[Bioperl-l] repeatmasker

Sendu Bala bix at sendu.me.uk
Tue Jan 2 11:16:57 EST 2007


Karen Buysse wrote:
> Dear all,
> 
> I want to use the BioPerl repeatmasker program.
> However, when I run the following program (=first lines of the synopsis):
> 
> use Bio::Tools::Run::RepeatMasker;
> 
>   my @params=("mam" => 1,"noint"=>1);
>   my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
> 
> I get the error message: *RepeatMasker program not found as  or not 
> executable.*
> I have the file *RepeatMasker.pm* in the following directories:
> C:/Perl/lib/Bio/Tools/Run
> C:/Perl/site/lib/Bio/Tools/Run
> 
> Can anyone please help me with this?

Bioperl run modules are not programs but front-ends ('wrappers') to 
external programs. You need to install the program that corresponds to 
the module before it will work.

Visit http://www.repeatmasker.org/ to get the program and database.


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