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On 12/14/09 3:16 PM, [email protected] wrote:
> Hi Alexander,
>
> I tried that and got this error:
>
> Can't locate Bio/SearchIO.pm in @INC (@INC contains:
> /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5
> /sw/lib/perl5/darwin /Library/Perl/Updates/5.10.0
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/5.10.0
> /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0
> /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
> /Network/Library/Perl/5.10.0 /Network/Library/Perl
> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.10.0 .) at blastparser.new.pl line 8.
> BEGIN failed--compilation aborted at blastparser.new.pl line 8.
>
How are you running the script? If you're using
perl somescript.pl
then that's going to be using perl-5.10.0, as the first 'perl'
executable in your PATH, unless you install the 'perl588' package from
Fink. Changing the #! line at the beginning of the script just sets the
interpreter if the script is set to be executable and you run it via
just e.g.
./somescript.pl
on the command line.
If you're not doing that, then something in other perl code that your
script is running is invoking perl-5.10.0, presumably via a
#!/usr/bin/perl line, so you'll need to go through those and fix every
occurrence.
If you're using modules from CPAN, you'll probably need to install them
separately. If you don't have "perl588" installed, but just
"perl588-core", then install perl588 and use the 'cpan' script from that
to make sure that the modules get set up in the proper area.
>
> ----- Original Message -----
> From: Alexander Hansen <[email protected]>
> Date: Monday, December 14, 2009 3:13 pm
> Subject: Re: [Fink-beginners] bioperl install
> To: [email protected]
> Cc: [email protected]
>
> On 12/14/09 2:33 PM, [email protected] wrote:
>> Hello everyone,
>
>> I am trying to install bioperl on my new macbook pro that is
> running Mac
>> OSX 10.6. I downloaded fink and was able to install the
> bioperl-pm588
>> packages (there were no package for 5100), but I keep getting
> an error
>> when trying to run a bioperl script. I think the problem
> is that I
>> installed bioperl to work with perl 5.8.8 and my default perl
> is 5.10.0;
>> but I do not know how to solve this problem.
>
>> Does anyone know how to install bioperl on mac os 10.6?
>
>> Thanks for your help,
>
>> Eric
>
>
>> Eric F. Donaldson, Ph.D. Research Assistant Professor, Ralph
> Baric Lab
>> University of North Carolina Department of Epidemiology
>
>
>
> Without seeing your script or the error it's hard to say what's going
> on, but in general, to make a script use a particular perl interpreter
> you'd want to replace the
>
> #!/usr/bin/perl
>
> at the beginning with e.g.
>
> #!/sw/bin/perl5.8.8
>
>>
> Eric F. Donaldson, Ph.D. Research Assistant Professor, Ralph Baric Lab
> University of North Carolina Department of Epidemiology
- --
Alexander Hansen
Fink User Liaison
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