Bio::Tools::Run::PiseWorkflow # First, create a Bio::Tools::Run::AnalysisFactory::Pise object: my $factory = new Bio::Tools::Run::AnalysisFactory::Pise(); # Then create the application objects (Pise::Run::Tools::PiseApplication): my $clustalw = $factory->program('clustalw'); $clustalw->infile($my_alignment_file); my $protpars = $factory->program('protpars'); # You can specify different servers for different applications : my $protdist = $factory->program('protpars' -remote => 'http://kun.homelinux.com/cgi-bin/Pise/5.a//protpars.pl', -email => 'your_email'); # Create a new workflow object : my $workflow = Bio::Tools::Run::PiseWorkflow->new(); # Define the workflow's methods using the application objects: # the application method $protpars will receive the output of # type 'readseq_ok_alig' from the application method $clustalw. $workflow->addpipe(-method => $clustalw, -tomethod => $protpars, -pipetype => 'readseq_ok_alig'); # The application method $clustalw will be piped to a second # application method ($protdist) using the output of type 'readseq_ok_alig'. $workflow->addpipe(-method => $clustalw, -tomethod => $protdist, -pipetype => 'readseq_ok_alig'); # The application method $protpars will be piped to the application # method $consense using the output of type 'phylip_tree'. my $consense = $factory->program('consense'); $workflow->addpipe(-method => $protpars, -tomethod => $consense, -pipetype => 'phylip_tree'); # Run the workflow. $workflow->run(); A class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication. Create the workflow object : my $workflow = Bio::Tools::Run::PiseWorkflow->new(); You can specify which application will be used as the first method at creation of the workflow object: (by default, this first method will be the one specified by the option -method at the First call of the function addpipe(). my $workflow = Bio::Tools::Run::PiseWorkflow->new($clustalw); Use the function addpipe to define the workflow : $workflow->addpipe(-method => $clustalw, -tomethod => $protpars, -pipetype => 'readseq_ok_alig'); One method may be piped to different methods in the workflow: $workflow->addpipe(-method => $clustalw, -tomethod => $protdist, -pipetype => 'readseq_ok_alig'); To run the workflow (processes will be forked when possible): $workflow->run(); An html temporary file summarising the jobs status will be created in the working directory. The html output file can also be specified: $workflow->run(-html => 'jobs.html');

new
Title : new() Usage : my $workflow = Bio::Tools::Run::PiseWorkflow->new(); Function: Creates a Bio::Tools::Run::PiseWorkflow object. Example : my $workflow = Bio::Tools::Run::PiseWorkflow->new(); Returns : An instance of Bio::Tools::Run::PiseWorkflow.

addpipe
Title : addpipe() Usage : $workflow = Bio::Tools::Run::PiseWorkflow->addpipe( -method => $clustalw, -tomethod => $protpars, -pipetype => 'readseq_ok_alig'); Function: Pipe two methods of class PiseApplication in the workflow object. Example : $workflow = Bio::Tools::Run::PiseWorkflow->addpipe($clustalw, $protpars, 'readseq_ok_alig'); Returns :

run
Title : run() Usage : $workflow = Bio::Tools::Run::PiseWorkflow->run(); Function: Run the defined workflow. You may provide an interval for jobs' completion checking and a file for html output. Examples : $workflow = Bio::Tools::Run::PiseWorkflow->run(); $workflow = Bio::Tools::Run::PiseWorkflow->run(-interval => '200', -html => 'jobs.html'); Returns :