How to use

getInstance

method

in

org.renci.common.exec.BashExecutor

@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()");
  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 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 Exception {
  logger.debug("ENTERING call()");
  StringBuilder command = new StringBuilder(getExecutable());
  command.append(" ").append(this.minimumAnchorWidth.toString());
  command.append(" ").append(this.maximumAnchor.toString());
  command.append(" ").append(this.maximumThresholdEach.toString());
  command.append(" ").append(this.maximumThresholdTotal.toString());
  command.append(" ").append(this.junction.getAbsolutePath());
  command.append(" 1");
  command.append(" ").append(this.fusionJunction.getAbsolutePath());
  command.append(" 1");
  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 {
  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 {
  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);
}

@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 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 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 {
  CommandOutput commandOutput = null;
  try {
    StringBuilder command = new StringBuilder();
    command.append("/bin/ln -s ").append(fastaDB).append(" ").append(symlinkFile.getAbsolutePath()).append(";");
    command.append(String.format("$%s_%s", getWorkflowName().toUpperCase(),
        getModuleClass().getAnnotation(Executable.class).value()));
    command.append(" ")
        .append(getModuleClass().getDeclaredField("algorithm").getAnnotation(InputArgument.class).flag())
        .append(" ").append(algorithm.getValue());
    command.append(" ").append(symlinkFile.getAbsolutePath());
    CommandInput commandInput = new CommandInput();
    File mapseqTmpDir = new File(System.getenv("MAPSEQ_HOME"), "tmp");
    commandInput.setWorkDir(mapseqTmpDir);
    commandInput.setCommand(command.toString());
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (Exception 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 ModuleException {
  CommandOutput commandOutput = null;
  try {
    StringBuilder command = new StringBuilder();
    command.append("/bin/ln -s ").append(fastaDB).append(" ").append(symlinkFile.getAbsolutePath()).append(";");
    command.append(String.format("$%s_%s", getWorkflowName().toUpperCase(),
        getModuleClass().getAnnotation(Executable.class).value()));
    command.append(" ")
        .append(getModuleClass().getDeclaredField("algorithm").getAnnotation(InputArgument.class).flag())
        .append(" ").append(algorithm.getValue());
    command.append(" ").append(symlinkFile.getAbsolutePath());
    CommandInput commandInput = new CommandInput();
    File mapseqTmpDir = new File(System.getenv("MAPSEQ_HOME"), "tmp");
    commandInput.setWorkDir(mapseqTmpDir);
    commandInput.setCommand(command.toString());
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  } catch (Exception 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 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 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);
}

@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 {
  logger.debug("ENTERING call()");
  CommandOutput commandOutput;
  try {
    StringBuilder command = new StringBuilder();
    command.append(getModuleClass().getAnnotation(Executable.class).value());
    command.append(" ").append(regularExpression);
    command.append(" > ").append(outputFile.getAbsolutePath());
    CommandInput commandInput = new CommandInput();
    commandInput.setWorkDir(directory);
    commandInput.setCommand(command.toString());
    Executor executor = BashExecutor.getInstance();
    commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
    if (mimeType != null) {
      FileData fileData = new FileData();
      fileData.setName(outputFile.getName());
      fileData.setMimeType(mimeType);
      addFileData(fileData);
    }
  } catch (ExecutorException e) {
    throw new ModuleException(e);
  }
  return new ShellModuleOutput(commandOutput);
}