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Using Bioperl module for first time.

by mastarr (Novice)
on Mar 19, 2013 at 03:53 UTC ( #1024194=perlquestion: print w/ replies, xml ) Need Help??
mastarr has asked for the wisdom of the Perl Monks concerning the following question:

use strict; require Bio::SeqiO;

the error message is:

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.

I can see the files from the module... so my best guess is that i need to change the path to bioperl or add the path to bioperl.

I'm trying to use the module "bioperl" in Komodo edit. I am on OSX 10.6.8 and downloaded the module using "fink" into /sw/.

Thanks for your help!

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Re: Using Bioperl module for first time.
by kielstirling (Scribe) on Mar 19, 2013 at 04:20 UTC

      Thank you very much! The How to install Perl modules on a Mac link was exactly what I needed.

      It said, "The only instructions I could find point to Fink, which basically installs modules in a path that isnít included in the Perl @INC variable" and this was exactly my problem.

      I reinstalled it using the directions there and everything seems perfect now. Thanks a lot.

Re: Using Bioperl module for first time.
by 7stud (Deacon) on Mar 19, 2013 at 04:29 UTC
    1. Spelling counts in computer programming. You wrote the equivalent of:

      require Dog::Poop;
    2. You don't write 'require' anyway--it should be 'use'.
    3. I am on OSX 10.6.8 and downloaded the module using "fink"

      Is there a reason you aren't using the cpan command that is provided to you by your perl installation to download perl modules, i.e. opening up the Terminal App, and in the window that appears typing:

      $ cpan Some::Module

      You wrote the equivalent of:

      --7stud

      You don't write 'require' anyway--it should be 'use'.

      Unless you need to conditionally require and import it at runtime.
      ;)

      Thanks. I can make those first two small changes.

      Yea, I didn't know about the cpan command which, now that I know, is much easier. Fink was actually the problem in the end.

        You need to install your own perl and leave the system perl alone. You might screw up your OS by messing with the system perl. If you have root permissions on the computer you're using, you can just download the latest version of perl and follow the installation instructions.

        If you don't have root permissions, you can download perlbrew and use it to install perl in your local directories. You may just want to do that anyway because perlbrew makes it easy to manage multiple versions of perl in case you decide to try different versions of perl or you want to install perl both with thread support and without, etc.

Re: Using Bioperl module for first time.
by kcott (Abbot) on Mar 19, 2013 at 04:41 UTC

    G'day mastarr,

    Welcome to the monastery.

    Firstly, it appears you're attempting to alter the Mac OS X System Perl. If you're not, ignore the rest of this paragraph and move on to the next one; if you are, be advised that this is generally considered to be a bad idea that could potentially cause you all manner of grief. I moved to a Mac OS X system about 18 months and received the same warning (see Are there any major Perl issues with Mac OS X Lion?). For what it's worth, while there's more than one option suggested, I went with perlbrew.

    For information on modules in the Bio:: namespace, you might want to look at the tutorial: Perl and Bioinformatics

    There are a number of tools available for installing Perl modules. cpan and cpanp come bundled with Perl (I generally use the former).

    -- Ken

      Firstly, it appears you're attempting to alter the Mac OS X System Perl.

      Oh, boy:

      /Library/Perl/Updates/5.10.0/System/
Re: Using Bioperl module for first time.
by Corion (Pope) on Mar 19, 2013 at 08:57 UTC

    The module name is Bio::SeqIO (note the capital I), not Bio::SeqiO (with a lowercase i).

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