[Bioperl-l] please some help

Sendu Bala bix at sendu.me.uk
Fri Aug 24 10:38:39 EDT 2007


mcons004 at fiu.edu wrote:
> Hello, I am new to this software and I am having some trouble
> starting. The version of Bioperl I am working on is v5.8.6. My OS is
> Unix (Mac OS X). I am trying to use Bioperl with a file called
> blastParser to process a file which is the output of a "blastall"
> operation.
> 
> The code that gives me error is:
>> perl blastParser.pl junk.out 1 1 1.0
> and the error message says: Can't locate Bio/SearchIO.pm in @INC
> (@INC contains: /System/Library/Perl/5.8.6/darwin-thread-multi-2level
> 
> 
> You online info says I probably means that the module
> Bio::SearchIO.pm is not instaled and I can either install
> Bundle::Bioperl or install that specific module by hand. Could you
> give me some tips in this? I am new working with Unix, and Bioperl so
> I am a little confused.

You need to install Bioperl first. You can find instructions here:
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix

If this is your own Mac (you have the root/admin password), when it 
tells you to run cpan (">perl -MCPAN -e shell" or ">cpan"), start the 
command with 'sudo'. So:

 >sudo cpan


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