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(); $obj->save_tempfiles($booleanflag) 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.

Mailing Lists
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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 email or the web: bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ Email jason@bioperl.org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

run
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

error_string
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)

no_param_checks
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)

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

outfile_name
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

tempdir
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

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

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

version
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

executable
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

program_path
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

program_dir
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

program_name
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