Uses of Class
biolockj.exception.DockerVolCreationException

Packages that use DockerVolCreationException

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.getData.sra
biolockj.module.rnaseq
biolockj.util	Static utilities centralize and organize reusable core methods.
biolockj.util.paths

Uses of DockerVolCreationException in biolockj

Methods in biolockj that throw DockerVolCreationException

Modifier and Type	Method and Description
static String	Config.convertRelativePath(String filePath, File CONFIG_DOT) Given a relative path (ie, one that starts with "."), get the absolute path---even when runnig in docker.
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.getFileObjectFromPath(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 String	BioLockJ.getProjectName() Extract the project name from the Config file.
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 void	Config.setConfigProperty(String name, Collection<?> data) Sets a property value in the props cache as a list
static void	Config.setConfigProperty(String name, Collection<?> data, BioModule module) Sets a property value in the props cache as a list
static void	Config.setFilePathProperty(String name, String val)
static void	Config.setFilePathProperty(String name, String val, BioModule module)

Uses of DockerVolCreationException in biolockj.launch

Methods in biolockj.launch that throw DockerVolCreationException

Modifier and Type	Method and Description
protected void	LaunchProcess.checkBasicArgCompatibility()
protected void	LaunchProcess.gatherEnvVars()
static void	Reset.main(String[] args) Reset a pipeline.

Constructors in biolockj.launch that throw DockerVolCreationException

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

Uses of DockerVolCreationException in biolockj.module

Methods in biolockj.module that throw DockerVolCreationException

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 DockerVolCreationException in biolockj.module.classifier

Methods in biolockj.module.classifier that throw DockerVolCreationException

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

Uses of DockerVolCreationException in biolockj.module.classifier.r16s

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

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

Uses of DockerVolCreationException in biolockj.module.classifier.wgs

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

Modifier and Type	Method and Description
List<String>	Metaphlan2Classifier.getClassifierParams() Obtain the metaphlan2 runtime params
File	Metaphlan2Classifier.getDB()
File	Humann2Classifier.getDB()
File	KrakenClassifier.getDB()
File	Kraken2Classifier.getDB()

Uses of DockerVolCreationException in biolockj.module.getData.sra

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

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

Uses of DockerVolCreationException in biolockj.module.rnaseq

Methods in biolockj.module.rnaseq that throw DockerVolCreationException

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

Uses of DockerVolCreationException in biolockj.util

Methods in biolockj.util that throw DockerVolCreationException

Modifier and Type	Method and Description
static void	MetaUtil.addColumn(String colName, Map<String,String> map, File fileDir, boolean removeMissingIds) Adds a column to the metadata file.
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.
static File	DockerUtil.containerizePath(File file) DockerUtil.containerizePath(String)
static String	DockerUtil.containerizePath(String path) If running in docker mode, convert this path to the form that can be used inside the docker container.
static File	DockerUtil.deContainerizePath(File innerFile) DockerUtil.deContainerizePath(String)
static String	DockerUtil.deContainerizePath(String innerPath) If running in docker mode, convert this path to the form that can be used on the host machine.
static boolean	RuntimeParamUtil.doRestart() Return TRUE if runtime parameters indicate attempt to restart pipeline
static File	RuntimeParamUtil.get_BLJ_PROJ() Runtime property getter for "-projectDir"
static File	RuntimeParamUtil.get_BLJ_PROJ(boolean dockerize)
static File	RuntimeParamUtil.getConfigFile() Runtime property getter for "-config"
static File	RuntimeParamUtil.getConfigFile(boolean dockerize)
static String	DockerUtil.getContainerId() Deprecated.
static File	RuntimeParamUtil.getFileParam(String paramName, boolean dockerize) Get a File that is given through a parameter; if in docker, get the in-container form of the path
static String	MetaUtil.getForcedColumnName(String name) Used to generate a guaranteed to be unique column name.
static String	RuntimeParamUtil.getJavaModuleArgs(JavaModule module) For cluster env, runtime params that need be forward to detached cluster Java modules.
static DockerMountMapper	DockerUtil.getMapper(boolean initAsNeeded) Intended for diagnostic purposes only.
static File	RuntimeParamUtil.getRestartDir() Return restart pipeline directory
static File	RuntimeParamUtil.getRestartDir(boolean dockerize)
static String	MetaUtil.getSystemMetaCol(BioModule module, String col) Return a system generated metadata column name based on the module status.
static void	BioLockJUtil.ignoreFile(File file) Method used to add a file to the ignore file list property.
protected static List<String>	BashScriptBuilder.initMainScript(ScriptModule module) Create the ScriptModule main script that calls all worker scripts.
static List<String>	TaxaUtil.initTaxaLevels() Set taxonomy levels ordered by level, from highest to lowest.
static void	RuntimeParamUtil.registerRuntimeParameters(String[] args) TODO: runtime params should always store the string as given on the command line, and that should be the host-file path, even when running in docker.
static void	MetaUtil.removeColumn(String colName, File fileDir) Remove the metadata column from the metadata file
static void	MetaUtil.setFile(File file) Set a new metadata file.
static void	DockerUtil.touchDockerInfo() Save a file with info about the current docker container.
static void	RuntimeParamUtil.validateParams()

Uses of DockerVolCreationException in biolockj.util.paths

Methods in biolockj.util.paths that throw DockerVolCreationException

Modifier and Type	Method and Description
String	DockerMountMapper.asInnerPath(String path) Convert path to inner path form.
String	BasicDockerMapper.asInnerPath(String path)
String	DockerMountMapper.asOuterPath(String path) Convert path to outer path form.
String	BasicDockerMapper.asOuterPath(String innerPath)
protected String	BasicDockerMapper.getDockerInfoCmd()
TreeMap<String,String>	DockerMountMapper.getMap() The map at represents the connection of inner path to outer path.
protected void	BasicDockerMapper.makeVolMap() This map is a link between file paths inside the container (the containerized path) and paths outside the container (the decontainerized path).

Constructors in biolockj.util.paths that throw DockerVolCreationException

Constructor and Description
BasicDockerMapper()
CommonDockerMapper()
SimpleDockerMapper()