[Bioperl-l] Ask help for Bio::Tools::Run::Primer3

[Jason Stajich]

yes of course - the question is what the default should be.  I've left 
it as 'primer3' but if people compile it and it produces 
'primer3_core'.... I've updated the Primer3.t test to figure it out and 
test both possiblities.

-jason
On Oct 1, 2004, at 1:51 PM, Brian Osborne wrote:

> Jason,
>
> And, as you know, one can also do:
>
>   my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>$seq,
>                                               -outfile=>"temp.out",
>                                               
> -path=>"/usr/bin/primer3_core"
> );
>
> Tested in Cygwin, not Windows.
>
> Brian O.
>
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason 
> Stajich
> Sent: Friday, October 01, 2004 10:01 AM
> To: Bioperl Mailing List
> Subject: Re: [Bioperl-l] Ask help for Bio::Tools::Run::Primer3
>
> In looking at the code some more, shouldn't we make the default
> 'primer3_core' instead?
>
> You can always override it with the program_name function.
> $primer3->program_name('my_superfast_primer3');
>
> -jason
> On Sep 29, 2004, at 4:38 PM, Ewing, Adam D. wrote:
>
>> Yes, it does matter... simply change the name of primer3_core to
>> primer3, put it in your path, and you should be good to go!
>>
>> Adam
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at portal.open-bio.org on behalf of Fengkai Zhang
>> (Tony)
>> Sent: Wed 9/29/2004 4:21 PM
>> To: bioperl-l at bioperl.org
>> Subject: [Bioperl-l] Ask help for Bio::Tools::Run::Primer3
>>
>> Hi, I am a newbie for bioperl and met the below question.
>>
>> I was trying to use Bio::Tools::Run::Primer3. When I run the example
>> code in the documentation of this module, I got the following error
>> message:
>> --------------------------------
>> <shell> $ perl -I ../primer3_1.0.0/src/ -w primer3run_test.pl
>>
>> Use of uninitialized value in concatenation (.) or string at
>> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Primer3.pm line 212,
>> <GEN0> line 1.
>> primer3 can not be found. Is it installed?
>> --------------------------------
>>
>> I already installed Primer3 according its instruction and it works
>> well to run the test and example. I also noticed that the
>> primer_test.pl in primer3 package calls "primer3_core" rather than
>> "primer3". Does it matter for Bio::Tools::Run::Primer3 module?
>>
>>
>> Thanks ahead for your help.
>>
>>
>>
>> Tony
>>
>> VIPBG at VCU
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> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
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>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/