@Override
public boolean isOperational(ExecutionContext executionContext) {
if (!new JellyfishCountV11(this.conanExecutorService).isOperational(executionContext)) {
log.warn("Jellyfish Count is not operational.");
return false;
}
if (!new JellyfishMergeV11(this.conanExecutorService).isOperational(executionContext)) {
log.warn("Jellyfish Merge is not operational.");
return false;
}
KatGcpV1 katGcpProc = new KatGcpV1();
katGcpProc.setConanProcessService(this.getConanProcessService());
if (!katGcpProc.isOperational(executionContext)) {
log.warn("KAT GCP is not operational.");
return false;
}
KatPlotDensityV1 katPlotDensityProc = new KatPlotDensityV1();
katPlotDensityProc.setConanProcessService(this.getConanProcessService());
if (!katPlotDensityProc.isOperational(executionContext)) {
log.warn("KAT Plot Density is not operational.");
return false;
}
log.info("Read Kmer counting stage is operational.");
return true;
}
private List<ExecutionResult> executeKatGcp(
JobOutputMap jfCountOutputs, String jobPrefix, int threads, int memory, boolean runInParallel)
throws InterruptedException, ProcessExecutionException, ConanParameterException {
List<ExecutionResult> output = new ArrayList<>();
for (Map.Entry<String, Set<File>> entry : jfCountOutputs.entrySet()) {
for (File inputFile : entry.getValue()) {
File outputPrefix = new File(inputFile.getAbsolutePath() + ".kat-gcp");
File matrixFile = new File(outputPrefix + ".mx");
File plotFile = new File(matrixFile.getAbsolutePath() + ".png");
KatGcpV1 katGcpProc = this.makeKatGcpProc(inputFile, outputPrefix, threads);
KatPlotDensityV1 katPlotDensityProc = this.makeKatPlotDensityProc(matrixFile, plotFile);
katGcpProc.addPostCommand(katPlotDensityProc.getCommand());
ExecutionResult result =
this.conanExecutorService.executeProcess(
katGcpProc,
inputFile.getParentFile(),
jobPrefix + "-" + inputFile.getName(),
threads,
memory,
runInParallel);
output.add(result);
}
}
return output;
}