NAME

Bio::Tools::Run::AnalysisFactory::Pise - A class to create Pise application objects.

SYNOPSIS

  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');

DESCRIPTION

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:

1 factory creation:

  my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(
                                 -location => 'http://somewhere/Pise/cgi-bin',
                                 -email => 'me@myhome');

2 program creation:

  my $program = $factory->program('water', 
                           -location => 'http://somewhere/Pise/cgi-bin/water.pl'
                                  );

3 any time before running:

  $program->location('http://somewhere/Pise/cgi-bin/water.pl');
  $job = $program->run();

4 when running:

  $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;

FEEDBACK

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/wiki/Mailing_lists  - 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.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

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.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

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.

cpanm Bio::Factory::EMBOSS

perl -MCPAN -e shell
install Bio::Factory::EMBOSS