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

[Jayararaman, Pushkala]

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