[Bioperl-l] bioperl on mac

Brian Osborne bosborne11 at verizon.net
Sat Jan 26 11:14:13 EST 2008


Katherine,

Perl keeps the addresses of all the module directories in its @INC  
array. What do you see when you do:

perl -e 'print @INC'

?

If '/sw/share/bioperl-pm586' is not in @INC then you need to put it  
there, perhaps by adding something like:

setenv PERL5LIB ${PERL5LIB}:/sw/share/bioperl-pm586

to the .tcshrc file in your home directory (if you use tcsh that is,  
most use bash, .bashrc, and 'set' these days).

You asked some other questions, the general answer is that all the  
modules you'll need are in the 2 packages you've installed, and you  
don't need to move them from /sw.


Brian O.


On Jan 24, 2008, at 1:19 PM, Katherine Wendelsdorf wrote:

> Dear one who knows,
>
> I have a macbook with Leopard OSX and I am having trouble running  
> scripts
> that call for bioperl modules.
>
> Here is my history: Using Fink I installed bioperl-pm586 version  
> 1.5.2-4
> and bioperl-run-pm586 version 1.5.2-1. when I type >which bioperl- 
> pm586 in
> to the command line I get nothing. Spotlight says that the path is
> /sw/share/bioperl-pm586. The same goes for bioperl-run-pm586.
>
> 1. I tried to run test2.pl script that was literally copied and pasted
> from the HOWTO manual, but it wouldnt run. The two attached docs are  
> the
> script I tried to run and the output (which is nonexistant). I read
> something that said to "go in to" Bioperl to execute a command. I  
> could
> not enter the bioperl directory when it was in the sw/shared  
> directory so
> I copied the bioperl folder to the Desktop just so I could try  
> executing
> the script inside bioperl. Where am I going wrong here?
>
> Should I place these folders (bioperl-pm586 and bioperl-run-pm586)
> somewhere else on my computer? Shoudl they be in the same directory as
> perl (usr/bin/perl)?
>
> 2. How do I know what modules are included in the bioperl-pm586 I
> downloaded? Specifically I want to use Bio::SeqIO.
>
> 3. What is the best way to download/install new modules as I need  
> them?
>
>
> Any answers you coudl give me for any of these questions would be  
> greatly
> appreciated!
>
> Thank you so much, kind volunteer!
> - 
> Kate 
> <test.txt><test2.pl>_______________________________________________
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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