How to use org.renci.common.exec

public static BashExecutor getInstance() {
  if (instance == null) {
    return new BashExecutor();
  }
  return instance;
}

  public CommandOutput execute(CommandInput input) throws ExecutorException {
    return execute(input, (File[]) null);
  }
}

  public void reschedule() throws CondorException {
    logger.debug("ENTERING reschedule()");
    try {
      Input input = new Input();
      input.setCommand(CONDOR_RESCHEDULE);
      Executor executor = Executor.getInstance();
      executor.run(input);
    } catch (ExecutorException e) {
      throw new CondorException("Problem running: " + CONDOR_RESCHEDULE);
    }
  }
}

@Override
public ModuleOutput call() throws Exception {
  CommandInput commandInput = new CommandInput();
  StringBuilder commandSB = new StringBuilder();
  commandSB.append(this.executable);
  if (argument != null) {
    for (String arg : argument) {
      commandSB.append(String.format(" %s", arg));
    }
  }
  commandInput.setCommand(commandSB.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

public void run() {
  for (LaunchDescriptorBean ldb : getLaunchDescriptorBeans()) {
    String command = ldb.getCommands().get(0);
    logger.debug("command = " + command);
    Executor sh = new Executor(command);
    sh.setEnvironment(new HashMap<String, String>());
    sh.setWorkDir(getWorkDirectory());
    try {
      sh.execute();
    } catch (ExecutorException e) {
      logger.error("Execution error: " + e.getMessage());
    }
    setStdOut(sh.getStdout());
    setStdErr(sh.getStderr());
    setExitCode(sh.getExitCode());
  }
}

@Override
public ModuleOutput call() throws ModuleException {
  CommandInput commandInput = new CommandInput();
  commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
      flagstatInput.getAbsolutePath(), output.getAbsolutePath()));
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput);
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws ModuleException {
  CommandInput commandInput = new CommandInput();
  commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
      flagstatInput.getAbsolutePath(), output.getAbsolutePath()));
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput);
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws ModuleException {
  CommandInput commandInput = new CommandInput();
  commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
      getWorkflowName().toUpperCase(), input.getAbsolutePath(), output.getAbsolutePath()));
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws Exception {
  logger.debug("ENTERING call()");
  StringBuilder command = new StringBuilder(getExecutable());
  command.append(" ").append(clusterDirectory.getAbsolutePath()).append("/");
  CommandInput commandInput = new CommandInput();
  logger.info("command.toString(): {}", command.toString());
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws Exception {
  CommandInput commandInput = new CommandInput();
  commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
      geneResults.getAbsolutePath(), origGeneResults.getAbsolutePath()));
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws Exception {
  logger.debug("ENTERING call()");
  StringBuilder command = new StringBuilder(getExecutable());
  command.append(" ").append(input.getAbsolutePath());
  command.append(" ").append(outputDirectory.getAbsolutePath());
  if (this.outputDirectory.isDirectory() && !this.outputDirectory.getAbsolutePath().endsWith("/")) {
    command.append("/");
  }
  CommandInput commandInput = new CommandInput();
  logger.info("command.toString(): {}", command.toString());
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws ModuleException {
  File userHome = new File(System.getProperty("user.home"));
  CommandInput commandInput = new CommandInput();
  StringBuilder command = new StringBuilder();
  command.append(String.format(getModuleClass().getAnnotation(Executable.class).value()));
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(userHome, ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws ModuleException {
  CommandInput commandInput = new CommandInput();
  commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
      getWorkflowName().toUpperCase(), input.getAbsolutePath(), output.getAbsolutePath()));
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws Exception {
  logger.debug("ENTERING call()");
  StringBuilder command = new StringBuilder(getExecutable());
  command.append(" ").append(output.getAbsolutePath());
  if (fastq) {
    command.append(" 1");
  }
  command.append(" ").append(input.getAbsolutePath());
  CommandInput commandInput = new CommandInput();
  logger.info("command.toString(): {}", command.toString());
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws ModuleException {
  CommandInput commandInput = new CommandInput();
  StringBuilder command = new StringBuilder();
  command.append(getModuleClass().getAnnotation(Executable.class).value());
  command.append(" ").append(inFile.getAbsolutePath());
  command.append(" ").append(outFile.getAbsolutePath());
  command.append(" ").append(transcriptDB.getAbsolutePath());
  command.append(" ").append(sqHeader.getAbsolutePath());
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws Exception {
  logger.debug("ENTERING call()");
  StringBuilder command = new StringBuilder(getExecutable());
  command.append(" ").append(this.minimumAnchor.toString());
  command.append(" ").append(this.maximumAnchor.toString());
  command.append(" ").append(this.maximumSequenceThreshold.toString());
  command.append(" ").append(this.junction.getAbsolutePath());
  command.append(" ").append(this.referenceSequenceDirectory.getAbsolutePath());
  if (this.referenceSequenceDirectory.isDirectory()
      && !this.referenceSequenceDirectory.getAbsolutePath().endsWith("/")) {
    command.append("/");
  }
  command.append(" ").append(this.output.getAbsolutePath());
  CommandInput commandInput = new CommandInput();
  logger.info("command.toString(): {}", command.toString());
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws Exception {
  CommandInput commandInput = new CommandInput();
  StringBuilder command = new StringBuilder();
  command.append(getModuleClass().getAnnotation(Executable.class).value());
  command.append(" -c ").append(column.toString());
  command.append(" -q ").append(quantile.toString());
  command.append(" -t ").append(target.toString());
  command.append(" -o ").append(output.getAbsolutePath());
  command.append(" ").append(input.getAbsolutePath());
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws Exception {
  logger.debug("ENTERING call()");
  Properties readLengthProperties = new Properties();
  FileInputStream fis = new FileInputStream(this.readLength);
  readLengthProperties.loadFromXML(fis);
  fis.close();
  StringBuilder command = new StringBuilder(getExecutable());
  command.append(" ").append(junction.getAbsolutePath());
  command.append(" ").append(readLengthProperties.getProperty("maxLength"));
  command.append(" ").append(minimumAnchor.toString());
  command.append(" ").append(referenceSequenceDirectory.getAbsolutePath());
  command.append(" ").append(sam.getAbsolutePath());
  CommandInput commandInput = new CommandInput();
  logger.info("command.toString(): {}", command.toString());
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws ModuleException {
  CommandInput commandInput = new CommandInput();
  StringBuilder command = new StringBuilder();
  command.append(getModuleClass().getAnnotation(Executable.class).value());
  try {
    command.append(output.getAbsolutePath());
    for (File f : entry) {
      command.append(" ").append(f.getAbsolutePath());
    }
  } catch (Exception e) {
    throw new ModuleException(e);
  }
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}

@Override
public ModuleOutput call() throws Exception {
  CommandInput commandInput = new CommandInput();
  StringBuilder command = new StringBuilder();
  command.append(getModuleClass().getAnnotation(Executable.class).value());
  command.append(" ").append(input.getAbsolutePath()).append(" ").append(output.getAbsolutePath());
  commandInput.setCommand(command.toString());
  CommandOutput commandOutput;
  try {
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  FileData fileData = new FileData();
  fileData.setMimeType(MimeType.APPLICATION_PDF);
  fileData.setName(output.getName());
  addFileData(fileData);
  return new ShellModuleOutput(commandOutput);
}