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.diy | |
biolockj.module.getData.sra | |
biolockj.module.implicit.qiime |
This package contains
BioModule s that are implicitly added to QIIME pipeline as needed. |
biolockj.module.rnaseq | |
biolockj.module.seq |
BioModule s used to prepare sequence files or update the metadata prior to classification. |
biolockj.util |
Static utilities centralize and organize reusable core methods.
|
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
|
Modifier and Type | Method and Description |
---|---|
protected void |
LaunchProcess.gatherEnvVars() |
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 |
---|---|
abstract File |
ClassifierModuleImpl.getDB() |
Modifier and Type | Method and Description |
---|---|
File |
RdpClassifier.getDB() |
Modifier and Type | Method and Description |
---|---|
File |
Metaphlan2Classifier.getDB() |
File |
Humann2Classifier.getDB() |
File |
KrakenClassifier.getDB() |
File |
Kraken2Classifier.getDB() |
Modifier and Type | Method and Description |
---|---|
protected String |
Rmarkdown.transferMarkdown() |
protected void |
GenMod.transferResources() |
protected void |
Rmarkdown.transferResources() |
protected String |
GenMod.transferScript() |
Modifier and Type | Method and Description |
---|---|
Set<String> |
SraMetaDB.getWriteDirs() |
Set<String> |
SraDownload.getWriteDirs() |
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"
|
Modifier and Type | Method and Description |
---|---|
String |
DESeq2.copyDEseqScript() |
String |
EdgeR.copyEdgeRScript() |
Modifier and Type | Method and Description |
---|---|
File |
KneadData.getDB() |
Modifier and Type | Method and Description |
---|---|
static File |
BioLockJUtil.getBljDir()
Get the program source (either the jar path or main class biolockj.BioLockJ);
|