Uses of Class
biolockj.exception.ConfigNotFoundException

Packages that use ConfigNotFoundException

Package	Description
biolockj	The root biolockj package contains core classes used by all BioLockJ pipelines.
biolockj.module	Pipeline modules are loaded based on the BioModules listed in the Config file. All modules (i.e., implement BioModule) are contained within this package or its sub-packages.
biolockj.module.classifier	This package contains Classifier specific BioModules that build bash scripts to generate taxonomy reports from the sequences files.
biolockj.module.classifier.r16s	This package contains RDP and QIIME classifier modules that assign taxonomy to 16s sequences. Output file formats are classifier specific so classifier requires a unique post-requisite ParserModule.
biolockj.module.classifier.wgs	This package contains Kraken, Kraken2, Humann2, MetaPhlAn classifier modules that assign taxonomy to WGS data. As with all BioLockJ classifiers, these modules generate raw classifier output files from the sequence data. Include the corresponding ParserModule in the Config file to generate standardized OTU abundance tables.
biolockj.module.diy
biolockj.module.implicit.qiime	This package contains BioModules that are implicitly added to QIIME pipeline as needed.
biolockj.module.seq	BioModules used to prepare sequence files or update the metadata prior to classification.
biolockj.util	Static utilities centralize and organize reusable core methods.

Uses of ConfigNotFoundException in biolockj

Methods in biolockj that throw ConfigNotFoundException

Modifier and Type	Method and Description
static void	Config.checkDependencies(BioModule module)
static Map<String,String>	Config.getEnvVarMap() Return the String, String map of environment variables and their values.
static boolean	Config.requireBoolean(BioModule module, String property) Required to return a valid boolean or
static Double	Config.requireDoubleVal(BioModule module, String property) Requires valid double value
static File	Config.requireExistingDir(BioModule module, String property) Requires valid existing directory.
static List<File>	Config.requireExistingDirs(BioModule module, String property) Requires valid list of file directories
static File	Config.requireExistingFile(BioModule module, String property) Require valid existing file
static Integer	Config.requireInteger(BioModule module, String property) Requires valid integer value
static List<String>	Config.requireList(BioModule module, String property) Require valid list property
static Double	Config.requirePositiveDouble(BioModule module, String property) Require valid positive double value
static Integer	Config.requirePositiveInteger(BioModule module, String property) Require valid positive integer value
static Set<String>	Config.requireSet(BioModule module, String property) Require valid Set value
static String	Config.requireString(BioModule module, String property) Require valid String value
protected String	Processor.runJob(String[] args, String label)
protected String	Processor.runJob(String[] args, String label, File workDir)
static void	Processor.submitJob(String[] args, String label) Instantiates a new Processor. String[] array used to control spacing between command/params. As if executing on terminal args[0] args[1]...
static String	Processor.submitQuery(String cmd, String label) Run script that expects a single result

Uses of ConfigNotFoundException in biolockj.module

Methods in biolockj.module that throw ConfigNotFoundException

Modifier and Type	Method and Description
File	DatabaseModule.getDB() Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Uses of ConfigNotFoundException in biolockj.module.classifier

Methods in biolockj.module.classifier that throw ConfigNotFoundException

Modifier and Type	Method and Description
abstract File	ClassifierModuleImpl.getDB()

Uses of ConfigNotFoundException in biolockj.module.classifier.r16s

Methods in biolockj.module.classifier.r16s that throw ConfigNotFoundException

Modifier and Type	Method and Description
(package private) String	RdpClassifier.getConfThreshold()
File	RdpClassifier.getDB()

Uses of ConfigNotFoundException in biolockj.module.classifier.wgs

Methods in biolockj.module.classifier.wgs that throw ConfigNotFoundException

Modifier and Type	Method and Description
File	Metaphlan2Classifier.getDB()
File	Humann2Classifier.getDB()
File	KrakenClassifier.getDB()
File	Kraken2Classifier.getDB()

Uses of ConfigNotFoundException in biolockj.module.diy

Methods in biolockj.module.diy that throw ConfigNotFoundException

Modifier and Type	Method and Description
protected List<String>	ForEachLoop.getLoopElements()

Uses of ConfigNotFoundException in biolockj.module.implicit.qiime

Methods in biolockj.module.implicit.qiime that throw ConfigNotFoundException

Modifier and Type	Method and Description
File	QiimeClassifier.getDB() Check DB parameters for the comment parent directory path, there are 3 parameters: "qiime.pynastAlignDB" "qiime.refSeqDB" "qiime.taxaDB"

Uses of ConfigNotFoundException in biolockj.module.seq

Methods in biolockj.module.seq that throw ConfigNotFoundException

Modifier and Type	Method and Description
File	KneadData.getDB()

Uses of ConfigNotFoundException in biolockj.util

Methods in biolockj.util that throw ConfigNotFoundException

Modifier and Type	Method and Description
static boolean	DemuxUtil.barcodeInHeader() Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence headers.
static boolean	DemuxUtil.barcodeInMapping() Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.
static boolean	DemuxUtil.barcodeInSeq() Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.
static void	BashScriptBuilder.checkDependencies(BioModule module)
static boolean	BioLockJUtil.copyInputFiles() Copy input files into an internal folder within the pipeline root direction named "input"
static Boolean	DemuxUtil.doDemux() Return TRUE if Config is setup to demultiplex the sequence data.
static String	DockerUtil.getDockerImage(BioModule module) Return the name of the Docker image needed for the given module.
static Integer	ModuleUtil.getMinSamplesPerWorker(BioModule module) Return the min number of samples that can be processed per worker script.
static Integer	ModuleUtil.getNumWorkers(BioModule module) Get the actual number of worker scripts generated for a given module, minimum value = 1.
static String	SeqUtil.getSeqType() Get sequence type
protected static String	BashScriptBuilder.getWorkerScriptPath(ScriptModule module) Build the file path for the numbered worker script.
static List<String>	TaxaUtil.initTaxaLevels() Set taxonomy levels ordered by level, from highest to lowest.
protected static List<String>	BashScriptBuilder.passEnvironmentVarVals(ScriptModule module)
static boolean	BioLockJUtil.pipelineInputType(String type) Convenience method to check pipeline input file type.
static boolean	SeqUtil.piplineHasSeqInput() Return TRUE if pipeline input files are sequence files.