Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BLJ_BASH_VAR |
"BLJ" |
public static final String |
BLJ_PROJ_VAR |
"BLJ_PROJ" |
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" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
RETURN |
"\n" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DIRECTORY |
"directory" |
public static final String |
FILE |
"file" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ERROR_MSG |
"ERROR MESSAGE: " |
public static final String |
ERROR_TYPE |
"ERROR TYPE: " |
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." |
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." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
EXTERNAL_MODULES_CONTAINER_DIR |
"/app/external_modules" |
public static final int |
GUI_PORT |
8080 |
Modifier and Type | Constant Field | Value |
---|---|---|
static final String |
BioLockJ_CLASS |
"biolockj.BioLockJ" |
Modifier and Type | Constant Field | Value |
---|---|---|
static final String |
anim |
"|/-\\" |
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" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
BLJ_OPTIONS |
"BLJ_OPTIONS" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PICK_OTU_SCRIPT |
"pick_de_novo_otus.py" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PICK_OTU_SCRIPT |
"pick_open_reference_otus.py" |
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" |
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" |
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" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SHANNON_COLUMN |
"ShannonDiversity" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
RESOURCES |
"rmarkdown.resources" |
protected static final String |
RMD_FILE |
"rmarkdown.rmarkdown" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DO_UPDATE |
"sra.forceDbUpdate" |
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\'." |
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\'." |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
NUM_LINES_TEMP_FILE |
2000000 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
NUM_READS |
"Num_Reads" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
NUM_OTUS |
"OTU_COUNT" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
HN2_KEEP_UNINTEGRATED |
"humann2.keepUnintegrated" |
protected static final String |
HN2_KEEP_UNMAPPED |
"humann2.keepUnmapped" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
SCRIPT_MERGE_OTU_TABLES |
"merge_otu_tables.py" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SUMMARY |
"summary" |
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" |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
HIT_RATIO |
"Hit_Ratio" |
public static final String |
META_MERGED |
"_metaMerged.tsv" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
LOG_10 |
"10" |
protected static final String |
LOG_E |
"e" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
FUNCTION_GUNZIP |
"openZip" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
DO_GZIP |
"multiplexer.gzip" |
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" |
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" |
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" |
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" |
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__" |
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" |
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" |
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 |
"_" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOWNLOAD_LIST |
"downloadList.txt" |
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" |
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" |
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" |
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" |
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:" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PIPELINE_STATUS |
"Pipeline Status" |
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" |
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" |