Package | Description |
---|---|
biolockj |
The root biolockj package contains core classes used by all BioLockJ pipelines.
|
biolockj.exception |
This package contains
Exception subclasses specific to BioLockJ. |
biolockj.launch | |
biolockj.module | |
biolockj.module.assembly | |
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.hello_world | |
biolockj.module.implicit |
The modules in this package are implicitly added to pipelines as needed.
These modules cannot be directly added to any pipeline unless overridden via pipeline.disableImplicitModules=Y. |
biolockj.module.implicit.qiime |
This package contains
BioModule s that are implicitly added to QIIME pipeline as needed. |
biolockj.module.report.r |
This package contains
BioModule s that build pipeline reports from the standard OTU abundance
tables by generating R scripts to produce the summary statistics and data visualizations output to PDF files. |
biolockj.module.rnaseq | |
biolockj.module.seq |
BioModule s used to prepare sequence files or update the metadata prior to classification. |
biolockj.node |
Package
biolockj.node contains core classes instantiated by the
ParserModule to hold Sample ID-(OTU name/count) data read in from
ClassifierModule output. |
biolockj.pipelines | |
biolockj.util |
Static utilities centralize and organize reusable core methods.
|
biolockj.util.paths |
Class and Description |
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BioLockJException
Superclass for all BioLockJ exception used to ensure message uniformity.
|
ConfigFormatException
ConfigFormatException is thrown if property is defined but the format is invalid.
|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
DockerVolCreationException |
SpecialPropertiesException
This type of exception is thrown if an error occurs while processing a special type of property such as "exe."
properties or defaultProps.
|
Class and Description |
---|
BioLockJException
Superclass for all BioLockJ exception used to ensure message uniformity.
|
ConfigException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
DockerVolumeException |
IntentionalStop
Parent exception for BioLockJ Exception that arise when the user explicitly intended to make the pipeline stop.
|
MetadataException
MetadataException is thrown if errors occur processing Metadata files.
|
Class and Description |
---|
BioLockJException
Superclass for all BioLockJ exception used to ensure message uniformity.
|
BioLockJStatusException |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
DockerVolCreationException |
InvalidPipelineException |
Class and Description |
---|
ConfigException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
ConfigFormatException
ConfigFormatException is thrown if property is defined but the format is invalid.
|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
DockerVolCreationException |
PipelineFormationException
PipelineFormationException is thrown when there is a problem in setting up the modules to run.
|
SequnceFormatException
SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.
|
Class and Description |
---|
ConfigException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
Class and Description |
---|
ConfigException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
DockerVolCreationException |
Class and Description |
---|
ConfigException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
ConfigFormatException
ConfigFormatException is thrown if property is defined but the format is invalid.
|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
DockerVolCreationException |
Class and Description |
---|
ConfigException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
DockerVolCreationException |
Class and Description |
---|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
Class and Description |
---|
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
DockerVolCreationException |
Class and Description |
---|
ConfigFormatException
ConfigFormatException is thrown if property is defined but the format is invalid.
|
Class and Description |
---|
BioLockJException
Superclass for all BioLockJ exception used to ensure message uniformity.
|
SequnceFormatException
SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.
|
Class and Description |
---|
ConfigException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
Class and Description |
---|
BioLockJException
Superclass for all BioLockJ exception used to ensure message uniformity.
|
ConfigFormatException
ConfigFormatException is thrown if property is defined but the format is invalid.
|
Class and Description |
---|
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
DockerVolCreationException |
Class and Description |
---|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
SequnceFormatException
SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.
|
Class and Description |
---|
ConfigFormatException
ConfigFormatException is thrown if property is defined but the format is invalid.
|
Class and Description |
---|
BioLockJStatusException |
InvalidPipelineException |
Class and Description |
---|
BioLockJException
Superclass for all BioLockJ exception used to ensure message uniformity.
|
BioLockJStatusException |
ConfigException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
ConfigFormatException
ConfigFormatException is thrown if property is defined but the format is invalid.
|
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
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. |
DockerVolCreationException |
DockerVolumeException |
MetadataException
MetadataException is thrown if errors occur processing Metadata files.
|
OtuFileException
OtuFileException is thrown if errors occur processing OTU files.
|
PipelineScriptException
PipelineScriptException is thrown by
BashScriptBuilder if errors occur writing MASTER & WORKER
scripts. |
RuntimeParamException
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
|
SequnceFormatException
SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.
|
SpecialPropertiesException
This type of exception is thrown if an error occurs while processing a special type of property such as "exe."
properties or defaultProps.
|
Class and Description |
---|
BioLockJException
Superclass for all BioLockJ exception used to ensure message uniformity.
|
DockerVolCreationException |