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);
}
protected String makeInputStringFromLib(Library lib) throws ProcessExecutionException {
uk.ac.ebi.fgpt.conan.util.StringJoiner sj = new StringJoiner(" ");
for (File file : lib.getFiles()) {
if (!file.exists()) {
throw new ProcessExecutionException(
2, "Couldn't locate: " + file.getAbsolutePath() + "; for kmer counting.");
}
sj.add(file.getAbsolutePath());
}
String inputFilesStr = sj.toString();
// Check we have something plausible to work with
if (inputFilesStr.isEmpty())
throw new ProcessExecutionException(2, "Couldn't locate raw library files: " + lib.getName());
return inputFilesStr;
}