[Bioperl-l] repeatmasker

Fairley, Derek Derek.Fairley at bll.n-i.nhs.uk
Tue Jan 2 11:13:54 EST 2007


Hi Karen,

RepeatMasker isn't a BioPerl program - although the
Bio::Tools::Run::RepeatMasker module can call it if it's properly
installed on your system. RepeatMasker also requires either Cross_Match
or WUBlast to be installed, in addition to a local database containing
repeat data.

Can you run RepeatMasker from the command line okay?

Derek.

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Karen Buysse
Sent: 02 January 2007 15:00
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] repeatmasker

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

-- 
ir. Karen Buysse
Center for Medical Genetics Ghent (CMGG)
Ghent University Hospital
Medical Research Building (MRB), 2nd floor, room 120.050
De Pintelaan 185, B-9000 Ghent, Belgium
+32 9 240 39 46 (phone) 
+32 9 240 65 49 (fax)
http://medgen.ugent.be
Karen.Buysse at UGent.be

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