[Bioperl-l] Help installing BioPerl

[Jason Stajich]

They are 2 different things.  See the website and FAQ for more 
information about the "core" and "run" distributions.

There may have been some issues with the dependancies of Bio::Perl and 
LWP in the 1.4 release I cannot remember.

If you want to make CPAN install something, just force the install.  
This will ignore the failed tests and still install the modules.

cpan>force install Bio::Perl

cpan>force install Bio::Tools::Run::Alignment::Clustalw

Setting PERL5LIB isn't that hard though and is what most people do when 
they can't get CPAN to behave or if they want to work with the most 
up-to-date version of the code.

% tar zxf ~/bioperl-1.4.tar.gz
% cd bioperl-1.4
% perl Makefile.PL LIB=$HOME/lib/perl
% make install

Add this to your .bashrc
export PERL5LIB=$HOME/lib/perl

An install without using CPAN. This is useful if you want to get the 
bugfixes that have been released since 1.4 which you can get via CVS.

-jason

On Sep 13, 2004, at 1:24 PM, Michael Robeson wrote:

> Actually the file on the CPAN was:
>  "B/BI/BIRNEY/bioperl-run-1.4.tar.gz"
>
> Maybe that's it? This file with the added "-run-" in the name might be 
> something different?
>
> But, yes "perldoc Bio::Perl" does return the Bio::Perl synopsis.
>
> -Mike
>
>
> On Sep 13, 2004, at 11:16 AM, Jason Stajich wrote:
>
>> But are you sure you installed bioperl-1.4.tar.gz....it doesn't sound 
>> like it.
>> "B/BI/BIRNEY/bioperl-1.4.tar.gz"
>>
>> Does this return anything?
>> % perldoc Bio::Perl
>>
>> On Sep 13, 2004, at 12:58 PM, Michael Robeson wrote:
>>
>>> In a sense , yes.
>>>
>>> When I try to run any script using Bio::Perl I get this error:
>>>
>>> "Can't locate Bio/Perl.pm in @INC".
>>>
>>> -Mike
>>>
>>> On Sep 13, 2004, at 6:08 AM, Brian Osborne wrote:
>>>
>>>> Mike,
>>>>
>>>> Do you mean that the test for Bio::Perl is failing?
>>>>
>>>> Brian O.
>>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at portal.open-bio.org
>>>> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Michael 
>>>> S.
>>>> Robeson II
>>>> Sent: Sunday, September 12, 2004 12:16 PM
>>>> To: bioperl-l at portal.open-bio.org
>>>> Subject: [Bioperl-l] Help installing BioPerl
>>>>
>>>> I have successfully installed BioPerl on several machines running 
>>>> Mac
>>>> OS X (10.3.5) w/o any trouble. However one of my machines (same OS) 
>>>> the
>>>> install is not working. Basically I keep getting "Error 2" problems 
>>>> at
>>>> the end of an install.
>>>>
>>>> I've used the "perl -MCPAN -eshell" as both a normal user and root 
>>>> and
>>>> it still does not work. I've tried this while installing the
>>>> "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz".
>>>>
>>>> Basically what it amounts to is that I get an error that says "Can't
>>>> locate Bio/Perl.pm in @INC". I basically know what this means but I 
>>>> am
>>>> not so sure how to fix this or what to do.
>>>>
>>>> Any help would be greatly appreciated.
>>>>
>>>> -Thanks
>>>> -Mike
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at portal.open-bio.org
>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>> --
>> Jason Stajich
>> jason.stajich at duke.edu
>> http://www.duke.edu/~jes12/
>>
>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/