[Bioperl-l] BioPerl-run Primer3 trouble

john herbert john.herbert at clinical-pharmacology.oxford.ac.uk
Wed Jan 28 10:25:33 EST 2004

Hello All.
Sorry if this is wrong place to ask this but here goes.
I have the following code in a script:
use strict;
use Data::Dumper;
use johnhutils;
use IO::File;
use Carp;
use Getopt::Declare;
use Bio::Tools::Run::Primer3;
use Bio::SeqIO;
  my $results;
 # Setting up the enviroment, well theoretically. Which I am guessing
tells BioPerl where the executable lives.
  my $seqio=Bio::SeqIO->new(-file=>'infile');
  my $seq=$seqio->next_seq;
  my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>$seq,
-outfile=>"temp.out", -program => 'primer3_core' );
  unless ($primer3->executable()) {print STDERR "primer3 can not be
found. Is it installed?\n"; exit(-1)}
This code then generates primer3 cannot be found Is it installed. 
However, if I combine the path and program, it runs at the command
line. (/usr/bin/primer3_core) 
Would be gratefull if someone could point me to how I can get primer3
to run in my script.
ps (The administrator has apparently installed BioPerl-run)

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