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

[Ben Bimber]

you're right, dumb mistake.  I just read through the bowtie wrapper
and commandexts and at least I think I have a better understanding of
how it works though.  bowtie's working great now.  thanks for the
help.

-ben





On Mon, Feb 22, 2010 at 6:41 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> 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).
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>
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