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

[Scott Cain]

Hi Pushkala,

I think mod_fcgi is much easier to work with than mod_perl, so I would
suggest that.

gd-devel is the rpm package for libgd and it C-headers so that things
that need to be compiled to use libgd can be (like the perl GD
module).  The package perl-GD contains the perl GD module, and asking
yum to install it would also get you libgd.  If the only thing you can
find is gd-devel, then that will be fine and cpan will install GD.

Scott


On Thu, Feb 18, 2010 at 12:55 PM, Jayararaman, Pushkala
<biohelp at cgb.indiana.edu> wrote:
> 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
>
>



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