[Bioperl-l] please some help
Nathan S. Haigh
n.haigh at sheffield.ac.uk
Sun Aug 26 03:35:36 EDT 2007
mcons004 at fiu.edu wrote:
> 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. Any information will be helpful for me. Thanks
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
From what you have said, it appears you need some basic info to
understand what you are trying to achieve.
The Perl programming language requires the Perl interpreter in order to
execute a Perl script. The Perl interpreter is usually installed as
standard with Unix/Linux based Operating Systems. The version you
mention (5.8.6) will not be the version of Bioperl but the version of
the Perl interpreter you have installed - you can check this by typing
"perl -v" at a command prompt.
Given your apparent lack of understanding of the Unix OS, it is likely
that you don't have Bioperl installed. You should have a look at:
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