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.
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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 analysus run is stored. Returns : value of error_string 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) Function: 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 after a PAML run Returns : none Args : none
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<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
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.