GMOD configurartion

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GMOD configurartion

Rajeswari Swaminathan

Hello,

My name is Rajeswari Swaminathan. I am trying to install and configure GMOD in my work machine, which is a Ubuntu based Desktop. I have finished downloading and installing the software. Now, when I try to run the demo volvox page on my browser, it throws the following error in the apache error log:


[Tue Aug 07 15:44:04 2012] [error] [client 127.0.0.1] attempt to invoke directory as script: /var/www/cgi-bin/
Can't locate Bio/DB/SeqFeature/Store/Alias.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 10, <DATA> line 192.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 10, <DATA> line 192.
Compilation failed in require at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2.pm line 16, <DATA> line 192.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2.pm line 16, <DATA> line 192.
Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 11, <DATA> line 192.
BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 11, <DATA> line 192.
[Tue Aug 07 15:44:10 2012] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
[Tue Aug 07 15:44:12 2012] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico


I am not sure as to what is the problem. I will be happy to get some assistance on this.

Thanks
Rajeswari Swaminathan

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Re: GMOD configurartion

girlwithglasses
Hi Rajeswari,

The problem that you're running into is that perl can't locate the
libraries it needs for GBrowse to function. Have you had a look at the
installation instructions on the GMOD wiki?

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

The easiest way to install GBrowse is using cpan, as that will
automatically load up all the libraries that you need.

Best wishes,
Amelia

On Tue, Aug 7, 2012 at 12:49 PM, Rajeswari Swaminathan
<[hidden email]> wrote:

>
> Hello,
>
> My name is Rajeswari Swaminathan. I am trying to install and configure GMOD
> in my work machine, which is a Ubuntu based Desktop. I have finished
> downloading and installing the software. Now, when I try to run the demo
> volvox page on my browser, it throws the following error in the apache error
> log:
>
>
> [Tue Aug 07 15:44:04 2012] [error] [client 127.0.0.1] attempt to invoke
> directory as script: /var/www/cgi-bin/
> Can't locate Bio/DB/SeqFeature/Store/Alias.pm in @INC (@INC contains:
> /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
> /usr/local/lib/site_perl .) at
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 10,
> <DATA> line 192.
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 10,
> <DATA> line 192.
> Compilation failed in require at
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2.pm line 16, <DATA> line
> 192.
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2.pm line 16, <DATA> line
> 192.
> Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 11,
> <DATA> line 192.
> BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 11,
> <DATA> line 192.
> [Tue Aug 07 15:44:10 2012] [error] [client 127.0.0.1] Premature end of
> script headers: gbrowse
> [Tue Aug 07 15:44:12 2012] [error] [client 127.0.0.1] File does not exist:
> /var/www/favicon.ico
>
>
> I am not sure as to what is the problem. I will be happy to get some
> assistance on this.
>
> Thanks
> Rajeswari Swaminathan
>
> ------------------------------------------------------------------------------
> 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-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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

------------------------------------------------------------------------------
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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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FW: GMOD configurartion

girlwithglasses
For archiving.

---------- Forwarded message ----------
From: Rajeswari Swaminathan <[hidden email]>
Date: Tue, Aug 7, 2012 at 5:04 PM
Subject: Re: [Gmod-gbrowse] GMOD configurartion
To: Amelia Ireland <[hidden email]>


Hi Amelia,

I realized that too and saw that there was one particular perl module
that was missing somehow. I was following the instructions given in
the GMOD :HOWTO page. But after I added the path as well as included
the missing module, it seems to be working fine now. Thank you so much
for the help. I will contact you in case if I fall into trouble again.

Thanks
Rajeswari

On Tue, Aug 7, 2012 at 7:59 PM, Amelia Ireland <[hidden email]> wrote:

>
> Hi Rajeswari,
>
> The problem that you're running into is that perl can't locate the
> libraries it needs for GBrowse to function. Have you had a look at the
> installation instructions on the GMOD wiki?
>
> http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO
>
> The easiest way to install GBrowse is using cpan, as that will
> automatically load up all the libraries that you need.
>
> Best wishes,
> Amelia
>
> On Tue, Aug 7, 2012 at 12:49 PM, Rajeswari Swaminathan
> <[hidden email]> wrote:
> >
> > Hello,
> >
> > My name is Rajeswari Swaminathan. I am trying to install and configure GMOD
> > in my work machine, which is a Ubuntu based Desktop. I have finished
> > downloading and installing the software. Now, when I try to run the demo
> > volvox page on my browser, it throws the following error in the apache error
> > log:
> >
> >
> > [Tue Aug 07 15:44:04 2012] [error] [client 127.0.0.1] attempt to invoke
> > directory as script: /var/www/cgi-bin/
> > Can't locate Bio/DB/SeqFeature/Store/Alias.pm in @INC (@INC contains:
> > /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1
> > /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
> > /usr/local/lib/site_perl .) at
> > /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 10,
> > <DATA> line 192.
> > BEGIN failed--compilation aborted at
> > /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 10,
> > <DATA> line 192.
> > Compilation failed in require at
> > /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2.pm line 16, <DATA> line
> > 192.
> > BEGIN failed--compilation aborted at
> > /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2.pm line 16, <DATA> line
> > 192.
> > Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 11,
> > <DATA> line 192.
> > BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 11,
> > <DATA> line 192.
> > [Tue Aug 07 15:44:10 2012] [error] [client 127.0.0.1] Premature end of
> > script headers: gbrowse
> > [Tue Aug 07 15:44:12 2012] [error] [client 127.0.0.1] File does not exist:
> > /var/www/favicon.ico
> >
> >
> > I am not sure as to what is the problem. I will be happy to get some
> > assistance on this.
> >
> > Thanks
> > Rajeswari Swaminathan
> >
> > ------------------------------------------------------------------------------
> > 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-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
>
>
>
> --
> Amelia Ireland
> GMOD Community Support Specialist || http://gmod.org




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

------------------------------------------------------------------------------
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-gbrowse mailing list
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