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

[Mark A. Jensen]

I believe we are using it, I think that the 'which' solution is somewhat crufty
at this stage ...
----- Original Message ----- 
From: "Jason Stajich" <jason.stajich at gmail.com>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>; "Ben Bimber" <bbimber at gmail.com>
Sent: Monday, February 22, 2010 11:41 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::BowtieandBio::Assembly::IO::bowtie now 
available BETA


> 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
>>
>>
>>
>>
>> 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
>>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>