[Bioperl-l] Re peatMasker not found

nisa_dar vdar at yorku.ca
Thu May 22 11:47:20 EDT 2008


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?






Jason Stajich-3 wrote:
> 
> 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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> 
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