Provided by: libbio-perl-run-perl_1.6.9-2_all bug


       Bio::Tools::Run::Analysis - Module representing any (remote or local) analysis tool


         # run analysis 'seqret' using a default location and a default
         # access method (which means using a Web Service at EBI)
         use Bio::Tools::Run::Analysis;
         print new Bio::Tools::Run::Analysis (-name => 'edit::seqret')
              ->wait_for ({ sequence_direct_data => 'tatatacgtatacga',
                            osformat => 'embl'
              ->result ('outseq');

         # run a longer job without waiting for its completion
         use Bio::Tools::Run::Analysis;
         my $job = Bio::Tools::Run::Analysis->new(-name => 'edit::seqret')
                        ->run ({ sequence_direct_data => 'tatatacgtatacga',
                                 osformat => 'embl'
         # ...and after a while
         $job->result ('outseq');

         # get all results in the same invocation (as a hash reference
         # with result names as keys) - let the module decide which
         # results are binary (images in this examples) and save those
         # in file (or files); it also shows how to tell that the module
         # should read input data from a local file first
         use Bio::Tools::Run::Analysis;
         my $results =
           Bio::Tools::Run::Analysis->new(-name => 'alignment_multiple::prettyplot')
              ->wait_for ( { msf_direct_data => '@/home/testdata/my.seq' } )
              ->results ('?');
         use Data::Dumper;
         print Dumper ($results);

         # get names, types of all inputs and results,
         # get short and detailed (in XML) service description
         use Bio::Tools::Run::Analysis;
         my $service = Bio::Tools::Run::Analysis->new(-name => 'edit::seqret');
         my $hash1 = $service->input_spec;
         my $hash2 = $service->result_spec;
         my $hash3 = $service->analysis_spec;
         my $xml = $service->describe;

         # get current job status
         use Bio::Tools::Run::Analysis;
         print new Bio::Tools::Run::Analysis (-name => 'edit::seqret')
           ->run ( { #...input data...
                   } )

         # run a job and print its job ID, keep the job un-destroyed
         use Bio::Tools::Run::Analysis;
         my $job =
           Bio::Tools::Run::Analysis->new(-name => 'edit::seqret',
                                          -destroy_on_exit => 0)
           ->run ( { sequence_direct_data => '@/home/testdata/mzef.seq' } );
         print $job->id . "\n";
         # prints (for example):
         #    edit::seqret/c8ef56:ef535489ac:-7ff4

         # another time, on another planet, you may say
         use Bio::Tools::Run::Analysis;
         my $job =
           Bio::Tools::Run::Analysis::Job->new(-name => 'edit::seqret',
                                               -id => 'edit::seqret/c8ef56:ef535489ac:-7ff4');
         print join ("\n",
                   'Finished: ' . $job->ended (1),   # (1) means 'formatted'
                   'Elapsed time: ' . $job->elapsed,
                   $job->result ('outseq')

         # ...or you may achieve the same keeping module
         # Bio::Tools::Run::Analysis::Job invisible
         use Bio::Tools::Run::Analysis;
         my $job =
           Bio::Tools::Run::Analysis->new(-name => 'edit::seqret')
               ->create_job ('edit::seqret/c8ef56:ef535489ac:-7ff4');
         print join ("\n",
                   # ...

         # ...and later you may free this job resources

         # --- See DESCRIPTION for using generator '':


       The module represents an access to the local and/or remote analysis tools in a unified way
       that allows adding new access methods (protocols) seamlessly.

       At the moment of writing, there is available a SOAP access to almost all EMBOSS
       applications, running at the European Bioinformatics Institute.

       The documentation of all "public" methods are to be found in "Bio::AnalysisI". A tutorial
       (and examples how to call almost all public methods) is in the script "panalysis.PLS" (go
       to the "scripts" directory and type "perldoc panalysis.PLS").

       The module "Bio::Tools::Run::Analysis" uses general approach allowing to set arbitrary
       input data and to retrieve results by naming them. However, sometimes is more convenient
       to use a specific module, representing one analysis tool, that already knows about
       available input and result names. Such analyses-specific Perl modules can be generated by
       "papplmaker.PLS" generator. Its features and usage are documented in the generator (go to
       the "scripts" directory and type "perldoc papplmaker.PLS").

         # this will generate module
         perl papplmaker.PLS -n edit.seqret -m Seqret

         # ...which can be used with data-specific methods
         use Seqret;
         my $outseq = new Seqret
           ->sequence_direct_data ('@/home/testdata/my.seq')
           ->osformat ('embl')
         print $outseq;


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       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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:


       Martin Senger (


       Copyright (c) 2003, Martin Senger and EMBL-EBI.  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.




       Here is the rest of the object methods.  Internal methods are preceded with an underscore

        Usage   : my $tool =
                    Bio::Tools::Run::Analysis->new(-access => 'soap',
                                                   -name => 'edit.seqret',
        Returns : a new Bio::Tools::Run::Analysis object representing the given tool
        Args    : There may be additional arguments which are specific
                  to the access method (see methods 'new' or '_initialize'
                  of the access-specific implementations (such as module
                  Bio::Tools::Run::Analysis::soap for a SOAP-based access).

                  The recognised and used arguments are:

       It builds, populates and returns a new "Bio::Tools::Run::Analysis" object. This is how it
       is seen from the outside. But in fact, it builds, populates and returns a more specific
       lower-level object, for example "Bio::Tools::Run::Analysis::soap" object - which one it
       depends on the "-access" parameter.

           It indicates what lower-level module to load.  Default is 'soap'.  Other (but future)
           possibilities may be:

              -access => 'novella'
              -access => 'local'

           A location of the service. The contents is access-specific (see details in the lower-
           level implementation modules).

           Default is "" ( services running at European
           Bioinformatics Institute on top of most of EMBOSS analyses, and on few others).

           A name of an analysis tool, or a name of its higher-level abstraction, possibly
           including a category where the analysis belong to. There is no default value (which
           usually means that this parameter is mandatory unless your -location parameter
           includes also the name (but it is then access-dependent).

       -destroy_on_exit => '0'
           Default value is '1' which means that all Bio::Tools::Run::Analysis::Job objects -
           when being finalised - will send a request to the remote site to forget the results of
           these jobs.

           If you change it to '0' make sure that you know the job identification - otherwise you
           will not be able to re-established connection with it (later, when you use your
           program again). This can be done by calling method "id" on the job object (such object
           is returned by any of these methods: "create_job", "run", "wait_for").

           In addition to the location parameter, you may need to specify also a location/URL of
           an HTTP proxy server (if your site requires one). The expected format is
           "http://server:port".  There is no default value. It is also an access-specific
           parameter which may not be used by all access methods.

           For long(er) running jobs the HTTP connection may be time-outed. In order to avoid it
           (or, vice-versa, to call timeout sooner) you may specify "timeout" with the number of
           seconds the connection will be kept alive. Zero means to keep it alive forever. The
           default value is two minutes.

   VERSION and Revision
        Usage   : print $Bio::Tools::Run::Analysis::VERSION;
                  print $Bio::Tools::Run::Analysis::Revision;

Module Bio::Tools::Run::Analysis::Job

       It represents a job, a single execution of an analysis tool. Usually you do not
       instantiate these objects - they are returned by methods "create_job", "run", and
       "wait_for" of "Bio::Tools::Run::Analysis" object.

       However, if you wish to re-create a job you need to know its ID (method "id" gives it to
       you). The ID can be passed directly to the "new" method, or again you may use "create_job"
       of a "Bio::Tools::Run::Analysis" object with the ID as parameter. See SYNOPSIS above for
       an example.

       Remember that all public methods of this module are described in details in interface
       module "Bio::AnalysisI" and in the tutorial in the "" script.

        Usage   : my $job = Bio::Tools::Run::Analysis::Job->new
                              (-access => 'soap',
                               -name => 'edit.seqret',
                               -id => 'xxxyyy111222333'
        Returns : a re-created object representing a job
        Args    : The same arguments as for Bio::Tools::Run::Analysis object:
                    (and perhaps others)
                  Additionally and specifically for this object:

       -id A job ID created some previous time and now used to re-create the same job (in order
           to re-gain access to this job results, for example).

           A "Bio::Tools::Run::Analysis" object whose properties (such as "-access" and
           "-location" are used to re-create this job object.

Module Bio::Tools::Run::Analysis::Utils

       It contains several general utilities. These are "functions", not methods. Therefore call
       them like, for example:

           &Bio::Tools::Run::Analysis::Utils::format_time (...);

        Usage   : Bio::Tools::Run::Analysis::Utils::format_time ($time);
        Returns : Slightly formatted $time
        Args    : $time is number of seconds from the beginning of Epoch

       It returns what "localtime" returns which means that return value is different in the
       array and scalar context (see localtime). If $time is ``-1'' it returns 'n/a' (in the
       scalar context) or an empty array (in the array context). If $time is too small to
       represent the distance from the beginning of the Epoch, it returns it unchanged (the same
       in any contex) - this is reasonable for $time representing an elapsed time.

       The function is used to format times coming back from various job time methods.

        Usage   : $class->_load_access_module ($access)
        Returns : 1 on success, undef on failure
        Args    : 'access' should contain the last part of the
                  name of a module who does the real implementation

       It does (in the run-time) a similar thing as

          require Bio::Tools::Run::Analysis::$access

       It prints an error on STDERR if it fails to find and load the module (for example, because
       of the compilation errors in the module).

        Usage   : Bio::Tools::Run::Analysis::Utils::guess_access ($rh_params)
        Returns : string with a guessed access protocol (e.g. 'soap'),
                  or undef if the guessing failed
        Args    : 'rh_params' is a hash reference containing parameters given
                  to the 'new' method.

       It makes an expert guess what kind of access/transport protocol should be used to access
       the underlying analysis. The guess is based on the parameters in rh_params. Rememeber that
       this method is called only if there was no -access parameter which could tell directly
       what access method to use.