[Bioperl-l] bioperl on mac

Jason Stajich jason at bioperl.org
Sat Jan 26 15:30:11 EST 2008


Usually this is done by fink by adding a line to your .tcshrc (if you  
are running that shell) or .bash_profile or .bashrc.

On my machine I have this at the top of my .bash_profile file:
test -r /sw/bin/init.sh && . /sw/bin/init.sh

if that is not there you need to add it to insure that all the fink  
tools are setup properly.

On Jan 26, 2008, at 8:14 AM, Brian Osborne wrote:

> 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>_____________________________________________ 
>> __
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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