- main(String[]) - Static method in class biolockj.api.BioLockJ_API
-
- main(String[]) - Static method in class biolockj.api.BuildDocs
-
For standard use case, pass in $BLJ/mkdocs/user-guide/docs/GENERATED
- main(String[]) - Static method in class biolockj.BioLockJ
-
- main(String[]) - Static method in class biolockj.launch.DockerLaunchProcess
-
- main(String[]) - Static method in class biolockj.launch.JavaLaunchProcess
-
- main(String[]) - Static method in class biolockj.launch.Launcher
-
- main(String[]) - Static method in class biolockj.launch.LaunchProcess
-
- main(String[]) - Static method in class biolockj.launch.ProgressMsgDemo
-
- main(String[]) - Static method in class biolockj.launch.Reset
-
Reset a pipeline.
- main(String[]) - Static method in class biolockj.module.implicit.parser.r16s.RdpHierParser
-
For stand-alone testing outside of a BioLockJ pipeline.
arg 0 - comma-separated list of taxonomic levels
arg 1 - comma-separated list of input files (one or more)
arg 2 - path/to/dir where the outputs will be saved
- main(String[]) - Static method in class biolockj.util.DockerUtil
-
Even outside of a BioLockJ instance, access the containerize() and decontainerze() methods.
- main(String[]) - Static method in class biolockj.util.UpdateJavaDocs
-
Main method updates the JavaDocs to replace undesirable auto-generated text.
- MAIN_DOCKER_IMAGE - Static variable in class biolockj.Constants
-
Docker image used for the BioLockJ head node.
- MAIN_DOCKER_OWNER - Static variable in class biolockj.Constants
-
Docker hub account that owns the .
- MAIN_SCRIPT_PREFIX - Static variable in interface biolockj.module.BioModule
-
Script prefix appended to start of file name to indicate the main script in the script directory.
Non-AWS pipelines execute worker scripts via executing the main shell script - named with the prefix:
"MAIN_"
- makeMapper() - Static method in class biolockj.util.DockerUtil
-
As version v1.3.18, the logic to do this mapping is not part of the DockerUtil class.
- makeMessage() - Method in class biolockj.module.hello_world.Hello_Friends
-
Create a message based on the modules properties.
- makeMessage() - Method in class biolockj.module.hello_world.Step5
-
Create a message based on the modules properties.
- makeRunAllScript(List<BioModule>) - Static method in class biolockj.util.DownloadUtil
-
This script allows a user to run all R scripts together from a single script.
- makeVolMap() - Method in class biolockj.util.paths.BasicDockerMapper
-
This map is a link between file paths inside the container (the containerized path) and paths outside the
container (the decontainerized path).
- MAPPING_FILE - Static variable in class biolockj.util.DemuxUtil
-
Config
String property "demultiplexer.mapping" lists the path to the mapping file to match
sequence headers to barcodes.
- markComplete(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Method creates a file named
"biolockjComplete" in module root directory to document module
has completed successfully.
- markDownReturn - Static variable in class biolockj.Constants
-
When writing mark down files, use this as a new line to start a new paragraph.
- markStarted(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Method creates a file named
"biolockjStarted" in module root directory to document module
has completed successfully.
- markStatus(String) - Method in class biolockj.module.JavaModuleImpl
-
This method sets the module status by saving the indicator file to the module root dir.
- markStatus(String, String) - Static method in class biolockj.pipelines.PipelineUtil
-
Set the status of a module or pipeline using a status flag file.
- markStatus(String) - Static method in class biolockj.pipelines.PipelineUtil
-
Set the status of a module or pipeline using a status flag file.
- markStatus(BioModule, String) - Static method in class biolockj.pipelines.PipelineUtil
-
Set the status of a module using a status flag file.
- MASTER_PREFIX - Static variable in class biolockj.Constants
-
Prefix added to the master Config file: "MASTER_"
- MasterConfigUtil - Class in biolockj.util
-
Simple utility containing String manipulation and formatting functions.
- MasterConfigUtil() - Constructor for class biolockj.util.MasterConfigUtil
-
- MATCHED_EXPECTATION - Static variable in class biolockj.util.ValidationUtil
-
The last column in a the output file, "MATCHED_EXPECTATION", indicates if the referenced file met all
expectations (PASS), or not (FAIL), or was not compared to any expectations (REPORT).
- MD5 - Static variable in class biolockj.util.ValidationUtil
-
- MemoryUtil - Class in biolockj.util
-
This Java memory report utility can be used to help identify memory leaks in the application.
- MemoryUtil() - Constructor for class biolockj.util.MemoryUtil
-
- MergeQiimeOtuTables - Class in biolockj.module.implicit.qiime
-
This BioModule will run immediately after QiimeClosedRefClassifier if multiple otu_table.biom files were created.
- MergeQiimeOtuTables() - Constructor for class biolockj.module.implicit.qiime.MergeQiimeOtuTables
-
- META_BARCODE_COLUMN - Static variable in class biolockj.util.MetaUtil
-
Config
property "metadata.barcodeColumn"
- META_COLUMN_DELIM - Static variable in class biolockj.util.MetaUtil
-
Config
property: "metadata.columnDelim"
- META_COMMENT_CHAR - Static variable in class biolockj.util.MetaUtil
-
Config
property: "metadata.commentChar"
- META_FILE_PATH - Static variable in class biolockj.util.MetaUtil
-
Config
String property: "metadata.filePath"
- META_FILENAME_COLUMN - Static variable in class biolockj.util.MetaUtil
-
Config
property "metadata.fileNameColumn"
- META_MERGED - Static variable in class biolockj.module.report.taxa.AddMetadataToTaxaTables
-
File suffix added to OTU table file name once merged with metadata.
- META_NULL_VALUE - Static variable in class biolockj.util.MetaUtil
-
Config
property: "metadata.nullValue"
- META_REQUIRED - Static variable in class biolockj.util.MetaUtil
-
Config
Boolean property: "metadata.required"
- METABAT_MEMORY - Static variable in class biolockj.module.assembly.GenomeAssembly
-
Config
Positive integer property defines total metabat memory per sample.
- METADATA_COL_DELIM - Static variable in class biolockj.util.MetaUtil
-
Default column delimiter = tab character
- METADATA_SRA_ID_COL_NAME - Static variable in class biolockj.module.getData.sra.SraDownload
-
- MetadataException - Exception in biolockj.exception
-
MetadataException is thrown if errors occur processing Metadata files.
- MetadataException(String) - Constructor for exception biolockj.exception.MetadataException
-
Create standard error to throw for Metadata related errors.
- MetadataWithoutFileException - Exception in biolockj.exception
-
- MetadataWithoutFileException(String) - Constructor for exception biolockj.exception.MetadataWithoutFileException
-
- METAPHLAN2_DB - Static variable in class biolockj.module.classifier.wgs.Metaphlan2Classifier
-
- METAPHLAN2_MPA_PKL - Static variable in class biolockj.module.classifier.wgs.Metaphlan2Classifier
-
Config
File property containing path to the mpa_pkl file used to reference an alternate DB
"metaphlan2.mpa_pkl"
Must always be paired with
"metaphlan2.db"
- Metaphlan2Classifier - Class in biolockj.module.classifier.wgs
-
This BioModule builds the bash scripts used to execute metaphlan2.py to classify WGS sequences with MetaPhlAn2.
- Metaphlan2Classifier() - Constructor for class biolockj.module.classifier.wgs.Metaphlan2Classifier
-
- Metaphlan2Parser - Class in biolockj.module.implicit.parser.wgs
-
This BioModules parses Metaphlan2Classifier output reports to build standard OTU abundance tables.
- Metaphlan2Parser() - Constructor for class biolockj.module.implicit.parser.wgs.Metaphlan2Parser
-
- MetaphlanNode - Class in biolockj.node.wgs
-
- MetaphlanNode(String, String) - Constructor for class biolockj.node.wgs.MetaphlanNode
-
Build the OtuNode by extracting the OTU names for each level from the line.
- METASPADES_MEMORY - Static variable in class biolockj.module.assembly.GenomeAssembly
-
Config
Positive integer property defines total metaspades memory per sample.
- MetaUtil - Class in biolockj.util
-
This utility is used to read, modify, or create a metadata file for the sequence data.
- millisToMinutes(long) - Static method in class biolockj.util.BioLockJUtil
-
Convert milliseconds to minutes - useful to convert Java millisecond output rounded to the nearest minute.
- minutesToMillis(int) - Static method in class biolockj.util.BioLockJUtil
-
Convert minutes to milliseconds - useful to convert Config props measure in minutes to milliseconds since many
Java functions have milliseconds args.
- MODULE_SEQ_PACKAGE - Static variable in class biolockj.Constants
-
BioLockJ SEQ module package: "biolockj.module.seq"
- MODULE_WGS_CLASSIFIER_PACKAGE - Static variable in class biolockj.Constants
-
BioLockJ WGS Classifier module package: "biolockj.module.classifier.wgs"
- moduleComplete() - Method in interface biolockj.module.JavaModule
-
This method will create the success flag file so the next module can run.
- moduleComplete() - Method in class biolockj.module.JavaModuleImpl
-
- moduleExists(String) - Static method in class biolockj.util.ModuleUtil
-
Check if a module was in the pipeline at least once.
- moduleFailed() - Method in interface biolockj.module.JavaModule
-
This method will create the fail flag file so the pipeline can move on..
- moduleFailed() - Method in class biolockj.module.JavaModuleImpl
-
- moduleInfo() - Static method in class biolockj.api.BioLockJ_API
-
Returns a json formatted list of all modules and for each module that
implements the gui interface, it lists the props used by the module,
and for each prop the info.
- ModuleUtil - Class in biolockj.util
-
This utility holds general methods useful for BioModule interaction and management.
- mostRecent - Variable in class biolockj.launch.LaunchProcess
-
- msgs - Variable in class biolockj.launch.LaunchProcess
-
- multiplex(File) - Method in class biolockj.module.seq.Multiplexer
-
Add file sequences to the multiplexed file.
- Multiplexer - Class in biolockj.module.seq
-
This BioModule will merge sequence files into a single combined sequence file, with either the sample ID or an
identifying bar-code (if defined in the metatata) is stored in the sequence header.
BioLockJ is designed to run on demultiplexed data so this must be the last module to run in its branch.
- Multiplexer() - Constructor for class biolockj.module.seq.Multiplexer
-