ProvisionDependenciesBundle (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.module.Module
- - net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

All Implemented Interfaces:

ModuleInterface
```
public class ProvisionDependenciesBundle
extends Module
```
Purpose: This module takes a software bundle and unzips it to the temporary directory. Software bundles let you create a directory structure containing binary applications and their associated files that can then be referenced by the module. See the SeqWare wiki at http://seqware.sf.net for information on creating these software bundles. TODO: move the download code to an S3 utility, factor out common code between this and ProvisionFiles object

Version:

$Id: $Id

Author:

boconnor

Field Summary
- Fields inherited from class net.sourceforge.seqware.pipeline.module.Module
  processingAccession, VERSION

Constructor Summary

Constructors
Constructor and Description

ProvisionDependenciesBundle()

Constructors
Constructor and Description
`ProvisionDependenciesBundle()`

Method Summary

Methods
Modifier and Type	Method and Description
`ReturnValue`	`do_run()` do_run.
`ReturnValue`	`do_test()` do_test.
`ReturnValue`	`do_verify_input()` do_verify_input.
`ReturnValue`	`do_verify_output()` do_verify_output.
`ReturnValue`	`do_verify_parameters()` do_verify_parameters.
`String`	`get_syntax()` get_syntax.
`protected joptsimple.OptionParser`	`getOptionParser()` getOptionParser.

Methods inherited from class net.sourceforge.seqware.pipeline.module.Module
clean_up, get_galaxy_xml, getAlgorithm, getMetadata, getParameters, getProcessingAccession, getStderrFile, getStdoutFile, init, setAlgorithm, setMetadata, setParameters, setProcessingAccession, setStderrFile, setStdoutFile

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - ProvisionDependenciesBundle
```
public ProvisionDependenciesBundle()
```
- Method Detail
  - getOptionParser
```
protected joptsimple.OptionParser getOptionParser()
```
    getOptionParser.
    
    Overrides:
    
    getOptionParser in class Module
    
    Returns:
    a OptionParser object.
  - get_syntax
```
public String get_syntax()
```
    get_syntax.
    
    Specified by:
    
    get_syntax in interface ModuleInterface
    
    Overrides:
    
    get_syntax in class Module
    
    Returns:
    a String object.
  - do_test
```
public ReturnValue do_test()
```
    do_test.
    Things to check: * FIXME
    
    Specified by:
    
    do_test in interface ModuleInterface
    
    Specified by:
    
    do_test in class Module
    
    Returns:
  - do_verify_parameters
```
public ReturnValue do_verify_parameters()
```
    do_verify_parameters.
    
    Specified by:
    
    do_verify_parameters in interface ModuleInterface
    
    Specified by:
    
    do_verify_parameters in class Module
    
    Returns:
  - do_verify_input
```
public ReturnValue do_verify_input()
```
    do_verify_input.
    
    Specified by:
    
    do_verify_input in interface ModuleInterface
    
    Specified by:
    
    do_verify_input in class Module
    
    Returns:
  - do_run
```
public ReturnValue do_run()
```
    do_run.
    
    Specified by:
    
    do_run in interface ModuleInterface
    
    Specified by:
    
    do_run in class Module
    
    Returns:
  - do_verify_output
```
public ReturnValue do_verify_output()
```
    do_verify_output.
    
    Specified by:
    
    do_verify_output in interface ModuleInterface
    
    Specified by:
    
    do_verify_output in class Module
    
    Returns:

Class ProvisionDependenciesBundle

Field Summary

Fields inherited from class net.sourceforge.seqware.pipeline.module.Module

Constructor Summary

Method Summary

Methods inherited from class net.sourceforge.seqware.pipeline.module.Module

Methods inherited from class java.lang.Object

Constructor Detail

ProvisionDependenciesBundle

Method Detail

getOptionParser

get_syntax

do_test

do_verify_parameters

do_verify_input

do_run

do_verify_output