[Bioperl-l] Re peatMasker not found

[Smithies, Russell]

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.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================