[Bioperl-l] Bio::Tools::Run::Bowtie and Bio::Assembly::IO::bowtie now available BETA

[Dan Kortschak]

Hi Ben,

Have you done a ./Build test? It would be nice to know if it passes that
(do you have bowtie's location in your $PATH?).

I've had a look through CommandExts, and I think you should pass
-program_dir, rather than -prog_dir (I know I've previously been saying
the latter, but I don't use that method, so you'll forgive me). You can
see this from line 454-474.

cheers
Dan

On Mon, 2010-02-22 at 18:12 -0600, Ben Bimber wrote:
> Hi Dan,
> 
> Maybe I'm missing something obvious, but this should work, right?
> 
> 	my $bowtiefac = Bio::Tools::Run::Bowtie->new(
>         -command             => 'single',
>         -prog_dir 			 => '/utils/bowtie/',
>         -max_seed_mismatches => 1,
>         -seed_length         => 28,
>         -max_qual_mismatch   => 70,
>         -quiet				 => 1,
>         -want 				 => 'raw',
> 	-unaligned_file		 => $output_dir . 'unaligned.fq',
> 	);
> 		
> 
> It throws this error for me:
> 
> MSG: Could not find the executable 'bowtie'. You can use
> $self->program_dir() and $self->program_name() to specify the location
> of the program.
> STACK Bio::Tools::Run::AssemblerBase::_check_executable
> C:/Perl/site/lib/Bio/Tools/Run/AssemblerBase.pm:178
> STACK Bio::Tools::Run::Bowtie::run C:/Perl/site/lib/Bio/Tools/Run/Bowtie.pm:295
> STACK Bimber::run_bowtie
> C:/Projects/PerlScripts/SequenceTools/Utilities/Bimber.pm:122
> STACK toplevel C:/Projects/PerlScripts/SequenceTools/test.pl:32
> 
> 
> Any chance this has something to do w/ inheriting from assemblerbase?
> other wrappers like StandAloneBlastPlus (program_dir() works on PC) do
> not.
> 
> The error is throw during creation, so I cannot set the program_dir
> after creation unless there is something I'm missing.
> 
> -Ben
> 
> 
> 
> 
> 
> 
> On Mon, Feb 22, 2010 at 5:27 PM, Dan Kortschak
> <dan.kortschak at adelaide.edu.au> wrote:
> > Hi Ben,
> >
> > That has been fixed in bioperl-run/trunk at 16869. Please check to see if
> > the fix works for you under Windows.
> >
> > If you want to use an environment variable, you will need to use the
> > executables method after constructing the factory unless you are keeping
> > all the executables in one directory in which case you can pass that
> > directory to the object during construction using the -prog_dir param.
> >
> > Dan
> >
> > On Mon, 2010-02-22 at 12:00 -0500, Ben Bimber wrote:
> >
> >> Hello,
> >>
> >> I just came across the bowtie wrapper and it looks very useful.
> >> However, I am having trouble with the current logic to find the bowtie
> >> executable path.  In Bio::Tools::Run::Bowtie, line 240, it uses the
> >> command 'which', which is not windows compatible as far as I know (i'm
> >> running a PC).
> >
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> >