[Bioperl-l] bioperl on MacOS X... a beginner's problems...

Thomas Keller kellert at ohsu.edu
Thu May 15 12:09:57 EDT 2003


Stefanie,
This sounds like your perl is not configured to look in the directory 
where fink is installing the modules.
You can inform perl where they are by adding:
use lib '/my/fink/perlmodulesdirectory';
to your script, then
use Bio::SeqIO; or whatever should work.

Refer to Jason Stajich's message for a more "universal" fix.
Also, from the command line, check @INC by typing:
% find `perl -e 'print "@INC"'` -name '*.pm' -print
## finds all perl modules in @INC, pipe to grep to find a specific 
module

good luck,
Tom K.

On Thursday, May 15, 2003, at 09:18  AM, Stefanie wrote:

>
> hi there!
>
> I'm not sure if this is even the right discussion board for my 
> question (if not: which is?)...
> Anyway, I am working under Mac OS X (10.2.6), I have Perl 5.8 
> installed, and I installed the BioPerl Bundle using fink. And: I am 
> quite new to all of this.
> Installation seems to have worked - but yet the bioperl modules are 
> not recognized / cannot be loaded.
> I think it's some problem related to a PATH not being set correctly, 
> but I'm not sure how to solve it.
> Is there anyone who can help or who can show me where to get help on 
> this?
> Thanks a lot!
>
> Stef
> _______________________________________________
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>
>
Tom Keller, Ph.D.
http://www.ohsu.edu/core
kellert at ohsu.edu
503-494-2442



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