[Bioperl-l] problem with install

[Jason Stajich]

Eric -
please CC the bioperl list when responding so others can help - I  
can't be the only answerer.

But since your @INC message doesn't include /sw/lib/perl5/5.8.8/ you  
would need to make sure that is added to your PERL5LIB.
There are some help docs on the perl sites I expect on how to get your  
PATHs in order.

Or you can just install via CPAN which will put it in the right path -  
there are docs on the bioperl website about installing via CPAN.

-jason
On Dec 13, 2009, at 9:02 PM, eric_donaldson at med.unc.edu wrote:

> Hi Jason,
>
> The fink package did not have support for perl 5.10, so I attempted  
> to install the perl 5.8.6 package.
>
> When I attempted: locate Bio/SearchIO.pm
> I got: -bash: $: command not found
>
> So even though I can find SearchIO.pm in sw/lib/perl5/5.8.8/Bio/ 
> SearchIO.pm  I cannot access it.  Do I need to use the older version  
> of perl?
>
> Would it be better to install with CPAN?  If so, can you send me to  
> a page that has instructions?
>
> Thank you so much!
>
> ERic
>
>
> ----- Original Message -----
> From: Jason Stajich <jason at bioperl.org>
> Date: Sunday, December 13, 2009 11:10 pm
> Subject: Re: [Bioperl-l] problem with install
> To: eric_donaldson at med.unc.edu
> Cc: BioPerl List <bioperl-l at bioperl.org>
>
>> So you installed perl-5.10 or using system perl?  I'm
>> confused if you
>> actually installed bioperl.pm or not via fink?
>>
>> It seems like since your @INC or $PERL5LIB points to
>> /sw/lib/perl5
>> which is one of the dirs it would have installed in, but I don't
>> think
>> you actually installed bioperl.
>>
>> you can try and do:
>> $ locate Bio/SearchIO.pm
>>
>> We'll see if any of the other osx/fink gurus are on the list
>> that can
>> help or you can install it via CPAN I guess.
>>
>> -jason
>> On Dec 13, 2009, at 6:39 PM, eric_donaldson at med.unc.edu wrote:
>>
>>>
>>> I actually tried a different blastparser that uses
>> BIO::SearchIO and
>>> got the same message:
>>>
>>> Can't locate Bio/SearchIO.pm in @INC (@INC contains:
>> /sw/lib/perl5/
>>> darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin
>> /
>>> Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-
>>
>>> thread-multi-2level /System/Library/Perl/5.10.0
>> /Library/Perl/5.10.0/
>>> darwin-thread-multi-2level /Library/Perl/5.10.0
>> /Network/Library/
>>> Perl/5.10.0/darwin-thread-multi-2level
>> /Network/Library/Perl/5.10.0 /
>>> Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-
>>
>>> thread-multi-2level /System/Library/Perl/Extras/5.10.0 .)
>> at
>>> blastparser.new.pl line 8.
>>> BEGIN failed--compilation aborted at blastparser.new.pl line 8.
>>>
>>> I suspect there is a path problem, but am not savvy enough to
>> know
>>> how to fix it.  I am really just a hacker.... I have
>> several scripts
>>> that I use regularly and that I know how to modify, but am
>> lost when
>>> they don't work...
>>>
>>> Thanks for any help,
>>>
>>> Eric
>>>
>>> ----- Original Message -----
>>> From: Jason Stajich <jason at bioperl.org>
>>> Date: Sunday, December 13, 2009 8:24 pm
>>> Subject: Re: [Bioperl-l] problem with install
>>> To: eric_donaldson at med.unc.edu
>>> Cc: bioperl-l at bioperl.org
>>>
>>>> Hi Eric -
>>>>
>>>> Bio::Tools::BPlite is no longer supported in Bioperl - it
>>>> was
>>>> deprecated several releases ago.
>>>> It was replaced with Bio::SearchIO
>>>>
>>>> -jason
>>>> On Dec 13, 2009, at 3:15 PM, eric_donaldson at med.unc.edu wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> Today I downloaded bioperl 1.61 on my new macbook pro using
>>>> fink.  I
>>>>> used the
>>>>>
>>>>> fink install bioperl.pm-588 as I could not get it to instal
>>>> using
>>>>> the perl version 5.10.
>>>>>
>>>>> But now I get an error when trying to run a bioperl script.
>>>>>
>>>>> Here is the error:
>>>>>
>>>>> Can't locate Bio/Tools/BPlite.pm in @INC (@INC contains:
>>>> /sw/lib/
>>>>> perl5/darwin-thread-multi-2level /sw/lib/perl5
>>>> /sw/lib/perl5/darwin /
>>>>> Library/Perl/Updates/5.10.0
>> /System/Library/Perl/5.10.0/darwin-
>>>>
>>>>> thread-multi-2level /System/Library/Perl/5.10.0
>>>> /Library/Perl/5.10.0/
>>>>> darwin-thread-multi-2level /Library/Perl/5.10.0
>>>> /Network/Library/
>>>>> Perl/5.10.0/darwin-thread-multi-2level
>>>> /Network/Library/Perl/5.10.0 /
>>>>> Network/Library/Perl
>> /System/Library/Perl/Extras/5.10.0/darwin-
>>>>
>>>>> thread-multi-2level /System/Library/Perl/Extras/5.10.0 .)
>>>> at
>>>>> blastparser.pl line 8.
>>>>> BEGIN failed--compilation aborted at blastparser.pl line 8.
>>>>>
>>>>>
>>>>> I am a novice at unix and bioperl so I do not know how
>>>> to
>>>>> troubleshoot this, would you please hleo me?
>>>>>
>>>>> Thank you,
>>>>>
>>>>> Eric
>>>>>
>>>>>
>>>>> Eric F. Donaldson, Ph.D.
>>>>> Research Assistant Professor, Ralph Baric Lab
>>>>> University of North Carolina
>>>>> Department of Epidemiology
>>>>>
>>>>>
>>>>>
>>>> <
>>>>
>> eric_donaldson.vcf>_______________________________________________>
>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> --
>>>> Jason Stajich
>>>> jason.stajich at gmail.com
>>>> jason at bioperl.org
>>>>
>>>>
>>>
>>> Eric F. Donaldson, Ph.D.
>>> Research Assistant Professor, Ralph Baric Lab
>>> University of North Carolina
>>> Department of Epidemiology
>>>
>>>
>>> <eric_donaldson.vcf>
>>
>> --
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>>
>>
>
> Eric F. Donaldson, Ph.D.
> Research Assistant Professor, Ralph Baric Lab
> University of North Carolina
> Department of Epidemiology
>
>
> <eric_donaldson.vcf>

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org