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

Matt mastarr9 at gmail.com
Fri Mar 15 00:54:49 EDT 2013


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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