Constant Field Values

Contents

• fr.ens.*

fr.ens.*

fr.ens.biologie.genomique.eoulsan.CommonHadoop

Modifier and Type	Constant Field	Value
public static final String	AWS_S3_ACCESS_KEY_ID_PARAM_KEY	"fs.s3n.awsAccessKeyId"
public static final String	AWS_S3_SECRET_ACCESS_KEY_PARAM_NAME	"fs.s3n.awsSecretAccessKey"
public static final int	CHECK_COMPLETION_TIME	5000
public static final String	HADOOP_PARAMETER_PREFIX	"hadoop.conf."
public static final String	HADOOP_REDUCER_TASK_COUNT_PARAMETER_NAME	"hadoop.reducer.task.count"

fr.ens.biologie.genomique.eoulsan.Globals

Modifier and Type	Constant Field	Value
public static final String	APP_NAME	"Eoulsan"
public static final boolean	BYPASS_PLATFORM_CHECKING	false
public static final String	DEFAULT_FILE_ENCODING	"UTF-8"
public static final double	DESIGN_FILE_VERSION	1.1
public static final String	EOULSAN_TOOLS_WEBSITE_URL	"https://raw.githubusercontent.com/GenomicParisCentre/eoulsan-tools"
public static final int	FASTA_FILE_WIDTH	60
public static final int	INTERNET_CHECK_PORT	443
public static final String	INTERNET_CHECK_SERVER	"raw.githubusercontent.com"
public static final String	LICENSE_TXT	"This program is developed under the GNU Lesser General Public License version 2.1 or later and CeCILL-C."
public static final String	LOG_EXTENSION	".log"
public static final int	MINIMAL_JAVA_VERSION_REQUIRED	8
public static final boolean	OBFUSCATE_DESIGN_DEFAULT	true
public static final boolean	OBFUSCATE_DESIGN_REMOVE_REPLICATE_INFO_DEFAULT	true
public static final String	OTHER_LOG_FILENAME	"additional.log"
public static final String	OUTPUT_TREE_TYPE_DEFAULT	"step"
public static final boolean	SAVE_WORKFLOW_IMAGE_DEFAULT	true
public static final boolean	STANDARD_EXTERNAL_MODULES_ENABLED_DEFAULT	true
public static final boolean	STD_OUTPUT_DEFAULT	false
public static final String	STEP_LOG_EXTENSION	".step.log"
public static final String	STEP_OUTPUT_DIRECTORY_SUFFIX	"_output"
public static final String	STEP_RESULT_EXTENSION	".step.result"
public static final String	STEP_RESULT_OLD_FORMAT_EXTENSION	".log"
public static final String	TASK_CONTEXT_EXTENSION	".task.context"
public static final String	TASK_DATA_EXTENSION	".task.data"
public static final String	TASK_DONE_EXTENSION	".task.done"
public static final String	TASK_JOB_ID	".task.job.id"
public static final String	TASK_LOG_EXTENSION	".task.log"
public static final String	TASK_RESULT_EXTENSION	".task.result"
public static final String	TASK_STDERR_EXTENSION	".task.err"
public static final String	TASK_STDOUT_EXTENSION	".task.out"
public static final String	UI_NAME_DEFAULT	"lanterna"
public static final boolean	USE_OLD_EOULSAN_RESULT_FORMAT_DEFAULT	false
public static final int	ZOOKEEPER_DEFAULT_PORT_DEFAULT	2181
public static final int	ZOOKEEPER_SESSION_TIMEOUT_DEFAULT	10000

fr.ens.biologie.genomique.eoulsan.Main

Modifier and Type	Constant Field	Value
public static final String	EOULSAN_CLASSPATH_JVM_ARG	"eoulsan.classpath"
public static final String	EOULSAN_MEMORY	"eoulsan.memory"
public static final String	EOULSAN_PATH	"eoulsan.path"
public static final String	EOULSAN_SCRIPT	"eoulsan.launch.script.path"

fr.ens.biologie.genomique.eoulsan.Settings

Modifier and Type	Constant Field	Value
public static final String	DATA_FORMAT_PATH_KEY	"main.format.path"
public static final String	GALAXY_TOOL_PATH_KEY	"main.galaxy.tool.path"
public static final String	STANDARD_EXTERNAL_MODULES_ENABLED_KEY	"main.standard.external.modules.enabled"

fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"clusterexec"

fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"clustertask"

fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"createdesign"

fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"createhadoopjar"

fr.ens.biologie.genomique.eoulsan.actions.ExecAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"exec"

fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"execjarhadoop"

fr.ens.biologie.genomique.eoulsan.actions.FormatsAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"formats"

fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"hadoopexec"

fr.ens.biologie.genomique.eoulsan.actions.InfoAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"info"

fr.ens.biologie.genomique.eoulsan.actions.ModulesAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"modules"

fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters

Modifier and Type	Constant Field	Value
public static final String	ENTRIES_READ	"Entries Read"
public static final String	ENTRIES_WRITTEN	"Entries Written"
public static final String	INPUT_ENTRIES	"Input Entries"

fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader

Modifier and Type	Constant Field	Value
public static final String	MAX_LINE_LENGTH	"mapreduce.input.linerecordreader.line.maxlength"

fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker

Modifier and Type	Constant Field	Value
public static final String	GENOME_DESCRIPTION	"genome_description"

fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker

Modifier and Type	Constant Field	Value
public static final int	MAX_READS_TO_CHECK	1000

fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_SINGLE_INPUT_PORT_NAME	"input"

fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_SINGLE_OUTPUT_PORT_NAME	"output"

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler

Modifier and Type	Constant Field	Value
public static final String	SCHEDULER_NAME	"htcondor"

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.PBSProTaskScheduler

Modifier and Type	Constant Field	Value
public static final String	SCHEDULER_NAME	"pbspro"

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.SLURMTaskScheduler

Modifier and Type	Constant Field	Value
public static final String	SCHEDULER_NAME	"slurm"

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler

Modifier and Type	Constant Field	Value
public static final String	SCHEDULER_NAME	"tgcc"

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TORQUETaskScheduler

Modifier and Type	Constant Field	Value
public static final String	SCHEDULER_NAME	"torque"

fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow

Modifier and Type	Constant Field	Value
protected static final String	WORKFLOW_COPY_FILENAME	"workflow.xml"

fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser

Modifier and Type	Constant Field	Value
public static final String	DESIGN_FILE_PATH_CONSTANT_NAME	"design.file.path"
public static final String	JOB_ID_CONSTANT_NAME	"job.id"
public static final String	JOB_PATH_CONSTANT_NAME	"job.path"
public static final String	JOB_UUID_CONSTANT_NAME	"job.uuid"
public static final String	OUTPUT_PATH_CONSTANT_NAME	"output.path"
public static final String	WORKFLOW_FILE_PATH_CONSTANT_NAME	"workflow.file.path"

fr.ens.biologie.genomique.eoulsan.data.DataFile

Modifier and Type	Constant Field	Value
public static final String	separator	"/"
public static final char	separatorChar	47

fr.ens.biologie.genomique.eoulsan.data.DataMetadata

Modifier and Type	Constant Field	Value
public static final String	FASTQ_FORMAT_KEY	"FastqFormat"
public static final String	PAIRED_END_KEY	"pairedend"
public static final String	SAMPLE_ID_KEY	"SampleId"
public static final String	SAMPLE_NAME_KEY	"SampleName"
public static final String	SAMPLE_NUMBER_KEY	"SampleNumber"

fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"annotation"

fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"file"

fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"ftp"

fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"ftp"

fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"genome"

fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"gff"

fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"gtf"

fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"hdfs"

fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"http"

fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"https"

fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"https"

fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_NAME	"http"

fr.ens.biologie.genomique.eoulsan.design.DesignMetadata

Modifier and Type	Constant Field	Value
public static final String	ADDITIONAL_ANNOTATION_FILE_KEY	"AdditionalAnnotationFile"
public static final String	GENOME_FILE_KEY	"GenomeFile"
public static final String	GFF_FILE_KEY	"GffFile"
public static final String	GTF_FILE_KEY	"GtfFile"

fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata

Modifier and Type	Constant Field	Value
public static final String	BUILD_CONTRAST_KEY	"buildContrast"
public static final String	COMPARISONS_KEY	"comparisons"
public static final String	CONTRAST_FILE_KEY	"contrastFile"
public static final String	CONTRAST_KEY	"contrast"
public static final String	DESIGN_FILE_KEY	"designFile"
public static final String	MODEL_KEY	"model"
public static final String	REFERENCE_KEY	"reference"
public static final String	SKIP_KEY	"skip"

fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata

Modifier and Type	Constant Field	Value
public static final String	CONDITION_KEY	"Condition"
public static final String	REFERENCE_KEY	"Reference"
public static final String	REP_TECH_GROUP_KEY	"RepTechGroup"

fr.ens.biologie.genomique.eoulsan.design.Sample

Modifier and Type	Constant Field	Value
public static final String	SAMPLE_ID_FIELD	"SampleId"
public static final String	SAMPLE_NAME_FIELD	"SampleName"
public static final String	SAMPLE_NUMBER_FIELD	"SampleNumber"

fr.ens.biologie.genomique.eoulsan.design.SampleMetadata

Modifier and Type	Constant Field	Value
public static final String	COMMENT_KEY	"Comment"
public static final String	CONDITION_KEY	"Condition"
public static final String	DATE_KEY	"Date"
public static final String	DESCRIPTION_KEY	"Description"
public static final String	FASTQ_FORMAT_KEY	"FastqFormat"
public static final String	OPERATOR_KEY	"Operator"
public static final String	READS_KEY	"Reads"
public static final String	REFERENCE_KEY	"Reference"
public static final String	REP_TECH_GROUP_KEY	"RepTechGroup"
public static final String	SERIAL_NUMBER_KEY	"SerialNumber"
public static final String	UUID_KEY	"UUID"

fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter

Modifier and Type	Constant Field	Value
public static final String	CALL_METHOD	"galaxy_dict.get"
public static final String	PYTHON_VARIABLES_DICT_NAME	"galaxy_dict"
public static final String	VAR_CMD_NAME	"cmd"

fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement

Modifier and Type	Constant Field	Value
public static final String	TYPE	"boolean"

fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement

Modifier and Type	Constant Field	Value
public static final String	TYPE	"boolean"

fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement

Modifier and Type	Constant Field	Value
public static final String	TAG_NAME	"data"
public static final String	TYPE	"data"

fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement

Modifier and Type	Constant Field	Value
public static final String	TYPE	"float"

fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement

Modifier and Type	Constant Field	Value
public static final String	TYPE	"integer"

fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement

Modifier and Type	Constant Field	Value
public static final String	TYPE	"select"

fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement

Modifier and Type	Constant Field	Value
public static final String	TYPE	"text"

fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement

Modifier and Type	Constant Field	Value
public static final String	SEP	"."

fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter

Modifier and Type	Constant Field	Value
public static final String	INTERPRETER_NAME	"default"

fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter

Modifier and Type	Constant Field	Value
public static final String	INTERPRETER_NAME	"docker"

fr.ens.biologie.genomique.eoulsan.io.FileCharsets

Modifier and Type	Constant Field	Value
public static final String	ASCII_ENCODING	"US-ASCII"
public static final String	LATIN1_FILE_ENCODING	"ISO-8859-1"
public static final String	UTF8_FILE_ENCODING	"UTF-8"

fr.ens.biologie.genomique.eoulsan.modules.CheckerModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"checker"

fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule

Modifier and Type	Constant Field	Value
public static final String	FORMAT_PARAMETER	"format"
public static final String	MODULE_NAME	"_copyinputformat"
public static final String	OUTPUT_COMPRESSION_PARAMETER	"output.compression"
public static final String	OUTPUT_COMPRESSIONS_ALLOWED_PARAMETER	"output.compressions.allowed"

fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule

Modifier and Type	Constant Field	Value
public static final String	FORMATS_PARAMETER	"formats"
public static final String	MODULE_NAME	"_copyoutputformat"
public static final String	PORTS_PARAMETER	"ports"

fr.ens.biologie.genomique.eoulsan.modules.DesignModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"design"

fr.ens.biologie.genomique.eoulsan.modules.FailModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"fail"

fr.ens.biologie.genomique.eoulsan.modules.FakeModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"fake"

fr.ens.biologie.genomique.eoulsan.modules.FirstModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"first"

fr.ens.biologie.genomique.eoulsan.modules.ImportModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"import"

fr.ens.biologie.genomique.eoulsan.modules.MergerModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"merger"

fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"requirementinstaller"

fr.ens.biologie.genomique.eoulsan.modules.SplitterModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"splitter"

fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"technicalreplicatemerger"

fr.ens.biologie.genomique.eoulsan.modules.TerminalModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"terminal"

fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"rmdup"

fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"peak_calling"

fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"sam_stats"

fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"deseq2"

fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"diffanaresultsannotation"

fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization

Modifier and Type	Constant Field	Value
protected static final String	NORMALIZATION_FUNCTIONS	"/DESeq1/normalization_anaDiff_RNAseq_Functions.R"
protected static final String	TARGET_CREATION	"/DESeq1/targetCreation.Rnw"

fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration

Modifier and Type	Constant Field	Value
public static final String	DOCKER_IMAGE_PARAMETER	"docker.image"
public static final String	EXECUTION_MODE_PARAMETER	"r.execution.mode"
public static final String	RSERVE_SERVER_PARAMETER	"rserve.servername"

fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"expression"
public static final String	COUNTER_PARAMETER_NAME	"counter"
public static final String	FEATURES_FILE_FORMAT_PARAMETER_NAME	"features.file.format"
public static final String	MODULE_NAME	"expression"
public static final String	OUTPUT_FILE_FORMAT_PARAMETER_NAME	"output.file.format"

fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule

Modifier and Type	Constant Field	Value
public static final String	COUNTER_GROUP	"expressionresultsannotation"
public static final String	MODULE_NAME	"expressionresultsannotation"

fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule

Modifier and Type	Constant Field	Value
public static final String	FASTQC_CASAVA_PARAMETER_NAME	"fastqc.casava"
public static final String	FASTQC_EXPGROUP_PARAMETER_NAME	"fastqc.expgroup"
public static final String	FASTQC_KMER_SIZE_PARAMETER_NAME	"fastqc.kmer.size"
public static final String	FASTQC_NOFILTER_PARAMETER_NAME	"fastqc.nofilter"
public static final String	FASTQC_NOGROUP_PARAMETER_NAME	"fastqc.nogroup"

fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"dummygenerator"

fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"genericstoragegenerator"

fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"genomedescgenerator"

fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"genericindexgenerator"

fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"gfffastagenerator"

fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"minimap2indexgenerator"

fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"starindexgenerator"

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"bam2sam"

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule

Modifier and Type	Constant Field	Value
protected static final String	GENOME_DESCRIPTION_PORT_NAME	"genomedescription"
protected static final int	HADOOP_TIMEOUT	3600000
protected static final String	MAPPER_INDEX_PORT_NAME	"mapperindex"
public static final String	MODULE_NAME	"filterandmap"
protected static final String	READS_PORT_NAME	"reads"

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"reads_filtering"
protected static final String	MODULE_NAME	"filterreads"

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"reads_mapping"
protected static final String	GENOME_DESCRIPTION_PORT_NAME	"genomedescription"
public static final String	HADOOP_THREADS_PARAMETER_NAME	"hadoop.threads"
public static final int	HADOOP_TIMEOUT	3600000
public static final String	LOCAL_THREADS_PARAMETER_NAME	"local.threads"
public static final String	MAPPER_ARGUMENTS_PARAMETER_NAME	"mapper.arguments"
public static final String	MAPPER_DOCKER_IMAGE_PARAMETER_NAME	"mapper.docker.image"
public static final String	MAPPER_FLAVOR_PARAMETER_NAME	"mapper.flavor"
protected static final String	MAPPER_INDEX_PORT_NAME	"mapperindex"
public static final String	MAPPER_NAME_PARAMETER_NAME	"mapper"
public static final String	MAPPER_VERSION_PARAMETER_NAME	"mapper.version"
public static final String	MAX_LOCAL_THREADS_PARAMETER_NAME	"max.local.threads"
public static final String	MODULE_NAME	"mapreads"
protected static final String	READS_PORT_NAME	"reads"
public static final String	USE_BUNDLED_BINARIES_PARAMETER_NAME	"mapper.use.bundled.binares"

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"sam2bam"

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"sam2fastq"

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"sam_filtering"

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule

Modifier and Type	Constant Field	Value
protected static final String	COUNTER_GROUP	"splice2bed"

fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils

Modifier and Type	Constant Field	Value
public static final String	HEADERMERGER_INPUTS_PROPERTY	"hadoopbam.headermerger.inputs"
public static final String	WORK_FILENAME_PROPERTY	"hadoopbam.work.filename"

fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule

Modifier and Type	Constant Field	Value
public static final String	MODULE_NAME	"_copy_design_params_to_output"

fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp.DuplicationException

Modifier and Type	Constant Field	Value
public static final int	ERROR_CODE	-2

fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload

Modifier and Type	Constant Field	Value
protected static final String	STEP_NAME	"defineformatstodownload"

fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule

Modifier and Type	Constant Field	Value
public static final String	DATAFORMATS_TO_DOWNLOAD_SETTING	"dataformat.to.download"
public static final String	MODULE_NAME	"_download"
public static final String	NO_HDFS_DOWNLOAD	"no.hdfs.download"

fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor

Modifier and Type	Constant Field	Value
public static final String	REPORT_NAME	"expression"

fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor

Modifier and Type	Constant Field	Value
public static final String	REPORT_NAME	"fastqc"

fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor

Modifier and Type	Constant Field	Value
public static final String	REPORT_NAME	"featurecounts"

fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor

Modifier and Type	Constant Field	Value
public static final String	REPORT_NAME	"mapreads"

fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement

Modifier and Type	Constant Field	Value
protected static final String	INSTALLABLE_PARAMETER	"installable"
public static final String	NAME_PARAMETER	"name"
protected static final String	OPTIONAL_PARAMETER	"optional"

fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement

Modifier and Type	Constant Field	Value
public static final String	REQUIREMENT_NAME	"docker"

fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement

Modifier and Type	Constant Field	Value
public static final String	REQUIREMENT_NAME	"path"

fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement

Modifier and Type	Constant Field	Value
public static final String	REQUIREMENT_NAME	"rserve"

fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock

Modifier and Type	Constant Field	Value
public static final int	ANY_VERSION	-1

fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor

Modifier and Type	Constant Field	Value
public static final String	REXECUTOR_NAME	"docker"

fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor

Modifier and Type	Constant Field	Value
protected static final String	DEFAULT_R_LANG	"C"
protected static final String	LANG_ENVIRONMENT_VARIABLE	"LANG"
public static final String	REXECUTOR_NAME	"process"
public static final String	RSCRIPT_EXECUTABLE	"Rscript"

fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor

Modifier and Type	Constant Field	Value
public static final String	REXECUTOR_NAME	"rserve"