[Gmod-help] [#19565] Re: RE: Re: RE: Re: RE: Re: GBrowse installation
Scott Cain
biohelp at cgb.indiana.edu
Thu Feb 18 14:11:38 EST 2010
Hi Pushkala,
I would suggest that you not try mod_perl or mod_fcgi until you have
GBrowse working--you don't need them, they just speed GBrowse up.
Messing around with Apache config file when you don't know what you
are doing can lead to all kinds of problems.
You don't need moderator approval to join the gbrowse mailing list.
You should have gotten an automated email with a confirmation link
that you needed to click. If you didn't get that, perhaps it is in
your spam folder, or you put a typo in the email address.
Scott
On Thu, Feb 18, 2010 at 1:17 PM, Jayararaman, Pushkala
<biohelp at cgb.indiana.edu> wrote:
> Thanks,
>
> I also tried to install mod_fast_cgi. Using this link:
> http://www.cyberciti.biz/tips/rhel-centos-fedora-apache2-fastcgi-php-configuration.html
>
> and then I went into the /etc/httpd/conf.d/perl.conf and commented the " LoadModule perl_module modules/mod_perl.so" line
> I did this because I have also installed mod_fastcgi and would like to use mod_fastcgi instead of mod_perl.
> would this actually help?
>
> Also,
> I get a delivery failure when I try and send emails to the gmod-gbrowse at lists.sourceforge.net. Apparently, I haven't yet received moderator approval to join the mailing lists. Please help as I am not able to receive any of the other emails as well.
>
>
> Thanks,
> Pushkala
>
> -----Original Message-----
> From: Scott Cain [mailto:biohelp at cgb.indiana.edu]
> Sent: Thursday, February 18, 2010 12:10 PM
> To: Jayararaman, Pushkala
> Subject: [#19565] Re: RE: Re: RE: Re: GBrowse installation
>
> 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
>
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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