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

[Jayararaman, Pushkala]

Hello, 
I had a mail delivery failure with gmod-gbrowse mailing lists. I
apologize for the inconvenience. 
It is apparently waiting moderator's approval. 
I will from now on send it via this mail chain. 

Pushkala

-----Original Message-----
From: Ram Podicheti [mailto:mnrusimh at indiana.edu] 
Sent: Thursday, February 18, 2010 11:58 AM
To: Jayararaman, Pushkala; Jayararaman, Pushkala 
Cc: gmod-gbrowse at lists.sourceforge.net; Scott Cain
Subject: Re: [#19565] RE: Re: GBrowse installation

I don't think this email exchange is reaching the intended audience
which is gmod-gbrowse at lists.sourceforge.net. You are communicating
through the CGB issue tracker. Not that we have any issues with it, but,
it sort of defeats the purpose of the GBrowse mailing list. So I am
copying the entire conversation to the mailing list.

Pushkala - can you start sending your further responses related to
GBrowse directly to gmod-gbrowse at lists.sourceforge.net? Of course, if
there is any thing related to WebGBrowse, please include
biohelp at cgb.indiana.edu in your recipient list.
Thanks,

Ram Podicheti


Scott Cain wrote:
> 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
>>
>>
>>     
>
>
>
>