[Bioperl-l] Fwd: [Volunteer] submitting modules (PiseWorkflow.pm)

[Catherine Letondal]

On Mon, Aug 25, 2003 at 10:04:26PM -0400, Jason Stajich wrote:
> submit it as a feature request at http://bugzilla.open-bio.org.
> 
> I'll leave it up to Catherine Letondal to make the okay for adding the
> code.

I'm rather Ok to add the code in CVS if it is ok with you. This is a
nice and light-weight module for building a workflow. I have tested it
and discuss with Samuel about its features. For instance, say you to
build a workflow with an alignment and a phylogeny: you first
instantiate the applications and set parameters, without running
them. You then build the workflow and run it. Parallel branches of the
workflow are submitted in parallel.

use Bio::Tools::Run::AnalysisFactory::Pise;
use Bio::Tools::Run::PiseWorkflow;

my $factory = new Bio::Tools::Run::AnalysisFactory::Pise();
my $clustalw = $factory->program('clustalw');
$clustalw->infile($ARGV[0]);
my $protdist = $factory->program('protdist');
my $protpars = $factory->program('protpars');
my $fitch = $factory->program('fitch');
my $consense = $factory->program('consense');
my $workflow = Bio::Tools::Run::PiseWorkflow->new();
$workflow->addpipe(-method => $clustalw,
                   -tomethod => $protdist,
                   -pipetype => 'readseq_ok_alig');
$workflow->addpipe(-method => $clustalw,
                   -tomethod => $protpars,
                   -pipetype => 'readseq_ok_alig');
$workflow->addpipe(-method => $protdist,
  	           -tomethod => $fitch,
		   -pipetype => 'phylip_dist');
$workflow->addpipe(-method => $protpars,
	           -tomethod => $consense,
	           -pipetype =>  'phylip_tree');
$workflow->run();

Results are reported in 2 forms:
an HTML file that is created at the beginning of the run, containing
jobs status and link to the results, and a perl file containing this
information in perl format. Errors a just reported. So, it's really
lightweight, compared to biopipe for instance, but I believe, still
very useful. 

> 
> -jason
> 
> On Mon, 25 Aug 2003, James Freeman wrote:
> 
> > See below.
> >
> > Begin forwarded message:
> >
> > > From: "Samuel Thoraval" <s.thoraval at imb.uq.edu.au>
> > > Date: Mon Aug 25, 2003  19:46:03 US/Eastern
> > > To: volunteer at open-bio.org
> > > Subject: [Volunteer] submitting modules
> > >
> > > Hello,
> > >
> > > I have written a module for the Bioperl/Pise API.
> > > I would like to submit it.
> > > To which email should i send the details, code and request to ?
> > >
> > > Regards,
> > >
> > > Samuel Thoraval

-- 
Catherine Letondal -- Pasteur Institute Computing Center