public SmallPedigreeCheckpointFactory(
IWorkDoer workDoer,
ILogger logger,
ExecutableProcessor executableProcessor,
IFileLocation pedigreefileNameStub,
CanvasWorkerFactory canvasWorkerFactory)
{
_workDoer = workDoer;
_logger = logger;
_executableProcessor = executableProcessor;
_pedigreefileNameStub = pedigreefileNameStub;
_canvasWorkerFactory = canvasWorkerFactory;
}
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 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 CanvasWorkerFactory(
ISettings sampleSettings,
IWorkDoer workDoer,
ILogger logger,
ExecutableProcessor executableProcessor,
DbSnpVcfProcessor dbSnpVcfProcessor,
bool detectCnvDefault,
TabixWrapper tabixWrapper, ICommandManager commandManager)
{
_workDoer = workDoer;
_sampleSettings = sampleSettings;
_logger = logger;
_executableProcessor = executableProcessor;
_dbSnpVcfProcessor = dbSnpVcfProcessor;
_detectCnvDefault = detectCnvDefault;
_tabixWrapper = tabixWrapper;
_commandManager = commandManager;
}
public int Launch()
{
try
{
var executableProcessor = new ExecutableProcessor(_settings, _logger);
var runtimeExecutable = new FileLocation(executableProcessor.GetEnvironmentExecutablePath("dotnet"));
ICommandFactory GetDotnetCommand(string component)
{
return(new CommandManager(executableProcessor).GetDotnetCommandFactory($"{component}.dll", component));
}
_logger.Info($"Running Canvas {_mode} {_version}");
_logger.Info($"Command-line arguments: {string.Join(" ", _args)}");
var runnerFactory = new CanvasRunnerFactory(_logger, _checkpointRunner, _workDoer, runtimeExecutable, GetDotnetCommand);
_modeRunner.Run(runnerFactory);
return(0);
}
catch (Exception e)
{
_logger.Error($"Canvas workflow error: {e}");
return(-1);
}
}
public int Launch()
{
CommonOptions commonOptions = _modeRunner.CommonOptions;
IDirectoryLocation outFolder = commonOptions.OutputDirectory;
var log = outFolder.GetFileLocation("CanvasLog.txt");
var error = outFolder.GetFileLocation("CanvasError.txt");
IsasConfiguration config = IsasConfiguration.GetConfiguration();
IDirectoryLocation genomeRoot = commonOptions.WholeGenomeFasta?.Parent?.Parent?.Parent?.Parent?.Parent;
int returnValue = 0;
IsasFrameworkFactory.RunWithIsasFramework(outFolder, log, error, commonOptions.StartCheckpoint, commonOptions.StopCheckpoint, 0,
config.MaximumMemoryGB, config.MaximumHoursPerProcess, false, genomeRoot,
frameworkServices =>
{
var logger = frameworkServices.Logger;
try
{
var executableProcessor = new ExecutableProcessor(new NullSampleSettings(), logger);
#if DotNetCore
var runtimeExecutable = new FileLocation(executableProcessor.GetEnvironmentExecutablePath("dotnet"));
#else
var runtimeExecutable = CrossPlatform.IsThisLinux() ? new FileLocation(executableProcessor.GetMonoPath()) : null;
#endif
frameworkServices.Logger.Info($"Running Canvas {_mode} {_version}");
logger.Info($"Command-line arguments: {string.Join(" ", _args)}");
_modeRunner.Run(logger, frameworkServices.Checkpointer, frameworkServices.WorkManager, runtimeExecutable);
returnValue = 0;
}
catch (Exception e)
{
logger.Error($"Canvas workflow error: {e}");
returnValue = -1;
}
});
return(returnValue);
}
