Uses of Class
biolockj.exception.ConfigPathException

Packages that use ConfigPathException

Package	Description
biolockj	The root biolockj package contains core classes used by all BioLockJ pipelines.
biolockj.launch
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.getData.sra
biolockj.module.implicit.qiime	This package contains BioModules that are implicitly added to QIIME pipeline as needed.
biolockj.module.rnaseq
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 ConfigPathException in biolockj

Methods in biolockj that throw ConfigPathException

Modifier and Type	Method and Description
static File	Config.getExistingDir(BioModule module, String property) Get a valid File directory or return null
static File	Config.getExistingFile(BioModule module, String property) Get a valid File or return null.
static List<File>	Config.getExistingFileList(BioModule module, String property)
static File	Config.getExistingFileObject(BioModule module, String property) Build File using module and property name.
static File	Config.getExistingFileObjectFromPath(String filePath) Build File using filePath.
static File	Config.getExistingFileObjectFromPath(String filePath, boolean convertRelativePath, boolean containerizePath) Build File using filePath.
static File	Config.getLocalConfigFile(String path) Return file for path after modifying if running in a Docker container and/or interpreting bash env vars.
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

Uses of ConfigPathException in biolockj.launch

Methods in biolockj.launch that throw ConfigPathException

Modifier and Type	Method and Description
protected void	LaunchProcess.gatherEnvVars()

Constructors in biolockj.launch that throw ConfigPathException

Constructor and Description
DockerLaunchProcess(String[] args)
JavaLaunchProcess(String[] args)
LaunchProcess(String[] args)

Uses of ConfigPathException in biolockj.module

Methods in biolockj.module that throw ConfigPathException

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.
Set<String>	OutsidePipelineWriter.getWriteDirs()

Uses of ConfigPathException in biolockj.module.classifier

Methods in biolockj.module.classifier that throw ConfigPathException

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

Uses of ConfigPathException in biolockj.module.classifier.r16s

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

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

Uses of ConfigPathException in biolockj.module.classifier.wgs

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

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

Uses of ConfigPathException in biolockj.module.diy

Methods in biolockj.module.diy that throw ConfigPathException

Modifier and Type	Method and Description
protected String	Rmarkdown.transferMarkdown()
protected void	GenMod.transferResources()
protected void	Rmarkdown.transferResources()
protected String	GenMod.transferScript()

Uses of ConfigPathException in biolockj.module.getData.sra

Methods in biolockj.module.getData.sra that throw ConfigPathException

Modifier and Type	Method and Description
Set<String>	SraMetaDB.getWriteDirs()
Set<String>	SraDownload.getWriteDirs()

Uses of ConfigPathException in biolockj.module.implicit.qiime

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

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 ConfigPathException in biolockj.module.rnaseq

Methods in biolockj.module.rnaseq that throw ConfigPathException

Modifier and Type	Method and Description
String	DESeq2.copyDEseqScript()
String	EdgeR.copyEdgeRScript()

Uses of ConfigPathException in biolockj.module.seq

Methods in biolockj.module.seq that throw ConfigPathException

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

Uses of ConfigPathException in biolockj.util

Methods in biolockj.util that throw ConfigPathException

Modifier and Type	Method and Description
static File	BioLockJUtil.getBljDir() Get the program source (either the jar path or main class biolockj.BioLockJ);