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

Ben Bimber bbimber at gmail.com
Mon Feb 22 17:23:01 EST 2010


I believe I did enter a bug this morning.  An env variable is not
necessary.  As long as we have some reasonable mechanism to specify
exe location when we run this on different servers that's all we need.
 thanks for making the change.


On Mon, Feb 22, 2010 at 4:18 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> 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).
> cheers
> Dan
> 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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