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

[Ben Bimber]

Mark,

Thanks for the reply.  I'll put in that bug.

I'm actually writing a couple wrappers for other utilities based on
bioperl.  Is there a preferred method to handle setting file path at
the moment?  Could you point me to a wrapper that uses this?

Ideally, I'd prefer to support both letting the user either set the
path via an environmental variable or when they create the factory:

	my $factory = Bio::Tools::Run::XXXXX->new(
            -command => 'blat',
            -prog_dir => '/myPath',
            );

-Ben


On Mon, Feb 22, 2010 at 10:01 AM, 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
>
>
>
>
> On Tue, Jan 19, 2010 at 3:18 PM, Dan Kortschak
> <dan.kortschak at adelaide.edu.au> wrote:
>>
>> Great.
>>
>> Thanks, Scott.
>>
>> Dan
>>
>> On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
>>>
>>> Dan,
>>>
>>> Life Tech has sample data for E. coli at
>>>
>>> http://solidsoftwaretools.com/gf/project/ecoli2x50/
>>>
>>> and
>>>
>>> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
>>>
>>> Reference sequences are included.
>>>
>>> Scott
>>>
>>> Scott Markel, Ph.D.
>>> Principal Bioinformatics Architect email: smarkel at accelrys.com
>>> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
>>> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
>>> San Diego, CA 92121 fax: +1 858 799 5222
>>> USA web: http://www.accelrys.com
>>>
>>> http://www.linkedin.com/in/smarkel
>>> Vice President, Board of Directors:
>>> International Society for Computational Biology
>>> Chair: ISCB Publications Committee
>>> Associate Editor: PLoS Computational Biology
>>> Editorial Board: Briefings in Bioinformatics
>>>
>>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
>>> Sent: Monday, 18 January 2010 6:48 PM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
>>> Bio::Assembly::IO::bowtie now available BETA
>>>
>>> Hi All,
>>>
>>> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
>>> short read aligner' are now available in the bioperl-live and
>>> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
>>> bioperl-run/trunk at 16726). Bowtie details are available here:
>>>
>>> http://bowtie-bio.sourceforge.net/index.shtml
>>>
>>> The modules can return a Bio::Assembly::Scaffold object (operating via
>>> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
>>> which requires lstein's Bio::DB::Sam, from CPAN). Note that Bio::DB::Sam
>>> uses large amounts of memory - the test suite works for me with >=2GB
>>> but not with 1GB due to this. (Is there a disk file system based tool
>>> for this for large projects?)
>>>
>>> Bowtie (>0.12.0) can align in colour space, but this is not currently
>>> supported by the wrapper though it should not be difficult to add. If
>>> someone can point me to a small set of colour space reads and a
>>> reference sequence I will be able to use these for testing.
>>>
>>> Thanks to the core devs for helping me with many of my problems in
>>> putting this together.
>>>
>>> Dan
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
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