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

Ben Bimber bbimber at gmail.com
Mon Feb 22 19:12:14 EST 2010

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
STACK Bio::Tools::Run::Bowtie::run C:/Perl/site/lib/Bio/Tools/Run/Bowtie.pm:295
STACK Bimber::run_bowtie
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

The error is throw during creation, so I cannot set the program_dir
after creation unless there is something I'm missing.


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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