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

Dan Kortschak dan.kortschak at adelaide.edu.au
Mon Feb 22 17:18:05 EST 2010

Hi Jason,

No I didn't use that, but I'm happy to change those part of the new
method so that it works with our cousins (MAJ, it's not that I don't
consider it a bug, I just very rarely even consider Windows at all - yes
that's bad, but I find my life works better that way ;) - though I'm
glad to have people find things that I am unable to test, and fix them
when found).

It should be a simple case of using the executable[s] methods which go
through B:R:IO->exists_exe.

Ben would you log a bug? Also note that as the module stands the
executable location[s] with WrapperBase[::CommandExts] derived modules
can be changed through the executable[s] methods, so your desire to have
a user specified executable path is available. The function of that
method was not completely resolved when I wrote the new method, so the
unix command was used - it will be fixed. As far as using an $ENV{} var,
I'd be happy to do that deeply if there is already an established
variable defining the executable locations, though I don't think this is
the case (there is a var for index locations - which I don't query, and
completely ignore, this may be a bug request).


On Mon, 2010-02-22 at 12:00 -0500, Jason Stajich wrote:
> We had a perl only executable funding routine in bio::root:: or the  
> runwrapper module - dan did you not want to use it?
> Sent from my iPod
> On Feb 22, 2010, at 11:01, "Mark A. Jensen" <maj at fortinbras.us> wrote:
> > Hi Ben-- this is definitely a valid issue. The newest wrappers are
> > works in progress; can you submit a bug report at  
> > bugzilla.bioperl.org ?
> > (as a Windows users, I call it a bug, but Dan may disagree!) (FYI,
> > some improvements to the wrapper interfaces are coming soon that
> > will attempt to standardize some of these kinds of issues, so stay  
> > tuned)
> > MAJ
> > ----- Original Message ----- From: "Ben Bimber" <bbimber at gmail.com>
> > To: <bioperl-l at lists.open-bio.org>
> > Sent: Sunday, February 21, 2010 9:28 PM
> > Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie  
> > andBio::Assembly::IO::bowtie now available BETA
> >
> >
> > 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).
> >
> > I made a crude hack to get it to work on my machine, but is this
> > something you would consider changing in bowtie.pm?  I'm not sure
> what
> > the most versatile approach to setting program path in a wrapper
> would
> > be, but I'd love to hear it.  I have still not entirely wrapped my
> > head around all the methods to handle program path in wrappers, so
> > perhaps there's a way to override this that I'm not aware of.
> >
> > Thanks,
> > Ben

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