[Bioperl-l] Bio::Tools::Run::Bowtie and Bio::Assembly::IO::bowtie now available BETA
bimber at wisc.edu
Mon Feb 22 21:15:28 EST 2010
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
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.
> 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
>> 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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