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

Fields, Christopher J cjfields at illinois.edu
Fri Mar 15 20:04:37 UTC 2013


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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