Uses of Class
biolockj.exception.ConfigException

Packages that use ConfigException

Package	Description
biolockj.exception	This package contains Exception subclasses specific to BioLockJ.
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.assembly
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.implicit.qiime	This package contains BioModules that are implicitly added to QIIME pipeline as needed.
biolockj.util	Static utilities centralize and organize reusable core methods.

Uses of ConfigException in biolockj.exception

Subclasses of ConfigException in biolockj.exception

Modifier and Type	Class and Description
class	ConfigConflictException
class	ConfigFormatException ConfigFormatException is thrown if property is defined but the format is invalid.
class	ConfigNotFoundException ConfigNotFoundException is thrown if a required Config property is undefined.
class	ConfigPathException ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ configuration file.
class	ConfigViolationException ConfigViolationException is thrown at runtime due to application state violations caused by invalid module I/O (sequences or metadata) as defined by Config properties.
class	SpecialPropertiesException This type of exception is thrown if an error occurs while processing a special type of property such as "exe." properties or defaultProps.

Uses of ConfigException in biolockj.module

Methods in biolockj.module that throw ConfigException

Modifier and Type	Method and Description
protected String	ScriptModuleImpl.getRuntimeParams(List<String> params, String numThreadsParam) Return all collectionProperty values separated by a space.

Uses of ConfigException in biolockj.module.assembly

Methods in biolockj.module.assembly that throw ConfigException

Modifier and Type	Method and Description
protected String	GenomeAssembly.getCheckmParams() Get standard Checkm runtime parameters.
protected String	GenomeAssembly.getMetabatParams() Get Metabat runtime parameters.
protected String	GenomeAssembly.getMetaspadeParams() Get Metaspade runtime parameters.

Uses of ConfigException in biolockj.module.classifier

Methods in biolockj.module.classifier that throw ConfigException

Modifier and Type	Method and Description
String	ClassifierModule.getClassifierExe() Get the executable required to classify your samples.
abstract String	ClassifierModuleImpl.getClassifierExe()
List<String>	ClassifierModule.getClassifierParams() Get optional list of parameters to append whenever the classifier executable is called.
abstract List<String>	ClassifierModuleImpl.getClassifierParams()

Uses of ConfigException in biolockj.module.classifier.r16s

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

Modifier and Type	Method and Description
protected List<String>	QiimeClosedRefClassifier.getBatch(List<String> lines, int batchNum, int index) Method returns batch script lines for one batch.
String	RdpClassifier.getClassifierExe() RDP uses java to run a JAR file, so no special command is required
List<String>	RdpClassifier.getClassifierParams() Do not accept -t to define a database, since that instead requires the specific property: "rdp.db" If "rdp.hierCounts" is true, then skip any parameter for it here, it will added per file.

Uses of ConfigException in biolockj.module.classifier.wgs

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

Modifier and Type	Method and Description
String	Metaphlan2Classifier.getClassifierExe() Metaphlan runs python scripts, so no special command is required
String	Humann2Classifier.getClassifierExe() Get HumanN2 executable command: "exe.humann2"
String	KrakenClassifier.getClassifierExe() Get kraken executable command: "exe.kraken"
String	Kraken2Classifier.getClassifierExe() Get kraken executable command: "exe.kraken2"
List<String>	Metaphlan2Classifier.getClassifierParams() Obtain the metaphlan2 runtime params
List<String>	Humann2Classifier.getClassifierParams() Obtain the humann2 runtime params
List<String>	KrakenClassifier.getClassifierParams() Obtain the kraken runtime params
List<String>	Kraken2Classifier.getClassifierParams() Obtain the kraken2 runtime params

Uses of ConfigException in biolockj.module.implicit.qiime

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

Modifier and Type	Method and Description
String	QiimeClassifier.getClassifierExe() QIIME calls python scripts, so no special command is required
List<String>	QiimeClassifier.getClassifierParams() Obtain the QIIME runtime params
protected String	QiimeClassifier.getParams() Subclasses call this method to check dependencies before picking OTUs to validate Config."qiime.params"
protected List<String>	QiimeClassifier.getPickOtuLines(String otuPickingScript, File fastaDir, String mapping, File outputDir) Subclasses call this method to add OTU picking lines by calling "add_qiime_labels.py" via OTU picking script.
protected String	QiimeClassifier.getVsearchParams() Return runtime parameters for "qiime.vsearchParams"

Uses of ConfigException in biolockj.util

Methods in biolockj.util that throw ConfigException

Modifier and Type	Method and Description
protected static void	BashScriptBuilder.buildMainScript(ScriptModule module) Build the MIAN script.
static List<String>	DockerUtil.buildSpawnDockerContainerFunction(BioModule module, String startedFlag) Build the "spawnDockerContainer" method, which takes container name, in/out port, and optionally script path parameters.
protected static List<String>	BashScriptBuilder.initMainScript(ScriptModule module) Create the ScriptModule main script that calls all worker scripts.