[Bioperl-l] HELP: script cannot find primer3, which has been properly installed

zhihua li lzhtom at hotmail.com
Sun Sep 24 23:46:28 EDT 2006


hi, netters

i installed primer3_1.0b and bioperl-run-1.4 following the instructions. 
the source of primer3 executables is in 
/home/zz/setup/primer3_1.0b/src/primer3_core.

then i tried the script in the documentation for bio::tool::run::primer3

use Bio::Tools::Run::Primer3;
use Bio::SeqIO;

  my $seqio = Bio::SeqIO->new(-file=>'input.1');
  my $seq = $seqio->next_seq;
  my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq,
                                              -outfile => "temp.out",
                                              -path => 
"/home/zz/setup/primer3_1.0b/src/primer3_core");
$primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
my $results = $primer3->run;

but when i ran it, there was an error message saying that primer3 couldn't 
be found.

i'm pretty sure primer3 has been properly installed. 'cause when i went to 
the source directory /home/zz/setup/primer3_1.0b/src/, i could run the 
program there using:

./primer3_core<input.2

why couldn't the perl script find primer3?

thanks a lot!




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