[Bioperl-l] Re:Installation under Mac OSX

Jason Stajich jason.stajich at duke.edu
Mon Oct 4 16:02:44 EDT 2004

err  this is just the stub directory leftover from a CPAN  build - 
eventually it will be removed so that's not really if you don't want to 
rely on CPAN for the install just download the tar file,untar it and 
point your @INC to that (or just set your PERL5LIB).  Lots of examples 
in the INSTALL document like installing bioperl in your home directory 
which show how to do this.

GET comes from LWP so depends on if you have updated it.

I'd really suggest fink and fink commander (GUI for fink) if you are 
not a computer expert and want to easily install OSX applications.

On Oct 4, 2004, at 3:30 PM, Todd Naumann wrote:

> Andrew,
> 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
> Todd Naumann
> Post-Doc, Stephen Benkovic lab
> Department of Chemistry
> Penn State University
> University Park, PA  16802
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Jason Stajich
jason.stajich at duke.edu

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