it is by default, but just in case. I am hoping this should be it. But, if there are more, don't hesitate notifying me. -Ram

-----Original Message-----
From: Prakhar Gaur [mailto:[hidden email]]
Sent: Tuesday, June 05, 2012 10:06 AM
To: Podicheti, Ram
Cc: [hidden email]
Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"

Hello,

I checked the path where the Gbrowse2 databases are, "/var/lib/gbrowse2/databases"
Should I change WWW2 = /var/lib/webgbrowse Though this folder will have to be created first.

Thanking you,
--
Prakhar Gaur


On Tue, 2012-06-05 at 13:52 +0000, Podicheti, Ram wrote:

> Prakhar,
> I am bemused. The WWW2 should be set to the location you provided as "root" at the time of installing GBrowse 2.0. The folder "gbrowse2/databases" will be created in the specified root when you install GBrowse. When you said /var/www/html/gbrowse2/databases/ does not exist, either GBrowse is not installed, or it is installed in a different location. I remember you mentioning GBrowse being already installed and it works.  So, it must be location then. Can you check the location for the GBrowse databases folder? It will also be listed on the GBrowse welcome page. Let me know if you are having issues.
> Thanks,
>
> Ram
>
> -----Original Message-----
> From: Prakhar Gaur [mailto:[hidden email]]
> Sent: Tuesday, June 05, 2012 9:39 AM
> To: Podicheti, Ram
> Cc: [hidden email]
> Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
>
> Hello,
>
> I checked the folders,
> /var/www/html/webgbrowse exist as well as, /var/www/html/gbrowse2/
> But, /var/www/html/webgbrowse/gbrowse2/databases
> or
> /var/www/html/gbrowse2/databases/
> Do not exist.
>
> Now after making the changes, to WWW2 the errors are still there.
> But the path for error changes from
> "/var/www/html/webgbrowse/gbrowse2/databases/" to "/var/www/html/gbrowse2/databases/"
> Which basically reflects the changes I just made to the variable WWW2.
> The new errors are these,
>
> ----------------------------------------------------------------------
> ---------------------------------------------------------------------
> [Tue Jun 05 18:39:37 2012] [error] [client 192.168.1.18] File does not
> exist: /var/www/html/favicon.ico
> [Tue Jun 05 18:40:03 2012] [error] [client 192.168.1.18] Could not
> open
> database: , referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] -------------
> EXCEPTION: Bio::Root::Exception -------------, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] MSG: Couldn't open /var/www/html/gbrowse2/databases/af06240c04f255392f5ccd56f4742bb7:
> No such file or directory, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Error::throw, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
> referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::Loader::load
> /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::memory::post_init
> /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::DB::SeqFeature::Store::new
> /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::DataBase::open_database
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::DataSource::open_database
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980,
> referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::init_database
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::init
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] STACK:
> Bio::Graphics::Browser2::Render::run
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18]
> STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] -----------------------------------------------------------, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7 [Tue Jun 05 18:40:03 2012] [error] [client
> 192.168.1.18] Premature end of script headers: gbrowse, referer:
> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=af06240c04
> f255392f5ccd56f4742bb7
> ----------------------------------------------------------------------
> ------------------------------------------------------------------
>
> Thanking you,
> --
> Prakhar Gaur
>
>
> On Tue, 2012-06-05 at 13:15 +0000, Podicheti, Ram wrote:
> > My apologies. Strike that previous email and read it this way.
> >
> > Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse ". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
> >
> >
> > -----Original Message-----
> > From: Podicheti, Ram
> > Sent: Tuesday, June 05, 2012 9:12 AM
> > To: 'Prakhar Gaur'; [hidden email]
> > Subject: RE: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
> >
> > Prakhar,
> > Check line #33 in the file WebGB.pm for the value you provided for the server setting WWW2. I am guessing, it must be "/var/www/html/webgbrowse/gbrowse2/databases/". Please check if this is a valid path which I don't think it is. If this is indeed the case, then try changing this value to "/var/www/html/gbrowse2/databases/". Also, make sure this new path exists. Let me know if anything I surmised is wrong.
> >
> > Ram
> >
> > -----Original Message-----
> > From: Prakhar Gaur [mailto:[hidden email]]
> > Sent: Tuesday, June 05, 2012 3:26 AM
> > To: [hidden email]
> > Cc: Podicheti, Ram
> > Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
> >
> > Hello,
> >
> > I have made sure that none of the errors are due to permission issues.
> > Also I checked the installation of Gbrowse2 on that system, that is also working fine.
> >
> > The apache error-log is,
> > 1st line, Which database is Apache talking about here?
> > The 3rd line, the folder "/var/www/html/webgbrowse/gbrowse2/" does not even exist.
> > --------------------------------------------------------------------
> > --
> > -------- [Tue Jun 05 11:34:10 2012] [error] [client 192.168.1.18]
> > Could not open
> > database: , referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] -------------
> > EXCEPTION: Bio::Root::Exception -------------, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] MSG: Couldn't open
> > /var/www/html/webgbrowse/gbrowse2/databases/aeccf6885062436a020e840b
> > 33
> > fb834a: No such file or directory, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Error::throw, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472,
> > referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::Loader::load
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:242, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::memory::post_init
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::DB::SeqFeature::Store::new
> > /usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::DataBase::open_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::DataSource::open_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:980,
> > referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::init_database
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1084, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::init
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:343, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] STACK:
> > Bio::Graphics::Browser2::Render::run
> > /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:285, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18]
> > STACK: /var/www/cgi-bin/gb2/gbrowse:50, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] -----------------------------------------------------------, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 11:34:10 2012] [error] [client
> > 192.168.1.18] Premature end of script headers: gbrowse, referer:
> > http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=aeccf688
> > 50 62436a020e840b33fb834a [Tue Jun 05 12:14:25 2012] [error] [client
> > 192.168.1.18] File does not
> > exist: /var/www/html/favicon.ico
> > -----------------------------------------
> >
> > The error log is also attached here.
> >
> > Thanking you,
> > --
> > Prakhar Gaur
>
>


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