public EverythingRunnerEngine(Tuple <string, Options> task, string outputFolder)
{
// set up directories to mount to docker container as volumes
AnalysisDirectory = task != null ? task.Item2.AnalysisDirectory : outputFolder;
var pathToConfig = Path.Combine(AnalysisDirectory, "configs");
if (!Directory.Exists(pathToConfig))
{
Directory.CreateDirectory(pathToConfig);
}
ConfigDirectory = pathToConfig;
var pathToDataFiles = Path.Combine(AnalysisDirectory, "data");
if (!Directory.Exists(pathToDataFiles))
{
Directory.CreateDirectory(pathToDataFiles);
}
DataDirectory = pathToDataFiles;
// path to workflow.txt
PathToWorkflow = Path.Combine(AnalysisDirectory, "workflow_" + DateTime.Now.ToString("yyyy-MM-dd-HH-mm-ss") + ".txt");
SpritzContainerName = $"spritz{PathToWorkflow.GetHashCode()}";
}
public static readonly bool PrebuiltSpritzMods = true; // always using prebuilt library now
public RunnerEngine(Tuple <string, SpritzOptions> task, string outputFolder)
{
// set up directories to mount to docker container as volumes
AnalysisDirectory = task != null ? task.Item2.AnalysisDirectory : outputFolder;
var pathToConfig = Path.Combine(AnalysisDirectory, "config");
if (!Directory.Exists(pathToConfig))
{
Directory.CreateDirectory(pathToConfig);
}
ConfigDirectory = pathToConfig;
ConfigFile = Path.Combine(ConfigDirectory, "config.yaml");
var resourcesPath = Path.Combine(Path.GetDirectoryName(AnalysisDirectory), "resources");
if (!Directory.Exists(resourcesPath))
{
Directory.CreateDirectory(resourcesPath);
}
ResourcesDirectory = resourcesPath;
// path to workflow.txt
PathToWorkflow = Path.Combine(AnalysisDirectory, "workflow_" + DateTime.Now.ToString("yyyy-MM-dd-HH-mm-ss") + ".txt");
SpritzContainerName = $"spritz{PathToWorkflow.GetHashCode()}";
}
public string GenerateCommandsDry(string dockerImageName)
{
string command = "";
if (dockerImageName.Contains("smithlab"))
{
command += $"docker pull {dockerImageName} ;";
}
command += $"docker run --rm -i -t --name {SpritzContainerName} " +
$"-v \"\"\"{AnalysisDirectory}:/app/analysis" + "\"\"\" " +
$"-v \"\"\"{DataDirectory}:/app/data" + "\"\"\" " +
$"-v \"\"\"{ConfigDirectory}:/app/configs\"\"\" " +
$"{dockerImageName}; docker stop spritz{PathToWorkflow.GetHashCode()}";
return(command);
}
public string GenerateCommandsDry(string dockerImageName, string spritzCmdCommand)
{
string imageWithVersion = dockerImageName.Contains(":") ? dockerImageName : $"{dockerImageName}:{CurrentVersion}";
string command = dockerImageName.Contains("smithlab") ?
$"docker pull {imageWithVersion};" :
"";
command +=
$"docker run --rm -i -t --user=root --name {SpritzContainerName} " +
$"-v \"\"\"{AnalysisDirectory}:/app/spritz/results/\"\"\" " +
$"-v \"\"\"{ResourcesDirectory}:/app/spritz/resources\"\"\" " +
$"{imageWithVersion} {spritzCmdCommand}; " +
$"docker stop spritz{PathToWorkflow.GetHashCode()}";
return(command);
}
public string GenerateTopComand()
{
return($"docker container top spritz{PathToWorkflow.GetHashCode()}");
}
