[Bioperl-l] Re peatMasker not found

Jason Stajich jason at bioperl.org
Tue May 13 17:06:31 EDT 2008


Dare I ask, did you install repeat masker?

http://www.repeatmasker.org/

On May 13, 2008, at 1:59 PM, nisa_dar wrote:

>
> Following is the path to repeatmasker.pm on my system
>
> /opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/RepeatMasker.pm
>
> but when I run my program, the error message comes
>
> RepeatMasker program not found as  or not executable
>
> Here is my piece of code which gives this error,
> #!/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} = '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/ 
> Tools/';
>
>  }
> 	
>
> my @params = ("mam" => 1,"noint"=>1);
> my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
> my $in  = Bio::SeqIO->new(-file => "boechera.fasta", -format =>  
> 'fasta');
>
> I tried finding RepeatMasker directory by typing
>
> which RepeatMasker
>
> but the error message was
>
> /usr/bin/which: no RepeatMasker in
> (/opt/openmpi/1.1.4/bin:/opt/lsfhpc/ego/1.2/linux2.6-glibc2.3- 
> x86_64/etc:/opt/lsfhpc/ego/1.2/linux2.6-glibc2.3-x86_64/bin:/opt/ 
> lsfhpc/7.0/linux2.6-glibc2.3-x86_64/etc:/opt/lsfhpc/7.0/linux2.6- 
> glibc2.3-x86_64/bin:/usr/kerberos/bin:/usr/java/jdk1.5.0_07/bin:/ 
> share/iNquiry/biotools/bin:/share/iNquiry/bin/lx24-x86:/share/ 
> iNquiry/bin/lx24-amd64:/opt/Bio/bin:/usr/local/bin:/bin:/usr/bin:/ 
> usr/X11R6/bin:/opt/modules/current/bin/:/opt/modules/bin/:/opt/Bio/ 
> glimmer/scripts:/opt/Bio/gromacs/bin:/opt/eclipse:/opt/ganglia/bin:/ 
> opt/maven/bin:/opt/rocks/bin:/opt/rocks/sbin:/home/vdar/bin)
>
>
> what should I do?
>
> Thanks
>
>
>
>
> -- 
> View this message in context: http://www.nabble.com/RepeatMasker- 
> not-found-tp17218229p17218229.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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