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D

DatabaseModule - Interface in biolockj.module
Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.
DB_DIR - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
 
DB_DIR_DESC - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
 
DB_NAME - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
 
DEBUG - Static variable in class biolockj.Log
DEBUG log message type:
debug(Class<?>, String) - Static method in class biolockj.Log
Print log level DEBUG message.
Do not print MetaUtil debug since these will always print since the Logger isn't initialized yet and logMesseges will print them as INFO after Log file initializes.
DEBUG_ARG - Static variable in class biolockj.launch.LaunchProcess
 
DEBUG_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
Flag argument; if present, BioLockJ will set the Conig property to DEBUG.
deContainerizePath(String) - Static method in class biolockj.util.DockerUtil
If running in docker mode, convert this path to the form that can be used on the host machine.
deContainerizePath(File) - Static method in class biolockj.util.DockerUtil
decrypt(String) - Method in class biolockj.module.report.Email
Used to authenticate the service email account defined in EMAIL_FROM.
DEFAULT_COMMENT_CHAR - Static variable in class biolockj.util.MetaUtil
Default comment character for any new metadata file created by a BioModule: ""
DEFAULT_DOCKER_MAPPER - Static variable in class biolockj.util.DockerUtil
 
DEFAULT_FORMAT - Static variable in class biolockj.Log
Standard BioLockJ log format includes date, time, severity type, and calling class before the msg.
DEFAULT_IMAGE_NAME - Static variable in class biolockj.util.DockerUtil
A light-weight docker image to use.
DEFAULT_IMAGE_OWNER - Static variable in class biolockj.util.DockerUtil
 
DEFAULT_IMAGE_TAG - Static variable in class biolockj.util.DockerUtil
 
DEFAULT_MOD_DEMUX - Static variable in class biolockj.Constants
Config property: "pipeline.defaultDemultiplexer"
DEFAULT_MOD_FASTA_CONV - Static variable in class biolockj.Constants
Config property: "pipeline.defaultFastaConverter"
DEFAULT_MOD_SEQ_MERGER - Static variable in class biolockj.Constants
Config property: "pipeline.defaultSeqMerger"
DEFAULT_NULL_VALUE - Static variable in class biolockj.util.MetaUtil
Default field value to represent null-value: "NA"
DEFAULT_STATS_MODULE - Static variable in class biolockj.Constants
Config property: "pipeline.defaultStatsModule"
DELIM_SEP - Static variable in class biolockj.Constants
In an otu string for multiple levels, each separated by "|", each otu has a level prefix ending with "__"
delimToLevelMap() - Static method in class biolockj.node.OtuNodeImpl
Map level delimeter to level names.
demultiplex(Map<String, Set<String>>) - Method in class biolockj.module.implicit.Demultiplexer
Demultiplex the file into separate small temp files, with 2000000 lines each for processing.
Demultiplexer - Class in biolockj.module.implicit
This BioModule splits multiplexed data into a separate file or pair of files (for paired reads) for each sample.
Demultiplexer() - Constructor for class biolockj.module.implicit.Demultiplexer
 
DEMUX_STRATEGY - Static variable in class biolockj.util.DemuxUtil
Config property "demultiplexer.strategy" tells BioLockJ how to match sequences with Sample IDs.
Options: barcode_in_header, barcode_in_mapping, barcode_in_seq, id_in_header, do_not_demux.
If using barcodes, metadata column "metadata.barcodeColumn" is required.
DemuxUtil - Class in biolockj.util
This utility contains standard methods used to handle multiplexed data.
DemuxUtil() - Constructor for class biolockj.util.DemuxUtil
 
demuxWithBarcode() - Static method in class biolockj.util.DemuxUtil
Return TRUE if barcode column is defined in the Config file and is populated in the metadata file
deprecatedPropMessage(String) - Static method in class biolockj.Properties
Returns a message telling the user that the property is deprecated.
deregisterThread(Thread) - Static method in class biolockj.Processor
De-register a thread, so it is not considered when shutting down the application.
DESeq2 - Class in biolockj.module.rnaseq
 
DESeq2() - Constructor for class biolockj.module.rnaseq.DESeq2
 
DEST_DIR - Static variable in class biolockj.module.getData.sra.SraDownload
 
DETACH_JAVA_MODULES - Static variable in class biolockj.Constants
Config property: "pipeline.detachJavaModules"
DEVELOPER_NOTE - Static variable in class biolockj.Constants
A prefix used for some messages.
DIRECT_FORMAT - Static variable in class biolockj.Log
Direct BioLockJ log prefix includes only the msg.
DIRECT_MODE - Static variable in class biolockj.util.RuntimeParamUtil
Direct mode runtime parameter switch: "-direct"
DirectModuleException - Exception in biolockj.exception
Some module are run as secondary instances of the BioLockJ program.
DirectModuleException(String) - Constructor for exception biolockj.exception.DirectModuleException
 
DirectModuleException() - Constructor for exception biolockj.exception.DirectModuleException
 
DIRECTORY - Static variable in exception biolockj.exception.ConfigPathException
One of 2 BioLockJ file path types that can be passed to the constructor "directory".
DISABLE_ADD_IMPLICIT_MODULES - Static variable in class biolockj.Constants
Config "boolean" property: "pipeline.disableAddImplicitModules"
DISABLE_PRE_REQ_MODULES - Static variable in class biolockj.Constants
Config property: "pipeline.disableAddPreReqModules"
discardPrecheckPipeline(File) - Static method in class biolockj.pipelines.PipelineUtil
 
displayArgVals() - Method in class biolockj.launch.LaunchProcess
 
displayAsciiArt() - Static method in class biolockj.util.SummaryUtil
Print the application name *bigly* with some ASCII art :-)
displayID(BioModule) - Static method in class biolockj.util.ModuleUtil
Return the module ID as a 2 digit display number (add leading zero if needed).
displayName(BioModule) - Static method in class biolockj.util.ModuleUtil
Return the name of the module (or an alias if it has one).
displaySignature(BioModule) - Static method in class biolockj.util.ModuleUtil
 
DO_GZIP - Static variable in class biolockj.module.seq.Multiplexer
Config boolean property: "multiplexer.gzip":
DO_UPDATE - Static variable in class biolockj.module.getData.sra.SraMetaDB
Config property: "sra.forceDbUpdate"
doChangePassword() - Static method in class biolockj.util.RuntimeParamUtil
Return TRUE if runtime parameters indicate change password request
DOCKER_ARG - Static variable in class biolockj.launch.LaunchProcess
 
DOCKER_BLJ_MOUNT_DIR - Static variable in class biolockj.util.DockerUtil
Docker container root user EFS directory: /mnt/efs
DOCKER_CONFIG_PATH - Static variable in class biolockj.Constants
Config property: "${BLJ}/resources/config/default/docker.properties" Default path for an additional configuration file used for any pipeline run in docker.
DOCKER_DB_DIR - Static variable in class biolockj.util.DockerUtil
Docker container root user DB directory: /mnt/efs/db
DOCKER_DEFAULT_DB_DIR - Static variable in class biolockj.util.DockerUtil
Docker container root user DB directory: /mnt/efs/db
DOCKER_EXE_PREFIX - Static variable in class biolockj.Constants
Prefix used in several Config String properties.
DOCKER_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
Flag argument; if present, BioLockJ will use a docker volume map.
DOCKER_HUB_USER - Static variable in class biolockj.util.DockerUtil
Config String property: "docker.imageOwner"

Docker Hub URL: https://hub.docker.com
By default the "biolockj" user is used to pull the standard modules, but advanced users can deploy their own versions of these modules and add new modules in their own Docker Hub account.
DOCKER_IMG - Static variable in class biolockj.util.DockerUtil
Config String property: "docker.imageName"
DOCKER_IMG_VERSION - Static variable in class biolockj.util.DockerUtil
Config String property: "docker.imageTag"
DOCKER_MAPPER - Static variable in class biolockj.util.RuntimeParamUtil
Argument giving the name of the class to use for the DockerMountMapper: "-docker-mapper"
DOCKER_MAPPER_ARG - Static variable in class biolockj.launch.LaunchProcess
 
DOCKER_MOUNT_SOCK - Static variable in class biolockj.util.DockerUtil
Config Boolean property: "docker.mountSock"
DOCKER_PIPELINE_DIR - Static variable in class biolockj.util.DockerUtil
All containers mount "internal.pipelineDir" to the container volume: /mnt/efs/output
DOCKER_USER - Static variable in class biolockj.util.DockerUtil
Docker container default $USER: "root"
DockerImageException - Exception in biolockj.exception
 
DockerImageException(BioModule, String, String) - Constructor for exception biolockj.exception.DockerImageException
 
DockerLaunchProcess - Class in biolockj.launch
 
DockerLaunchProcess(String[]) - Constructor for class biolockj.launch.DockerLaunchProcess
 
DockerMountMapper - Interface in biolockj.util.paths
Introduced with BioLockJ v1.3.18.
DockerUtil - Class in biolockj.util
DockerUtil for Docker integration.
DockerUtil() - Constructor for class biolockj.util.DockerUtil
 
DockerVolCreationException - Exception in biolockj.exception
 
DockerVolCreationException(String) - Constructor for exception biolockj.exception.DockerVolCreationException
 
DockerVolCreationException() - Constructor for exception biolockj.exception.DockerVolCreationException
 
DockerVolCreationException(Exception) - Constructor for exception biolockj.exception.DockerVolCreationException
 
DockerVolumeException - Exception in biolockj.exception
 
DockerVolumeException(String) - Constructor for exception biolockj.exception.DockerVolumeException
 
doDebug() - Static method in class biolockj.Log
Return TRUE if = DEBUG.
doDemux() - Static method in class biolockj.util.DemuxUtil
Return TRUE if Config is setup to demultiplex the sequence data.
DOMAIN - Static variable in class biolockj.Constants
Config option for "report.taxonomyLevels": "domain"
DOMAIN_DELIM - Static variable in class biolockj.node.OtuNodeImpl
Standard classifier output level delimiter for DOMAIN
doRestart() - Static method in class biolockj.util.RuntimeParamUtil
Return TRUE if runtime parameters indicate attempt to restart pipeline
DOWNLOAD_DIR - Static variable in class biolockj.Constants
Config String property: "pipeline.downloadDir"
DOWNLOAD_LIST - Static variable in class biolockj.util.DownloadUtil
Name of the file holding the list of pipeline files to include when running DownloadUtil
downloadDB(String[], String) - Static method in class biolockj.util.DockerUtil
Download a database for a Docker container
DownloadUtil - Class in biolockj.util
This utility is used to validate the metadata to help ensure the format is valid R script input.
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