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

zhihua li lzhtom at hotmail.com
Mon Sep 25 21:08:37 EDT 2006


I'm using Suse 10.0


>From: Brian Osborne <osborne1 at optonline.net>
>To: zhihua li <lzhtom at hotmail.com>, bioperl-l at lists.open-bio.org
>Subject: Re: [Bioperl-l] HELP: script cannot find primer3, which has been 
properly installed
>Date: Mon, 25 Sep 2006 14:13:19 -0400
>
>zhihua li,
>
>Are you on a Unix machine or Cygwin?
>
>Brian O.
>
>
>On 9/24/06 11:46 PM, "zhihua li" <lzhtom at hotmail.com> wrote:
>
> > 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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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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