[Bioperl-l] BioPerl-run Primer3 trouble

[Rob Edwards]

John,

This is exactly the right place to ask the question.

The problem is simple -- on your system primer3 is run as primer3_core, 
and in Bio::Tools::Run::Primer3 it is hard-coded (incorrectly) to be 
primer3 -- and simply bad coding on my behalf.

I have put one fix in CVS, that appears to work for me, although I 
think the whole Primer3 code needs revisiting and cleaning up.

If you can not install this send me an email and I will explain how to 
set this up to work correctly in one of your own directories.

Rob



On Jan 28, 2004, at 9:25 AM, john herbert wrote:

> 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.
>   $ENV{PRIMER3}="/usr/bin/";
>   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.
>
> Thanks.
>
> ps (The administrator has apparently installed BioPerl-run)
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