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);
}
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);
}