@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); }