[Bioperl-l] Re peatMasker not found

[vdar at yorku.ca]

I have tried it and it gives the following message

RepeatMasker could not find the repeat library at:
    /home/vdar/RepeatMasker/Libraries/RepeatMasker.lib
 or
    /home/vdar/RepeatMasker/Libraries/RepeatMaskerLib.embl
Please download the latest RepeatMasker library from
http://www.girinst.org and install before using RepeatMasker


I've downloaded and installed censor-4.2 from www.girinst.org already but of no
use. I have seen that RepeatMasker/Libraries/RepeatMasker.lib is empty. What
should I do?



Quoting "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>:

> Have you had tried RepeatMasker running on the command line?
> If it doesn't run there, it's very unlikely to run through BioPerl.
>
> Eg. 	/home/vdar/RepeatMasker/RepeatMasker  -species Ruminantia
> -xsmall test.fa
>
>
> --Russell
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-
> > bio.org] On Behalf Of nisa_dar
> > Sent: Friday, 23 May 2008 7:29 a.m.
> > To: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] Re peatMasker not found
> >
> >
> > Finally I have put my whole code inside the Directory RepeatMasker and
> now
> > this error message comes
> >
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: Repeat Masker Call(RepeatMasker  -noint -mam
> > /tmp/uZzDGdH78C/oyiUOrQOer
> > 2> /dev/null 1>/dev/null) crashed: 32512
> >
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw
> > /opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:328
> > STACK: Bio::Tools::Run::RepeatMasker::_run
> > /opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/RepeatMasker.pm:266
> > STACK: Bio::Tools::Run::RepeatMasker::run
> > /opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/RepeatMasker.pm:220
> > STACK: try.pl:28
> > -----------------------------------------------------------
> >
> >
> > Here is my code
> >
> > #!/usr/bin/perl
> >
> > use strict;
> > use warnings;
> >
> > use Bio::Seq;
> > use Bio::Tools::Run::StandAloneBlast;
> > use Bio::Search::Hit::HitI;
> > use Bio::Search::Hit::BlastHit;
> > use Bio::Search::HSP::BlastHSP;
> > use Bio::Search::HSP::HSPI;
> > use Bio::SearchIO;
> > use Bio::Tools::Run::RepeatMasker;
> >
> > BEGIN {
> >
> >         $ENV{REPEATMASKERDIR} = '/home/vdar/RepeatMasker';
> >
> >  }
> >
> >
> > my @params = ("mam" => 1,"noint"=>1);
> > my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
> > my $in  = Bio::SeqIO->new(-file => "boechera.fasta", -format =>
> 'fasta');
> >   my $seq = $in->next_seq();
> > #
> >   #return an array of Bio::SeqFeature::FeaturePair objects
> >   my @feats = $factory->run($seq);
> > #
> > #  # or
> > #
> > #  $factory->run($seq);
> > #  my @feats = $factory->repeat_features;
> > #
> > #  #return the masked sequence, a Bio::SeqI object
> >   my $masked_seq = $factory->run;
> > #
> >   if ($masked_seq){
> >         print "yes\n";
> > #
> >   }
> >
> >
> > Does anyone know what does that mean and what to do now? bcs I have
> seen
> > that RepeatMasker program resides in this directory and I didn't get
> the
> > previous message this time that program not found.
> >
> > Thanks!
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Sendu Bala-2 wrote:
> > >
> > > nisa_dar wrote:
> > >> please see my full message and all the approaches that i have been
> doing
> > >> to
> > >> tell my pogram where repeat masker is...what else is correct if
> these are
> > >> not?
> > >
> > > We don't know where you installed RepeatMasker. Only you do. You
> need to
> > > supply that installation directory to $ENV{REPEATMASKERDIR} in your
> code.
> > >
> > >
> > >> Sendu Bala-2 wrote:
> > >>> nisa_dar wrote:
> > >>>> ok now I have installed repeat masker, with its prerequisites as
> given
> > >>>> on
> > >>>> http://www.repeatmasker.org/
> > >>>> but now I am getting this error message.
> > >>>>
> > >>>> RepeatMasker program not found as  or not executable.
> > >>>>
> > >>>> what should I do?
> > >>> Well now you have to correct your code to tell it where you
> installed
> > >>> RepeatMasker:
> > >>>
> > >>>
> > >>>>> On May 13, 2008, at 1:59 PM, nisa_dar wrote:
> > >>> [...]
> > >>>>>> BEGIN {
> > >>>>>>
> > >>>>>> 	$ENV{REPEATMASKERDIR} =
> > >>>>>> '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/';
> > >>>>>>
> > >>>>>>  }
> > >>> _______________________________________________
> > >>> Bioperl-l mailing list
> > >>> Bioperl-l at lists.open-bio.org
> > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >>>
> > >>>
> > >>
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > >
> >
> > --
> > View this message in context:
> http://www.nabble.com/RepeatMasker-not-found-
> > tp17218229p17411731.html
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
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