예제 #1
0
  protected JobOutput executeJellyfishMerger(
      Args args, String ecqName, Set<File> fileSet, File outputDir)
      throws InterruptedException, ProcessExecutionException, ConanParameterException, IOException {

    String suffix = "jellyfish_" + ecqName + "_all.jf31_0";

    String jobName = args.getJobPrefix() + "-merge-" + suffix;

    List<File> files = new ArrayList<>();
    files.addAll(fileSet);

    File outputFile = new File(outputDir, suffix);

    JellyfishMergeV11 jellyfishMerge =
        this.makeJellyfishMerge(files, outputFile, args.getOrganism());

    ExecutionResult id =
        this.conanExecutorService.executeProcess(
            jellyfishMerge,
            args.getOutputDir(),
            jobName,
            args.getThreadsPerProcess(),
            args.getMemoryPerProcess(),
            args.isRunParallel());

    id.setName("merge-" + suffix);

    return new JobOutput(id, outputFile);
  }
예제 #2
0
  protected JobOutput executeJellyfishCount(Args args, String ecqName, File outputDir, Library lib)
      throws ProcessExecutionException, InterruptedException, ConanParameterException, IOException {
    String suffix = "jellyfish_" + ecqName + "_" + lib.getName() + ".jf31";

    // Create the process
    JellyfishCountV11 jellyfishProcess =
        this.makeJellyfishCount(
            this.makeInputStringFromLib(lib),
            new File(new File(outputDir, ecqName), suffix).getAbsolutePath(),
            args.getOrganism(),
            args.getThreadsPerProcess());

    File outputFile = jellyfishProcess.getArgs().getOutputFile();

    // Create a job name
    String jobName = args.getJobPrefix() + "-count-" + suffix;

    // Start jellyfish
    final ExecutionResult id =
        this.conanExecutorService.executeProcess(
            jellyfishProcess,
            new File(outputDir, ecqName),
            jobName,
            args.getThreadsPerProcess(),
            args.getMemoryPerProcess(),
            args.isRunParallel());

    id.setName("count-" + suffix);

    return new JobOutput(id, outputFile);
  }