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); }