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

Mon Feb 22 12:53:25 EST 2010

Hi Ben--
I'd direct you to Bio::Tools::Run::WrapperBase and 
B:T:R:WrapperBase::CommandExts
(in bioperl-live). You'll want your wrapper to inherit from B:T:R:WrapperBase; 
then
(as Jason pointed out) the executable() and program_dir() methods will be 
available
to it. You can rely on executable() to find the path using the PATH variable, or 
you can
use executable/program_dir to set these paths explicitly. ComandExts adds 
methods
to WrapperBase that allow more complex programs or groups of programs to be
defined in a set of global config variables: Bowtie, BWA, Maq, and Samtools use 
this
module.
(What I'm secretly working on is a package called WrapperMaker, that uses XML
based on an XML Schema to define program names, commands, inputs and other 
details
(rather than an ugly Config module exporting hard to remember global variables),
passing them to CommandExts and providing a nice WrapperBase object
transparently. This is getting there, but isn't ready for primetime.)
cheers MAJ
----- Original Message ----- 
From: "Ben Bimber" <bimber at wisc.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Monday, February 22, 2010 11:40 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie andBio::Assembly::IO::bowtie 
now available BETA

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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