Bio::Tools::Run::AnalysisFactory::Pise - A class to create Pise application objects. use Bio::Tools::Run::AnalysisFactory::Pise; # Build a Pise factory my $factory = new Bio::Tools::Run::AnalysisFactory::Pise(); # Then create an application object (Pise::Run::Tools::PiseApplication): my $program = $factory->program('genscan'); # Set parameters $program->seq($ARGV[0]); # Next, run the program # (notice that you can set some parameters at run time) my $job = $program->run(-parameter_file => "Arabidopsis.smat"); # Test for submission errors: if ($job->error) { print "Job submission error (",$job->jobid,"):\n"; print $job->error_message,"\n"; exit; } # Get results print STDERR $job->content('genscan.out'); # or: my $result_file = $job->save('genscan.out'); Bio::Tools::Run::AnalysisFactory::Pise is a class to create Pise application objects, that let you submit jobs on a Pise server. my $factory = new Bio::Tools::Run::AnalysisFactory::Pise( -email => 'me@myhome'); The email is optional (there is default one). It can be useful, though. Your program might enter infinite loops, or just run many jobs: the Pise server maintainer needs a contact (s/he could of course cancel any requests from your address...). And if you plan to run a lot of heavy jobs, or to do a course with many students, please ask the maintainer before. The location parameter stands for the actual CGI location, except when set at the factory creation step, where it is rather the root of all CGI. There are default values for most of Pise programs. You can either set location at: my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new( -location => 'http://somewhere/Pise/cgi-bin', -email => 'me@myhome'); my $program = $factory->program('water', -location => 'http://somewhere/Pise/cgi-bin/water.pl' ); $program->location('http://somewhere/Pise/cgi-bin/water.pl'); $job = $program->run(); $job = $program->run(-location => 'http://somewhere/Pise/cgi-bin/water.pl'); You can also retrieve a previous job results by providing its url: $job = $factory->job($url); You get the url of a job by: $job->jobid;

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. This software is provided "as is" without warranty of any kind. Bio::Tools::Run::PiseApplication Bio::Tools::Run::PiseJob

new
Title : new() Usage : my $program = Bio::Tools::Run::AnalysisFactory::Pise->new( -location => 'http://somewhere/cgi-bin/Pise', -email => $email); Function: Creates a Bio::Tools::Run::AnalysisFactory::Pise object, which function is to create interface object (Bio::Tools::Run::PiseApplication::program) for programs. Example : Returns : An instance of Bio::Tools::Run::AnalysisFactory::Pise.

program
Title : program() Usage : my $program = Bio::Tools::Run::AnalysisFactory::Pise->program( $program, -location => 'http://somewhere/cgi-bin/Pise', -email => $email, @params); Function: Creates a representation of a single Pise program. Example : Returns : An instance of Bio::Tools::Run::PiseApplication::$program.

job
Title : job(url) Usage : my $job = Bio::Tools::Run::AnalysisFactory::Pise->job( 'http://somewhere/cgi-bin/Pise/tmp/dnapars/A3459687595869098'); Function: Creates a previously run job by providing its jobid (url of results). Example : Returns : An instance of Bio::Tools::Run::PiseJob.