[Bioperl-l] using a bioperl module after installing.

[Fields, Christopher J]

Even if you use fink, you may still need to set the PERL5LIB path to point to that location.  Have you done that?

chris
 
On Mar 14, 2013, at 11:54 PM, Matt <mastarr9 at gmail.com> wrote:

> I used "fink" to install bioperl. I see that the installation had no problems and that the Bio/SeqIO module exists in hard drive/sw/lib/perl5/5.10.0/Bio/SeqIO but I am still unable to actually make any use of bioperl in a script.
> 
> On the bioperl wiki I see that this common error message comes from the module sometimes not being installed but, in my case, I think that it is installed but "lost".  How can I reinstall or move or change the path to make bioperl actually work?
> Thanks!
> 
> Information:
> 
> * perl v5.10.0
> * Bioperl-pm5.10.0
> * OSX 10.6.8
> * Goal: To simply use a bioperl module
> * The code that gives the error (Using komodo edit):
>     o #!/usr/bin/perl -w
>       use strict;
>       require Bio::SeqiO;
> * The error message:
>     o Can't locate Bio/SeqiO.pm in @INC (@INC contains:
>       /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 /Users/Matt/bioperl
>       test.pl line 3.
> 
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