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

[Dan Kortschak]

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).