[Bioperl-l] Re peatMasker not found

nisa_dar vdar at yorku.ca
Tue May 13 16:59:00 EDT 2008


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.



More information about the Bioperl-l mailing list