Constant Field Values

Contents

• biolockj.*

biolockj.*

biolockj.Config

Modifier and Type	Constant Field	Value
public static final String	BLJ_BASH_VAR	"BLJ"
public static final String	BLJ_PROJ_VAR	"BLJ_PROJ"

biolockj.Constants

Modifier and Type	Constant Field	Value
public static final String	ASSIGN_ALIAS	" AS "
public static final String	AWS_S3_XFER_TIMEOUT	"aws.s3TransferTimeout"
public static final String	BASH_PROFILE	".bash_profile"
public static final String	BASH_RC	".bashrc"
public static final String	BLJ_COMPLETE	"biolockjComplete"
public static final String	BLJ_FAILED	"biolockjFailed"
public static final String	BLJ_MODULE_TAG	"#BioModule"
public static final String	BLJ_STARTED	"biolockjStarted"
public static final String	BLJ_VERSION_PROP	"biolockj.version"
public static final String	BLJ_VERSION_PROP_DESC	"Property giving the biolockj version that was used to generate the config file."
public static final String	BLJ_WIKI	"https://github.com/msioda/BioLockJ/wiki"
public static final String	CLASS	"class"
public static final String	CLUSTER_HOST	"cluster.host"
public static final String	DEFAULT_MOD_DEMUX	"pipeline.defaultDemultiplexer"
public static final String	DEFAULT_MOD_FASTA_CONV	"pipeline.defaultFastaConverter"
public static final String	DEFAULT_MOD_SEQ_MERGER	"pipeline.defaultSeqMerger"
public static final String	DEFAULT_STATS_MODULE	"pipeline.defaultStatsModule"
public static final String	DELIM_SEP	"__"
public static final String	DETACH_JAVA_MODULES	"pipeline.detachJavaModules"
public static final String	DEVELOPER_NOTE	"Developer note: "
public static final String	DISABLE_ADD_IMPLICIT_MODULES	"pipeline.disableAddImplicitModules"
public static final String	DISABLE_PRE_REQ_MODULES	"pipeline.disableAddPreReqModules"
public static final String	DOCKER_CONFIG_PATH	"${BLJ}/resources/config/default/docker.properties"
public static final String	DOCKER_EXE_PREFIX	"dockerExe."
public static final String	DOMAIN	"domain"
public static final String	DOWNLOAD_DIR	"pipeline.downloadDir"
public static final String	EXE_AWK	"exe.awk"
public static final String	EXE_DOCKER	"exe.docker"
public static final String	EXE_GZIP	"exe.gzip"
public static final String	EXE_JAVA	"exe.java"
public static final String	EXE_PREFIX	"exe."
public static final String	EXE_PYTHON	"exe.python"
public static final String	EXE_RSCRIPT	"exe.Rscript"
public static final String	FALSE	"N"
public static final String	FAMILY	"family"
public static final String	FASTA	"fasta"
public static final String	FASTQ	"fastq"
public static final String	GENUS	"genus"
public static final String	GZIP_EXT	".gz"
public static final String	HELP	"-help"
public static final String	HN2_DISABLE_GENE_FAMILIES	"humann2.disableGeneFamilies"
public static final String	HN2_DISABLE_PATH_ABUNDANCE	"humann2.disablePathAbundance"
public static final String	HN2_DISABLE_PATH_COVERAGE	"humann2.disablePathCoverage"
public static final String	HN2_GENE_FAM_SUM	"geneFam"
public static final String	HN2_PATH_ABUND_SUM	"pAbund"
public static final String	HN2_PATH_COVG_SUM	"pCovg"
public static final String	HN2_TOTAL_PATH_COUNT	"Total_Pathways"
public static final String	HN2_UNIQUE_PATH_COUNT	"Unique_Pathways"
public static final String	HOST_EXE_PREFIX	"hostExe."
public static final String	INDENT	" "
public static final String	INPUT_ALLOW_DUPS	"input.allowDuplicateNames"
public static final String	INPUT_DIRS	"input.dirPaths"
public static final String	INPUT_FORWARD_READ_SUFFIX	"input.suffixFw"
public static final String	INPUT_IGNORE_FILES	"input.ignoreFiles"
public static final String	INPUT_REQUIRE_COMPLETE_PAIRS	"input.requireCompletePairs"
static final String	INPUT_REQUIRE_COMPLETE_PAIRS_DESC	"Require all sequence input files have matching paired reads"
public static final String	INPUT_REVERSE_READ_SUFFIX	"input.suffixRv"
public static final String	INPUT_TRIM_PREFIX	"input.trimPrefix"
public static final String	INPUT_TRIM_SUFFIX	"input.trimSuffix"
public static final String	INPUT_TYPES	"pipeline.inputTypes"
public static final String	INTERNAL_ALL_MODULES	"internal.allModules"
public static final String	INTERNAL_BLJ_MODULE	"internal.configModules"
public static final String	INTERNAL_DEFAULT_CONFIG	"internal.defaultConfig"
public static final String	INTERNAL_IS_MULTI_LINE_SEQ	"internal.isMultiLineSeq"
public static final String	INTERNAL_MULTIPLEXED	"internal.multiplexed"
public static final String	INTERNAL_PAIRED_READS	"internal.pairedReads"
public static final String	INTERNAL_PIPELINE_DIR	"internal.pipelineDir"
public static final String	INTERNAL_PIPELINE_ID	"internal.pipelineInstanceId"
public static final String	INTERNAL_PIPELINE_NAME	"internal.pipelineName"
public static final String	INTERNAL_PREFIX	"internal."
public static final String	INTERNAL_SEQ_HEADER_CHAR	"internal.seqHeaderChar"
public static final String	INTERNAL_SEQ_TYPE	"internal.seqType"
public static final String	JAR_ARG	"-jar"
public static final String	LIMIT_DEBUG_CLASSES	"pipeline.limitDebugClasses"
public static final String	LOG_EXT	".log"
public static final String	LOG_LEVEL_PROPERTY	"pipeline.logLevel"
public static final String	LOG_SPACER	"========================================================================"
public static final String	MAIN_DOCKER_IMAGE	"biolockj_controller"
public static final String	MAIN_DOCKER_OWNER	"biolockjdevteam"
public static final String	MASTER_PREFIX	"MASTER_"
public static final String	MODULE_SEQ_PACKAGE	"biolockj.module.seq"
public static final String	MODULE_WGS_CLASSIFIER_PACKAGE	"biolockj.module.classifier.wgs"
public static final String	ORDER	"order"
public static final String	OTU_COUNT	"otuCount"
public static final String	OTU_SEPARATOR	"|"
public static final String	OTU_TABLE_PREFIX	"otu_table"
public static final String	P_VAL_CUTOFF	"r.pvalCutoff"
public static final String	PDF_EXT	".pdf"
public static final String	PHYLUM	"phylum"
public static final String	PIPELINE_COPY_FILES	"pipeline.copyInput"
public static final String	PIPELINE_DEFAULT_PROPS	"pipeline.defaultProps"
public static final String	PIPELINE_DESC	"pipeline.desc"
public static final String	PIPELINE_ENV	"pipeline.env"
public static final String	PIPELINE_ENV_AWS	"aws"
public static final String	PIPELINE_ENV_CLUSTER	"cluster"
public static final String	PIPELINE_ENV_LOCAL	"local"
public static final String	PIPELINE_ENV_VARS	"pipeline.envVars"
public static final String	PIPELINE_ENV_VARS_DESC	"list of variables that should be passed into the runtime environment for all modules."
public static final String	PIPELINE_LOCATION_KEY	"Pipeline root directory: "
public static final String	PIPELINE_NAME	"pipeline.name"
protected static final String	PIPELINE_PRIVS	"pipeline.permissions"
public static final String	PIPELINE_USE_EVARS	"pipeline.useEnvVars"
public static final String	PIPELINE_USE_EVARS_DESC	"when evaluating variables in the ${VAR} format, should environment variables be used. Regardless, priority is given to variable values defined in the config file."
public static final String	PRECHECK_COMPLETE	"precheckComplete"
public static final String	PRECHECK_FAILED	"precheckFailed"
public static final String	PRECHECK_STARTED	"precheckStarted"
public static final String	PROCESSED	"_reported.tsv"
public static final String	PROJECT_DEFAULT_PROPS	"project.defaultProps"
public static final String	PROJECT_DESC	"project.description"
public static final String	PROJECT_NAME	"project.name"
public static final String	PROPS_EXT	".properties"
public static final String	QIIME	"qiime"
public static final String	QIIME_ALPHA_DIVERSITY_METRICS	"qiime.alphaMetrics"
public static final String	QIIME_BARCODE_SEQ_COL	"BarcodeSequence"
public static final String	QIIME_DEMUX_COL	"BioLockJFileName"
public static final String	QIIME_DESC_COL	"Description"
public static final String	QIIME_LINKER_PRIMER_SEQ_COL	"LinkerPrimerSequence"
public static final String	R_COLOR_BASE	"r.colorBase"
public static final String	R_COLOR_FILE	"r.colorFile"
public static final String	R_COLOR_HIGHLIGHT	"r.colorHighlight"
public static final String	R_COLOR_PALETTE	"r.colorPalette"
public static final String	R_COLOR_POINT	"r.colorPoint"
public static final String	R_DEBUG	"r.debug"
public static final String	R_EXT	".R"
public static final String	R_FUNCTION_LIB	"BioLockJ_Lib.R"
public static final String	R_INTERNAL_RUN_HN2	"R_internal.runHumann2"
public static final String	R_MAIN_SCRIPT	"BioLockJ_MAIN.R"
public static final String	R_PCH	"r.pch"
public static final String	R_RARE_OTU_THRESHOLD	"r.rareOtuThreshold"
public static final String	R_SAVE_R_DATA	"r.saveRData"
public static final String	R_TIMEOUT	"r.timeout"
public static final String	R_USE_UINQUE_COLORS	"r.useUniqueColors"
public static final String	RDP_THRESHOLD_SCORE	"rdp.minThresholdScore"
public static final String	REPORT_LOG_BASE	"report.logBase"
public static final String	REPORT_MIN_COUNT	"report.minCount"
public static final String	REPORT_NUM_HITS	"report.numHits"
public static final String	REPORT_NUM_READS	"report.numReads"
public static final String	REPORT_SAMPLE_CUTOFF	"report.scarceSampleCutoff"
public static final String	REPORT_SCARCE_CUTOFF	"report.scarceCountCutoff"
public static final String	REPORT_TAXONOMY_LEVELS	"report.taxonomyLevels"
public static final String	REPORT_UNCLASSIFIED_TAXA	"report.unclassifiedTaxa"
public static final String	RETURN	"\n"
public static final String	RM_TEMP_FILES	"pipeline.deleteTempFiles"
public static final String	RSCRIPT	"Rscript"
public static final String	SCRIPT_DEFAULT_HEADER	"script.defaultHeader"
public static final String	SCRIPT_DEFAULT_HEADER_DESC	"Store default script header for MAIN script and locally run WORKER scripts."
public static final String	SCRIPT_DELAY_FOR_FILE_UPDATES	"script.fileRefreshDelay"
public static final String	SCRIPT_DIR	"script"
public static final String	SCRIPT_FAILURES	"Failures"
public static final String	SCRIPT_NUM_THREADS	"script.numThreads"
public static final String	SCRIPT_NUM_THREADS_DESC	"Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter."
public static final String	SCRIPT_NUM_WORKERS	"script.numWorkers"
public static final String	SCRIPT_NUM_WORKERS_DESC	"Set number of samples to process per script (if parallel processing)"
public static final String	SCRIPT_PERMISSIONS	"script.permissions"
public static final String	SCRIPT_PERMISSIONS_DESC	"Used as chmod permission parameter (ex: 774)"
public static final String	SCRIPT_STARTED	"Started"
public static final String	SCRIPT_SUCCESS	"Success"
public static final String	SCRIPT_TIMEOUT	"script.timeout"
public static final String	SCRIPT_TIMEOUT_DESC	"Sets # of minutes before worker scripts times out."
public static final String	SET_SEED	"pipeline.setSeed"
public static final String	SH_EXT	".sh"
public static final String	SPECIES	"species"
public static final String	STANDARD_CONFIG_PATH	"${BLJ}/resources/config/default/standard.properties"
public static final String	STATUS_MARK_KEY	"STATUS_MARK_KEY"
public static final String	STATUS_START_KEY	"STATUS_START_KEY"
public static final String	TAB_DELIM	"\t"
public static final String	TRUE	"Y"
public static final String	TSV_EXT	".tsv"
public static final String	TXT_EXT	".txt"
public static final String	UNCLASSIFIED	"Unclassified"
public static final String	UNVERIFIED_PROPS_FILE	"unverified.properties"
public static final String	USER_PROFILE	"pipeline.userProfile"
public static final String	VALIDATION_ENABLED	"This pipeline has validation enabled."
public static final String	VERSION	"-version"
public static final String	YEAR_AND_OWNER	"UNCC Fodor Lab 2021"

biolockj.Log

Modifier and Type	Constant Field	Value
protected static final String	DEFAULT_FORMAT	"%d{yyyy-MM-dd HH:mm:ss} %p %c{1}: %m%n"
protected static final String	DIRECT_FORMAT	"%m%n"
protected static final String	LOG_APPEND	"LOG_APPEND"
protected static final String	LOG_FILE	"LOG_FILE"
protected static final String	LOG_FORMAT	"LOG_FORMAT"

biolockj.Properties

Modifier and Type	Constant Field	Value
public static final String	BOOLEAN_TYPE	"boolean"
public static final String	EXE_PATH	"executable"
public static final String	FILE_PATH	"file path"
public static final String	FILE_PATH_LIST	"list of file paths"
public static final String	INTEGER_TYPE	"integer"
public static final String	LIST_TYPE	"list"
public static final String	NO_BROAD_USE	" Only use the module-specific-override form of this property."
public static final String	NUMERTIC_TYPE	"numeric"
public static final String	POS_INTEGER_TYPE	"positive integer"
public static final String	REQUIRED	"required "
public static final String	STRING_TYPE	"string"

biolockj.exception.*

biolockj.exception.BioLockJException

Modifier and Type	Constant Field	Value
protected static final String	RETURN	"\n"

biolockj.exception.ConfigPathException

Modifier and Type	Constant Field	Value
public static final String	DIRECTORY	"directory"
public static final String	FILE	"file"

biolockj.exception.FatalExceptionHandler

Modifier and Type	Constant Field	Value
public static final String	ERROR_MSG	"ERROR MESSAGE: "
public static final String	ERROR_TYPE	"ERROR TYPE: "

biolockj.exception.MetadataException

Modifier and Type	Constant Field	Value
protected static final String	howToLinkMetaWithFile	"\nFile to sample associations can be controlled using [input.trimPrefix] and [input.trimSuffix] for sequence files and [metadata.fileNameColumn] for any file type."

biolockj.exception.PipelineScriptException

Modifier and Type	Constant Field	Value
public static final String	COMMON_CAUSES	"Most often, this means there is not valid input for this module; this results from an upstream error, or a mis-match between the data and the metadata."

biolockj.launch.*

biolockj.launch.DockerLaunchProcess

Modifier and Type	Constant Field	Value
public static final String	EXTERNAL_MODULES_CONTAINER_DIR	"/app/external_modules"
public static final int	GUI_PORT	8080

biolockj.launch.JavaLaunchProcess

Modifier and Type	Constant Field	Value
static final String	BioLockJ_CLASS	"biolockj.BioLockJ"

biolockj.launch.biolockj.launch.LabeledSpinner

Modifier and Type	Constant Field	Value
static final String	anim	"|/-\\"

biolockj.launch.LaunchProcess

Modifier and Type	Constant Field	Value
protected static final String	AWS_ARG	"aws"
public static final String	BIOLOCKJ_TEST_MODE	"BIOLOCKJ_TEST_MODE"
protected static final String	BLJ_ARG	"blj"
protected static final String	CONFIG_ARG	"config-override"
protected static final String	DEBUG_ARG	"verbose"
static final String	DOCKER_ARG	"docker"
protected static final String	DOCKER_MAPPER_ARG	"docker-mapper"
protected static final String	ENV_ARG	"env-var"
protected static final String	EXT_MODS_ARG	"external-modules"
protected static final String	FG_ARG	"foreground"
static final String	GUI_ARG	"gui"
protected static final String	PASSWORD_ARG	"password"
public static final String	PLS_USE_INSTALL	"The install script packaged with BioLockJ sets this value. You may need to start a new terminal window."
protected static final String	PRECHECK_ARG	"precheck-only"
protected static final String	PROJ_ARG	"blj_proj"
protected static final String	RESTART_ARG	"restart"
protected static final String	UNUSED_PROPS_ARG	"unused-props"
protected static final String	WAIT_ARG	"wait-for-start"

biolockj.module.*

biolockj.module.BioModule

Modifier and Type	Constant Field	Value
public static final String	LOG_DIR	"log"
public static final String	MAIN_SCRIPT_PREFIX	"MAIN_"
public static final String	NO_VERSION	"0.0.0"
public static final String	OUTPUT_DIR	"output"
public static final String	RES_DIR	"resources"
public static final String	TEMP_DIR	"temp"

biolockj.module.BioModuleImpl

Modifier and Type	Constant Field	Value
public static final String	GZIP_EXT	".gz"
public static final String	LOG_EXT	".log"
public static final String	PDF_EXT	".pdf"
public static final String	RETURN	"\n"
public static final String	SH_EXT	".sh"
public static final String	TAB_DELIM	"\t"
public static final String	TSV_EXT	".tsv"
public static final String	TXT_EXT	".txt"

biolockj.module.JavaModuleImpl

Modifier and Type	Constant Field	Value
protected static final String	BLJ_OPTIONS	"BLJ_OPTIONS"

biolockj.module.assembly.GenomeAssembly

Modifier and Type	Constant Field	Value
protected static final String	EXE_CHECKM	"exe.checkm"
protected static final String	EXE_CHECKM_PARAMS	"exe.checkmParams"
protected static final String	EXE_METABAT2	"exe.metabat2"
protected static final String	EXE_METABAT2_PARAMS	"exe.metabat2Params"
protected static final String	EXE_METASPADES_PARAMS	"exe.metaspade2Params"
protected static final String	EXE_METASPADES2	"exe.metaspades2"
protected static final String	FUNCTION_ASSEMBLY	"runAssembly"
protected static final String	METABAT_MEMORY	"metabat.memory"
protected static final String	METASPADES_MEMORY	"metaspades.memory"

biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Modifier and Type	Constant Field	Value
protected static final String	BATCH_MAPPING	"batchMapping.tsv"
protected static final String	FUNCTION_CREATE_BATCH_MAPPING	"createBatchMapping"
public static final String	PICK_OTU_SCRIPT	"pick_closed_reference_otus.py"

biolockj.module.classifier.r16s.QiimeDeNovoClassifier

Modifier and Type	Constant Field	Value
public static final String	PICK_OTU_SCRIPT	"pick_de_novo_otus.py"

biolockj.module.classifier.r16s.QiimeOpenRefClassifier

Modifier and Type	Constant Field	Value
public static final String	PICK_OTU_SCRIPT	"pick_open_reference_otus.py"

biolockj.module.classifier.r16s.RdpClassifier

Modifier and Type	Constant Field	Value
protected static final String	FUNCTION_RDP	"runRdp"
public static final String	HIER_COUNTS	"rdp.hierCounts"
public static final String	HIER_SUFFIX	"_hierarchicalCount.tsv"
protected static final String	JAVA_PARAMS	"rdp.javaParams"
protected static final String	RDP_DB	"rdp.db"
protected static final String	RDP_DOCKER_JAR	"rdp.containerJar"
protected static final String	RDP_JAR	"rdp.jar"
protected static final String	RDP_PARAMS	"rdp.params"

biolockj.module.classifier.wgs.Humann2Classifier

Modifier and Type	Constant Field	Value
protected static final String	EXE_HUMANN2	"exe.humann2"
protected static final String	EXE_HUMANN2_JOIN_PARAMS	"humann2.humann2JoinTableParams"
protected static final String	EXE_HUMANN2_PARAMS	"humann2.humann2Params"
protected static final String	EXE_HUMANN2_RENORM_PARAMS	"humann2.humann2RenormTableParams"
protected static final String	HN2_NUCL_DB	"humann2.nuclDB"
protected static final String	HN2_PROT_DB	"humann2.protDB"

biolockj.module.classifier.wgs.Kraken2Classifier

Modifier and Type	Constant Field	Value
protected static final String	EXE_KRAKEN2	"exe.kraken2"
protected static final String	FUNCTION_KRAKEN	"runKraken2"
protected static final String	KRAKEN_DATABASE	"kraken2.db"
protected static final String	KRAKEN_FILE	"_kraken2_out.txt"
protected static final String	KRAKEN2_PARAMS	"kraken2.kraken2Params"

biolockj.module.classifier.wgs.KrakenClassifier

Modifier and Type	Constant Field	Value
protected static final String	EXE_KRAKEN	"exe.kraken"
protected static final String	FUNCTION_KRAKEN	"runKraken"
protected static final String	FUNCTION_TRANSLATE	"translate"
protected static final String	KRAKEN_DATABASE	"kraken.db"
protected static final String	KRAKEN_FILE	"_kraken_out.txt"
protected static final String	KRAKEN_PARAMS	"kraken.krakenParams"

biolockj.module.classifier.wgs.Metaphlan2Classifier

Modifier and Type	Constant Field	Value
protected static final String	EXE_METAPHLAN	"exe.metaphlan2"
protected static final String	EXE_METAPHLAN_PARAMS	"metaphlan2.metaphlan2Params"
protected static final String	METAPHLAN2_DB	"metaphlan2.db"
protected static final String	METAPHLAN2_MPA_PKL	"metaphlan2.mpa_pkl"

biolockj.module.diversity.ShannonDiversity

Modifier and Type	Constant Field	Value
public static final String	SHANNON_COLUMN	"ShannonDiversity"

biolockj.module.diy.GenMod

Modifier and Type	Constant Field	Value
protected static final String	CODE_LINE	"genMod.codeLine"
protected static final String	LAUNCHER	"genMod.launcher"
protected static final String	PARAM	"genMod.param"
protected static final String	RESOURCES	"genMod.resources"
protected static final String	SCRIPT	"genMod.scriptPath"

biolockj.module.diy.Rmarkdown

Modifier and Type	Constant Field	Value
protected static final String	RESOURCES	"rmarkdown.resources"
protected static final String	RMD_FILE	"rmarkdown.rmarkdown"

biolockj.module.getData.sra.SequenceReadArchive

Modifier and Type	Constant Field	Value
public static final String	DB_DIR	"sra.metaDataDir"
protected static final String	DB_DIR_DESC	"path to the directory where the *SRAmetadb.sqlite* database is stored."
protected static final String	DB_NAME	"SRAmetadb.sqlite"
public static final String	SRA_ACC_LIST	"sra.sraAccList"
protected static final String	SRA_ACC_LIST_DESC	"A file that has one SRA accession per line and nothing else."
public static final String	SRP	"sra.sraProjectId"
protected static final String	SRP_DESC	"The project id(s) referencesing a project in the NCBI SRA. example: SRP009633, ERP016051"

biolockj.module.getData.sra.SraDownload

Modifier and Type	Constant Field	Value
public static final String	DEST_DIR	"sra.destinationDir"
public static final String	EXE_FASTERQ	"exe.fasterq-dump"
public static final String	METADATA_SRA_ID_COL_NAME	"sra.accessionIdColumn"

biolockj.module.getData.sra.SraMetaDB

Modifier and Type	Constant Field	Value
public static final String	DO_UPDATE	"sra.forceDbUpdate"

biolockj.module.hello_world.Hello_Friends

Modifier and Type	Constant Field	Value
public static final String	EXCITE_PROP	"helloFriends.excitmentLevel"
public static final String	EXCITE_PROP_DESC	"The number of ! to use with the phrase."
public static final String	NAME_PROP	"helloFriends.friendsName"
public static final String	NAME_PROP_DEFAULT	"world"
public static final String	NAME_PROP_DESC	"A name to use instead of \'world\'."

biolockj.module.hello_world.Step3

Modifier and Type	Constant Field	Value
public static final String	EXCITE_PROP	"hello.excitmentLevel"
public static final String	EXCITE_PROP_DESC	"The number of ! to use with the phrase."
public static final String	NAME_PROP	"hello.myName"
public static final String	NAME_PROP_DEFAULT	"world"
public static final String	NAME_PROP_DESC	"A name to use instead of \'world\'."

biolockj.module.implicit.Demultiplexer

Modifier and Type	Constant Field	Value
protected static final int	NUM_LINES_TEMP_FILE	2000000

biolockj.module.implicit.RegisterNumReads

Modifier and Type	Constant Field	Value
protected static final String	NUM_READS	"Num_Reads"

biolockj.module.implicit.parser.ParserModuleImpl

Modifier and Type	Constant Field	Value
protected static final String	NUM_OTUS	"OTU_COUNT"

biolockj.module.implicit.parser.wgs.Humann2Parser

Modifier and Type	Constant Field	Value
protected static final String	HN2_KEEP_UNINTEGRATED	"humann2.keepUnintegrated"
protected static final String	HN2_KEEP_UNMAPPED	"humann2.keepUnmapped"

biolockj.module.implicit.qiime.BuildQiimeMapping

Modifier and Type	Constant Field	Value
protected static final String	FUNCTION_REORDER_FIELDS	"reorderColumns"
protected static final String	QIIME_COMMENT	"BioLockJ Generated Mapping"
protected static final String	QIIME_ID	"#SampleID"
protected static final String	SCRIPT_VALIDATE_MAPPING	"validate_mapping_file.py"
protected static final String	VALIDATED_MAPPING	"_corrected.txt"

biolockj.module.implicit.qiime.MergeQiimeOtuTables

Modifier and Type	Constant Field	Value
protected static final String	SCRIPT_MERGE_OTU_TABLES	"merge_otu_tables.py"

biolockj.module.implicit.qiime.QiimeClassifier

Modifier and Type	Constant Field	Value
protected static final String	ALPHA_DIV_NULL_VALUE	"N/A"
protected static final String	ALPHA_DIVERSITY_TABLE	"alphaDiversity.txt"
protected static final String	CITE_QIIME	"QIIME allows analysis of high-throughput community sequencing data\nJ Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303"
protected static final String	COMBINED_FNA	"combined_seqs.fna"
protected static final String	EXE_VSEARCH	"exe.vsearch"
protected static final String	EXE_VSEARCH_PARAMS	"qiime.vsearchParams"
protected static final String	OTU_SUMMARY_FILE	"otuSummary.txt"
protected static final String	OTU_TABLE	"otu_table.biom"
protected static final String	QIIME_PARAMS	"qiime.params"
protected static final String	QIIME_PYNAST_ALIGN_DB	"qiime.pynastAlignDB"
protected static final String	QIIME_REF_SEQ_DB	"qiime.refSeqDB"
protected static final String	QIIME_REMOVE_CHIMERAS	"qiime.removeChimeras"
protected static final String	QIIME_TAXA_DB	"qiime.taxaDB"
protected static final String	REP_SET	"rep_set"
protected static final String	SCRIPT_ADD_ALPHA_DIVERSITY	"add_alpha_to_mapping_file.py"
protected static final String	SCRIPT_ADD_LABELS	"add_qiime_labels.py"
protected static final String	SCRIPT_CALC_ALPHA_DIVERSITY	"alpha_diversity.py"
protected static final String	SCRIPT_FILTER_OTUS	"filter_otus_from_otu_table.py"
protected static final String	SCRIPT_PRINT_CONFIG	"print_qiime_config.py"
protected static final String	SCRIPT_SUMMARIZE_BIOM	"biom summarize-table"
protected static final String	SCRIPT_SUMMARIZE_TAXA	"summarize_taxa.py"
protected static final String	SUMMARIZE_TAXA_SUPPRESS_BIOM	"suppress_biom_table_output"

biolockj.module.report.Email

Modifier and Type	Constant Field	Value
protected static final String	EMAIL_ENCRYPTED_PASSWORD	"mail.encryptedPassword"
protected static final String	EMAIL_FROM	"mail.from"
protected static final String	EMAIL_HOST	"mail.smtp.host"
protected static final String	EMAIL_PORT	"mail.smtp.port"
protected static final String	EMAIL_SMTP_AUTH	"mail.smtp.auth"
protected static final String	EMAIL_START_TLS_ENABLE	"mail.smtp.starttls.enable"
protected static final String	EMAIL_TO	"mail.to"

biolockj.module.report.otu.CompileOtuCounts

Modifier and Type	Constant Field	Value
public static final String	SUMMARY	"summary"

biolockj.module.report.otu.RarefyOtuCounts

Modifier and Type	Constant Field	Value
protected static final String	LOW_ABUNDANT_CUTOFF	"rarefyOtuCounts.lowAbundantCutoff"
protected static final String	NUM_ITERATIONS	"rarefyOtuCounts.iterations"
protected static final String	QUANTILE	"rarefyOtuCounts.quantile"
protected static final String	REMOVE_LOW_ABUNDANT_SAMPLES	"rarefyOtuCounts.rmLowSamples"

biolockj.module.report.r.R_CalculateStats

Modifier and Type	Constant Field	Value
protected static final String	ADJ_PVAL_ATTRIBUTE	"ATTRIBUTE"
protected static final String	ADJ_PVAL_GLOBAL	"GLOBAL"
protected static final String	ADJ_PVAL_LOCAL	"LOCAL"
protected static final String	ADJ_PVAL_TAXA	"TAXA"
protected static final String	P_VALS_NP	"nonParametricPvals"
protected static final String	P_VALS_NP_ADJ	"adjNonParPvals"
protected static final String	P_VALS_PAR	"parametricPvals"
protected static final String	P_VALS_PAR_ADJ	"adjParPvals"
protected static final String	R_ADJ_PVALS_SCOPE	"r_CalculateStats.pAdjustScope"
protected static final String	R_PVAL_ADJ_METHOD	"r_CalculateStats.pAdjustMethod"
protected static final String	R_SQUARED_VALS	"rSquaredVals"

biolockj.module.report.r.R_PlotMds

Modifier and Type	Constant Field	Value
protected static final String	R_MDS_DISTANCE	"r_PlotMds.distance"
protected static final String	R_MDS_NUM_AXIS	"r_PlotMds.numAxis"
protected static final String	R_MDS_REPORT_FIELDS	"r_PlotMds.reportFields"

biolockj.module.report.taxa.AddMetadataToTaxaTables

Modifier and Type	Constant Field	Value
public static final String	HIT_RATIO	"Hit_Ratio"
public static final String	META_MERGED	"_metaMerged.tsv"

biolockj.module.report.taxa.LogTransformTaxaTables

Modifier and Type	Constant Field	Value
protected static final String	LOG_10	"10"
protected static final String	LOG_E	"e"

biolockj.module.seq.AwkFastaConverter

Modifier and Type	Constant Field	Value
protected static final String	FUNCTION_CONVERT_454	"convert454"
protected static final String	FUNCTION_CONVERT_TO_FASTA	"convertToFastA"
protected static final String	FUNCTION_GUNZIP	"decompressGzip"

biolockj.module.seq.Gunzipper

Modifier and Type	Constant Field	Value
protected static final String	FUNCTION_GUNZIP	"openZip"

biolockj.module.seq.KneadData

Modifier and Type	Constant Field	Value
protected static final String	EXE_KNEADDATA	"exe.kneaddata"
protected static final String	EXE_KNEADDATA_PARAMS	"kneaddata.kneaddataParams"
protected static final String	FUNCTION_SANATIZE	"sanatizeData"
protected static final String	KNEAD_DBS	"kneaddata.dbs"

biolockj.module.seq.Multiplexer

Modifier and Type	Constant Field	Value
protected static final String	DO_GZIP	"multiplexer.gzip"

biolockj.module.seq.PearMergeReads

Modifier and Type	Constant Field	Value
protected static final String	EXE_PEAR	"exe.pear"
protected static final String	EXE_PEAR_PARAMS	"pearMergeReads.pearParams"
protected static final String	FUNCTION_PEAR_MERGE	"mergeReads"
public static final String	NUM_MERGED_READS	"Num_Merged_Reads"

biolockj.module.seq.RarefySeqs

Modifier and Type	Constant Field	Value
protected static final String	INPUT_RAREFYING_MAX	"rarefySeqs.max"
protected static final String	INPUT_RAREFYING_MIN	"rarefySeqs.min"
public static final String	NUM_RAREFIED_READS	"Num_Rarefied_Reads"

biolockj.module.seq.SeqFileValidator

Modifier and Type	Constant Field	Value
protected static final String	INPUT_SEQ_MAX	"seqFileValidator.seqMaxLen"
protected static final String	INPUT_SEQ_MIN	"seqFileValidator.seqMinLen"
public static final String	NUM_VALID_READS	"Num_Valid_Reads"
protected static final String	REQUIRE_EUQL_NUM_PAIRS	"seqFileValidator.requireEqualNumPairs"

biolockj.module.seq.TrimPrimers

Modifier and Type	Constant Field	Value
protected static final String	INPUT_REQUIRE_PRIMER	"trimPrimers.requirePrimer"
public static final String	INPUT_TRIM_SEQ_FILE	"trimPrimers.filePath"
public static final String	NUM_TRIMMED_READS	"Num_Trimmed_Reads"

biolockj.node.*

biolockj.node.r16s.QiimeNode

Modifier and Type	Constant Field	Value
protected static final String	QIIME_DOMAIN_DELIM	"k__"
protected static final String	SILVA_CLASS_DELIM	"D_2__"
protected static final String	SILVA_DOMAIN_DELIM	"D_0__"
protected static final String	SILVA_FAMILY_DELIM	"D_4__"
protected static final String	SILVA_GENUS_DELIM	"D_5__"
protected static final String	SILVA_ORDER_DELIM	"D_3__"
protected static final String	SILVA_PHYLUM_DELIM	"D_1__"
protected static final String	SILVA_SPECIES_DELIM	"D_6__"

biolockj.util.*

biolockj.util.BashScriptBuilder

Modifier and Type	Constant Field	Value
protected static final String	CLUSTER_BATCH_COMMAND	"cluster.batchCommand"
protected static final String	CLUSTER_HAS_BATCH_IDS	"cluster.returnsBatchIds"
protected static final String	CLUSTER_MODULES	"cluster.modules"
protected static final String	CLUSTER_PROLOGUE	"cluster.prologue"
protected static final String	CLUSTER_STATUS_COMMAND	"cluster.statusCommand"
protected static final String	SCRIPT_JOB_HEADER	"cluster.jobHeader"

biolockj.util.BioLockJUtil

Modifier and Type	Constant Field	Value
public static final String	INTERNAL_PIPELINE_INPUT_TYPES	"internal.pipelineInputTypes"
public static final String	PIPELINE_HUMANN2_COUNT_TABLE_INPUT_TYPE	"hn2"
public static final String	PIPELINE_LOG_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE	"taxa_count_log_norm"
public static final String	PIPELINE_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE	"taxa_count_norm"
public static final String	PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE	"otu_count"
public static final String	PIPELINE_PAIRED_READS_INPUT_TYPE	"paired"
public static final String	PIPELINE_PARSER_INPUT_TYPE	"classifier_output"
public static final String	PIPELINE_R_INPUT_TYPE	"R"
public static final String	PIPELINE_SEQ_INPUT_TYPE	"seq"
public static final String	PIPELINE_STATS_TABLE_INPUT_TYPE	"stats"
public static final String	PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE	"taxa_count"
public static final String	RETURN	"\n"

biolockj.util.DemuxUtil

Modifier and Type	Constant Field	Value
public static final String	BARCODE_CUTOFF	"demultiplexer.barcodeCutoff"
public static final String	BARCODE_USE_REV_COMP	"demultiplexer.barcodeRevComp"
public static final String	DEMUX_STRATEGY	"demultiplexer.strategy"
public static final String	MAPPING_FILE	"demultiplexer.mapping"
public static final String	OPTION_BARCODE_IN_HEADER	"barcode_in_header"
public static final String	OPTION_BARCODE_IN_MAPPING	"barcode_in_mapping"
public static final String	OPTION_BARCODE_IN_SEQ	"barcode_in_seq"
public static final String	OPTION_DO_NOT_DEMUX	"do_not_demux"
public static final String	OPTION_ID_IN_HEADER	"id_in_header"
protected static final String	SAMPLE_ID_SUFFIX_TRIM_DEFAULT	"_"

biolockj.util.DockerUtil

Modifier and Type	Constant Field	Value
public static final String	AWS_EC2_HOME	"/home/ec2-user"
public static final String	CONTAINER_BLJ_DIR	"/app/biolockj"
public static final String	CONTAINER_ID_KEY	"Current container id: "
public static final String	DEFAULT_DOCKER_MAPPER	"biolockj.util.paths.CommonDockerMapper"
public static final String	DEFAULT_IMAGE_NAME	"ubuntu"
public static final String	DEFAULT_IMAGE_OWNER	"library"
public static final String	DEFAULT_IMAGE_TAG	"latest"
public static final String	DOCKER_BLJ_MOUNT_DIR	"/mnt/efs"
public static final String	DOCKER_DB_DIR	"/mnt/efs/db"
public static final String	DOCKER_DEFAULT_DB_DIR	"/mnt/db"
public static final String	DOCKER_HUB_USER	"docker.imageOwner"
public static final String	DOCKER_IMG	"docker.imageName"
public static final String	DOCKER_IMG_VERSION	"docker.imageTag"
public static final String	DOCKER_MOUNT_SOCK	"docker.mountSock"
public static final String	DOCKER_PIPELINE_DIR	"/mnt/efs/pipelines"
public static final String	DOCKER_USER	"root"
public static final String	PURE_DOCKER_PIPELINE_DIR	"/workspace/pipelines"
static final String	SAVE_CONTAINER_ON_EXIT	"docker.saveContainerOnExit"
static final String	SPAWN_DOCKER_CONTAINER	"spawnDockerContainer"

biolockj.util.DownloadUtil

Modifier and Type	Constant Field	Value
public static final String	DOWNLOAD_LIST	"downloadList.txt"

biolockj.util.MetaUtil

Modifier and Type	Constant Field	Value
protected static final String	DEFAULT_COMMENT_CHAR	""
protected static final String	DEFAULT_NULL_VALUE	"NA"
public static final String	META_BARCODE_COLUMN	"metadata.barcodeColumn"
public static final String	META_COLUMN_DELIM	"metadata.columnDelim"
public static final String	META_COMMENT_CHAR	"metadata.commentChar"
public static final String	META_FILE_PATH	"metadata.filePath"
public static final String	META_FILENAME_COLUMN	"metadata.fileNameColumn"
public static final String	META_NULL_VALUE	"metadata.nullValue"
public static final String	META_REQUIRED	"metadata.required"
protected static final String	METADATA_COL_DELIM	"\t"
public static final String	USE_EVERY_ROW	"metadata.useEveryRow"

biolockj.util.NextflowUtil

Modifier and Type	Constant Field	Value
public static final String	AWS_CONFIG_DIR	"config"
public static final String	AWS_COPY_DB_TO_S3	"aws.copyDbToS3"
public static final String	AWS_COPY_PIPELINE_TO_S3	"aws.copyPipelineToS3"
public static final String	AWS_COPY_REPORTS_TO_S3	"aws.copyReportsToS3"
public static final String	AWS_PURGE_EFS_INPUTS	"aws.purgeEfsInputs"
public static final String	AWS_PURGE_EFS_OUTPUT	"aws.purgeEfsOutput"
public static final String	AWS_RAM	"aws.ram"
public static final String	AWS_REPORT_DIR	"reports"
public static final String	AWS_S3	"aws.s3"
protected static final String	EC2_ACQUISITION_STRATEGY	"aws.ec2AcquisitionStrategy"
protected static final String	EC2_INSTANCE_TYPE	"aws.ec2InstanceType"
protected static final String	NF_LOG	"/.nextflow.log"

biolockj.util.RMetaUtil

Modifier and Type	Constant Field	Value
protected static final String	BINARY_FIELDS	"R_internal.binaryFields"
protected static final String	NUM_META_COLS	"R_internal.numMetaCols"
protected static final String	QIIME_PLOT_ALPHA_METRICS	"qiime.plotAlphaMetrics"
protected static final String	R_EXCLUDE_FIELDS	"r.excludeFields"
protected static final String	R_MDS_REPORT_FIELDS	"r_PlotMds.reportFields"
protected static final String	R_NOMINAL_FIELDS	"r.nominalFields"
protected static final String	R_NUMERIC_FIELDS	"r.numericFields"
protected static final String	R_REPORT_FIELDS	"r.reportFields"

biolockj.util.RuntimeParamUtil

Modifier and Type	Constant Field	Value
public static final String	AWS_FLAG	"-aws"
public static final String	BLJ_PROJ_DIR	"-projectDir"
public static final String	CONFIG_FILE	"-config"
public static final String	DEBUG_FLAG	"-verbose"
public static final String	DIRECT_MODE	"-direct"
public static final String	DOCKER_FLAG	"-docker"
public static final String	DOCKER_MAPPER	"-docker-mapper"
protected static final String	HOME_DIR	"-homeDir"
public static final String	PASSWORD	"-password"
public static final String	PRECHECK_FLAG	"-precheck"
public static final String	RESTART_DIR	"-restartDir"
protected static final String	SYSTEM_OUT_FLAG	"-systemOut"
public static final String	UNUSED_PROPS_FLAG	"-unusedProps"

biolockj.util.SeqUtil

Modifier and Type	Constant Field	Value
public static final String	FASTA_HEADER_DEFAULT_DELIM	">"
public static final String	ILLUMINA_FW_READ_IND	" 1:N:"
public static final String	ILLUMINA_RV_READ_IND	" 2:N:"

biolockj.util.SummaryUtil

Modifier and Type	Constant Field	Value
public static final String	PIPELINE_STATUS	"Pipeline Status"

biolockj.util.TaxaUtil

Modifier and Type	Constant Field	Value
public static final String	FILE_EXT	".tsv"
public static final String	NORMALIZED	"norm"
protected static final String	TAXA_TABLE	"taxaCount"

biolockj.util.ValidationUtil

Modifier and Type	Constant Field	Value
protected static final String	COMPARE_ON	"validation.compareOn"
public static final String	EXPECTATION_FILE	"validation.expectationFile"
protected static final int	FAIL	0
protected static final String	HALT_PIPELINE	"validation.stopPipeline"
protected static final String	MATCHED_EXPECTATION	"MATCHED_EXPECTATION"
protected static final String	MD5	"md5"
protected static final String	NAME	"name"
protected static final String	OUTPUT_FILE_SUFFIX	"_validation.txt"
protected static final int	PASS	1
protected static final int	REPORT	2
protected static final String	REPORT_ON	"validation.reportOn"
protected static final String	SIZE	"size"
protected static final String	SIZE_WITHIN_PERCENT	"validation.sizeWithinPercent"
protected static final String	VALIDATION_FOLDER	"validation"