[Bioperl-l] Re:Installation under Mac OSX

Todd Naumann tan10 at psu.edu
Mon Oct 4 15:30:50 EDT 2004


I have recently had to migrate from a linux system to MacOSX and I am 
no computer expert. Under linux I installed bioperl using CPAN and it 
made a system-wide install and everything worked. Under MacOSX I had 
the same results that you describe when using CPAN. Despite the 
warnings, bioperl does install in my case. It is a local copy that you 
can locate under ~/.cpan/build/bioperl-1.4. I assume that the warning 
for your test script simply says that it can't find module Bio::SeqIO 
(or whatever) in directories in @INC. If you add the following line to 
your code:

use lib "/Users/todd/.cpan/build/bioperl-1.4;

it will add the directory to @INC and your script should run. Two 
things that I have noticed do not work by default are:

1) Bio::Graphics does not work for me. I think that there is some 
problem in communication between GD.pm and the GD libraries.
2) While web retrieval does work I can no longer use the GET alias from 
the command line (I think that GET comes from bioperl installation but 
I am not sure??).

Hope this helps.


Todd Naumann
Post-Doc, Stephen Benkovic lab
Department of Chemistry
Penn State University
University Park, PA  16802

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