Package | Description |
---|---|
biolockj |
The root biolockj package contains core classes used by all BioLockJ pipelines.
|
biolockj.launch | |
biolockj.module | |
biolockj.module.classifier |
This package contains Classifier specific
BioModule s 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 |
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) |
Modifier and Type | Method and Description |
---|---|
protected void |
LaunchProcess.checkBasicArgCompatibility() |
protected void |
LaunchProcess.gatherEnvVars() |
static void |
Reset.main(String[] args)
Reset a pipeline.
|
Constructor and Description |
---|
DockerLaunchProcess(String[] args) |
JavaLaunchProcess(String[] args) |
LaunchProcess(String[] args) |
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() |
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() |
Modifier and Type | Method and Description |
---|---|
File |
RdpClassifier.getDB() |
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() |
Modifier and Type | Method and Description |
---|---|
Set<String> |
SraMetaDB.getWriteDirs() |
Set<String> |
SraDownload.getWriteDirs() |
Modifier and Type | Method and Description |
---|---|
String |
DESeq2.copyDEseqScript() |
String |
EdgeR.copyEdgeRScript() |
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)
|
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)
|
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() |
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).
|
Constructor and Description |
---|
BasicDockerMapper() |
CommonDockerMapper() |
SimpleDockerMapper() |