[Gmod-help] [#19565] RE: Re: RE: Re: GBrowse installation

[Jayararaman, Pushkala]

Oh yes, 
I have created a virtual Linux machine over my window system and will need to install everything from scratch. This way I will be root and get to understand pre-requisites for Gbrowse2. 

I have httpd installed through yum and I have perl 5.10 installed separately. 
I have currently installed mod_perl through yum and I just read the thread in which Lincoln suggested that mod_fcgi works much better as mod-perl seems to "identify obscure bugs" 

Should I proceed with installing mod_fcgi or continue with mod_perl. 

Also, Is there any difference in:
Yum install gd-devel and yum install perl-GD 
I cannot find a package for the latter. 
Is it okay for me to continue installation?


Thanks again, 
Pushkala

-----Original Message-----
From: Scott Cain [mailto:biohelp at cgb.indiana.edu] 
Sent: Thursday, February 18, 2010 11:24 AM
To: Jayararaman, Pushkala
Subject: [#19565] Re: RE: Re: GBrowse installation

Oh, sorry, I didn't realize how minimal a linux system you were using.
 Yes, you definitely need apache2 and perl (5.8 or 5.10 are fine).
The others are optional, and you can only use mod_fastcgi or mod_perl,
not both.  And yes, I would suggest yum for installing those, as cpan
will only install perl modules.

Scott


On Thu, Feb 18, 2010 at 11:51 AM, Jayararaman, Pushkala
<biohelp at cgb.indiana.edu> wrote:
> Thanks Scott,
>
> Just one last question:
> 1. I would still have to install
> Apache2
> Perl 5.10
> Mod_fastcgi
> Mod_perl
> Mysql
>
> The above right? Should I simply try yum for these as well?
>
> Or would simply cpan> install Bio::Graphics::Browser2
> Install these for me as well?
>
> Thanks again,
> Pushkala
>
>
> -----Original Message-----
> From: Scott Cain [mailto:biohelp at cgb.indiana.edu]
> Sent: Thursday, February 18, 2010 10:45 AM
> To: Jayararaman, Pushkala
> Subject: [#19565] Re: GBrowse installation
>
> Hi Pushkala,
>
> The only thing you'll need to install before using cpan is libgd.
> Using yum, you'll want to do something like
>
>  yum install libgd2-dev  (I think that's the name of the package)
>
> Also, some minimal linux installations don't have fundamental things
> like gcc and make installed.  You should make sure you have those too.
>  After that, in the cpan shell, if you just enter
>
>  cpan> install Bio::Graphics::Browser2
>
> it should install GBrowse2 and all required prerequisites.
>
> Scott
>
>
> On Thu, Feb 18, 2010 at 11:28 AM, Jayararaman, Pushkala
> <biohelp at cgb.indiana.edu> wrote:
>> Hello,
>>
>> I had a query regarding installation of Gbrowse 2.0 pre requisites:
>>
>> This is what it says:
>>
>> " It is easiest to use the Perl CPAN shell to install these modules. If you
>> use the CPAN shell to install GBrowse, then the required modules will be
>> installed automatically, however the optional ones will still need to be
>> installed by hand:
>>
>> % perl -MCPAN -e shell
>>
>> cpan shell -- CPAN exploration and modules installation (v1.9301)
>>
>> cpan[2]> install GD::SVG
>>
>> cpan[3]> install DBI
>>
>> cpan[4]> install DB_File::Lock
>>
>> ...etc...
>>
>> Please install libgd2 and your distribution's compiler tools (e.g.
>> "libc6-dev" on Debian systems) before you attempt to install
>> Bio::Graphics::Browser from the CPAN shell. Otherwise it will fail at the GD
>> library installation step."
>>
>> Does that mean all I have to do is
>>
>> ·       Perl -MCPAN -e shell
>>
>> ·       Cpan> install Module::Build
>>
>> ·       Cpan> install GD
>>
>> ·       Cpan> install Bio::Perl ...etc..
>>
>> Until I install all the modules and the pre requisites?? Also will I have to
>> then install gbrowse2.0 also from CPAN?
>>
>> It says here that:
>>
>> " It is easiest to use the Perl CPAN shell to install these modules. If you
>> use the CPAN shell to install GBrowse, then the required modules will be
>> installed automatically, however the optional ones will still need to be
>> installed by hand:"
>>
>> Does that mean I do not have to install all the modules individually(except
>> for the optional modules) and that Gbrowse2.0 installation will install the
>> required modules for me?
>>
>> I have an RPM based system I am currently running a CentOS 5 virtual
>> machine. "yum"
>>
>> Does not seem to have all the packages required. But now that I am using
>> CPAN to install everything Do I have to do install anything else with yum?
>>
>> Would I not have to configure any paths at all? Would CPAN take care of the
>> paths for me?
>>
>> Thanks,
>>
>> Pushkala
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>



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