@Override protected void setup(Context context) throws IOException, InterruptedException { super.setup(context); isFirstAttempt = taskId.endsWith("_0"); isRNA = HalvadeConf.getIsRNA(context.getConfiguration()); scc = HalvadeConf.getSCC(context.getConfiguration(), isRNA); sec = HalvadeConf.getSEC(context.getConfiguration(), isRNA); try { gff = HalvadeFileUtils.downloadGFF(context, taskId); } catch (URISyntaxException ex) { Logger.EXCEPTION(ex); throw new InterruptedException("Error when downloading GFF file"); } filterBedFile = HalvadeConf.getFilterBed(context.getConfiguration()); filterDBsnp = HalvadeConf.getFilterDBSnp(context.getConfiguration()); useUnifiedGenotyper = HalvadeConf.getUseUnifiedGenotyper(context.getConfiguration()); redistribute = HalvadeConf.getRedistribute(context.getConfiguration()); containers = HalvadeConf.getMapContainerCount(context.getConfiguration()); tasksLeft = Integer.parseInt(context.getConfiguration().get("mapred.map.tasks")) - taskNr; // get task number: if (redistribute && tasksLeft < containers) { threads = 6; } }