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

Brian Osborne osborne1 at optonline.net
Tue Sep 26 10:57:04 EDT 2006


Zhihua Li,

Your code is correct and code just like it runs correctly on my machine. My
only suggestion is to upgrade your Bioperl core and run packages to version
1.5.1, 1.4 is quite old and 1.5.1 is a significant improvement.

Brian O.


On 9/25/06 9:08 PM, "zhihua li" <lzhtom at hotmail.com> wrote:

> 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!
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
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