Sendu Bala
and 1 contributors


Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables


  # do not use this object directly, it provides the following methods
  # for its subclasses

  my $errstr = $obj->error_string();
  my $exe    = $obj->executable();
  my $outfile= $obj->outfile_name();
  my $tempdir= $obj->tempdir(); # get a temporary dir for executing
  my $io     = $obj->io;  # Bio::Root::IO object
  my $cleanup= $obj->cleanup(); # remove tempfiles

  $obj->run({-arg1 => $value});


This is a basic module from which to build executable wrapper modules. It has some basic methods to help when implementing new modules.


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AUTHOR - Jason Stajich



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : run
 Usage   : $wrapper->run({ARGS HERE});
 Function: Support generic running with args passed in
           as a hashref
 Returns : Depends on the implementation, status OR data
 Args    : hashref of named arguments


 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysis run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)


 Title   : arguments
 Usage   : $obj->arguments($newval)
 Function: Commandline parameters 
 Returns : value of arguments
 Args    : newvalue (optional)


 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values
 Returns : value of no_param_checks
 Args    : newvalue (optional)


 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Returns : value of save_tempfiles
 Args    : newvalue (optional)


 Title   : outfile_name
 Usage   : my $outfile = $wrapper->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to


 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none


 Title   : cleanup
 Usage   : $wrapper->cleanup();
 Function: Will cleanup the tempdir directory
 Returns : none
 Args    : none


 Title   : io
 Usage   : $obj->io($newval)
 Function: Gets a Bio::Root::IO object
 Returns : Bio::Root::IO object
 Args    : none


 Title   : version
 Usage   : $version = $wrapper->version()
 Function: Returns the program version (if available)
 Returns : string representing version of the program 
 Args    : [Optional] value to (re)set version string


 Title   : executable
 Usage   : my $exe = $factory->executable();
 Function: Finds the full path to the executable
 Returns : string representing the full path to the exe
 Args    : [optional] name of executable to set path to
           [optional] boolean flag whether or not warn when exe is not found


 Title   : program_path
 Usage   : my $path = $factory->program_path();
 Function: Builds path for executable 
 Returns : string representing the full path to the exe
 Args    : none


 Title   : program_dir
 Usage   : my $dir = $factory->program_dir();
 Function: Abstract get method for dir of program. To be implemented
           by wrapper.
 Returns : string representing program directory 
 Args    : none 


 Title   : program_name
 Usage   : my $name = $factory->program_name();
 Function: Abstract get method for name of program. To be implemented
           by wrapper.
 Returns : string representing program name
 Args    : none