public static SGEWorkManager GetSGEWorkManager(ILogger logger, IDirectoryLocation analysisFolder,
ISampleSettings settings, IsasConfiguration config)
{
LocalWorkManager local = GetLocalWorkManager(logger, analysisFolder, settings, config);
return new SGEWorkManager(logger, local,
config.ClusterQueueName, config.ClusterParallelEnvironmentName);
}
public static LocalWorkManager GetLocalWorkManager(ILogger logger, IDirectoryLocation analysisFolder,
ISampleSettings settings, IsasConfiguration config)
{
int maxThreadCount = settings.GetIntegerSetting(SampleSheetUtils.MaximumThreadCount, 0);
float maxMemGB = settings.GetFloatSetting(SampleSheetUtils.MaximumMemoryGB, config.MaximumMemoryGB);
var loggingFolder = IsasFilePaths.GetLoggingFolder(analysisFolder);
return new LocalWorkManager(logger, loggingFolder, maxThreadCount, maxMemGB, config.MaximumHoursPerProcess);
}
public SmallPedigreeCheckpointFactory(
ISampleSettings sampleSettings,
IWorkManager workManager,
ILogger logger,
ExecutableProcessor executableProcessor,
DbSnpVcfProcessor dbSnpVcfProcessor,
bool detectCnvDefault, IFileLocation pedigreefileNameStub)
{
_workManager = workManager;
_logger = logger;
_executableProcessor = executableProcessor;
_pedigreefileNameStub = pedigreefileNameStub;
_canvasWorkerFactory = new CanvasWorkerFactory(sampleSettings, workManager, logger, executableProcessor, dbSnpVcfProcessor, detectCnvDefault);
}
public static IWorkManager GetWorkManager(ILogger logger, IDirectoryLocation analysisFolder,
ISampleSettings settings, IsasConfiguration config)
{
bool useSGE = settings.GetBooleanSetting(SampleSheetUtils.UseSGE, config.UseCluster);
config.UseCluster = useSGE;
if (config.UseCluster)
{
return GetSGEWorkManager(logger, analysisFolder, settings, config);
}
else
{
return GetLocalWorkManager(logger, analysisFolder, settings, config);
}
}
public CanvasWorkerFactory(
ISampleSettings sampleSettings,
IWorkManager workManager,
ILogger logger,
ExecutableProcessor executableProcessor,
DbSnpVcfProcessor dbSnpVcfProcessor,
bool detectCnvDefault)
{
_workManager = workManager;
_sampleSettings = sampleSettings;
_logger = logger;
_executableProcessor = executableProcessor;
_dbSnpVcfProcessor = dbSnpVcfProcessor;
_detectCnvDefault = detectCnvDefault;
}
public DbSnpVcfProcessor(ISampleSettings sampleSettings)
{
_sampleSettings = sampleSettings;
}
public DbSnpVcfProcessor(ISampleSettings sampleSettings) : this((ISettings)sampleSettings)
{
}
