[Bioperl-l] repeatmasker

Nathan S. Haigh n.haigh at sheffield.ac.uk
Tue Jan 2 11:18:53 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?
>
> Many thanks in advance and a happy new year,
> Karen
>
>   
Hi Karen,

Bioperl only supplies a wrapper for the repeatmasker software. You need
to download and install the RepeatMasker software from:
http://www.repeatmasker.org/RMDownload.html

Have another bash at it from here, and post again if you have problems.

Cheers
Nath



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