Uses of Class
fr.ens.biologie.genomique.eoulsan.data.DataFile
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Packages that use DataFile Package Description fr.ens.biologie.genomique.eoulsan.core This package contains Eoulsan workflow core class.fr.ens.biologie.genomique.eoulsan.core.workflow This package contains Eoulsan workflow dedicated classes.fr.ens.biologie.genomique.eoulsan.data This package contains classes for data files, data types and data formats.fr.ens.biologie.genomique.eoulsan.data.protocols This package contains class for protocols used by theDataFile
classes.fr.ens.biologie.genomique.eoulsan.data.storages This package contains and define data storages.fr.ens.biologie.genomique.eoulsan.design This package contains classes to handle experimental designs.fr.ens.biologie.genomique.eoulsan.design.io This package contains I/O classes to read and write design files.fr.ens.biologie.genomique.eoulsan.modules.diffana This package contain all the classes related to the differential analysis step.fr.ens.biologie.genomique.eoulsan.modules.expression This package contain all the classes related to the expression step.fr.ens.biologie.genomique.eoulsan.modules.fastqc This package contain all the classes related to FastQC.fr.ens.biologie.genomique.eoulsan.modules.generators This package contain generator steps.fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload This package contain classes related to upload data to HDFS and Cloud.fr.ens.biologie.genomique.eoulsan.splitermergers This package contains splitter and merger used when running Eoulsan on a standard cluster to get more parallelization efficiency.fr.ens.biologie.genomique.eoulsan.util This package contain utility classes.fr.ens.biologie.genomique.eoulsan.util.r This package contain utility classes for R usage. -
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Uses of DataFile in fr.ens.biologie.genomique.eoulsan.core
Methods in fr.ens.biologie.genomique.eoulsan.core that return DataFile Modifier and Type Method Description DataFile
StepConfigurationContext. getDesignFile()
Get the design file path.static DataFile
ContextUtils. getHadoopWorkingDirectory(TaskContext context)
Get the Hadoop working directory.static DataFile
ContextUtils. getJarPathname(TaskContext context)
Get the application jar file.static DataFile
ContextUtils. getJobDirectory(TaskContext context)
Get the job directory.DataFile
StepConfigurationContext. getJobDirectory()
Get the job path.static DataFile
ContextUtils. getLocalWorkingDirectory(TaskContext context)
Get the local working directory.DataFile
StepConfigurationContext. getOutputDirectory()
Get the output path.DataFile
StepConfigurationContext. getStepOutputDirectory()
Get the step working directory.static DataFile
ContextUtils. getTaskOutputDirectory(TaskContext context)
Get the task output directory.DataFile
StepConfigurationContext. getWorkflowFile()
Get the workflow file path.Methods in fr.ens.biologie.genomique.eoulsan.core that return types with arguments of type DataFile Modifier and Type Method Description static List<DataFile>
DataUtils. getDataFiles(Data data)
Get the list of the DataFile objects in a Data object.Methods in fr.ens.biologie.genomique.eoulsan.core with parameters of type DataFile Modifier and Type Method Description static boolean
FileNaming. dataEquals(DataFile file1, DataFile file2)
Test if two files are related to the same data.void
Workflow. deleteOnExit(DataFile file)
Delete a file on the exit of the workflow.static boolean
FileNaming. isFilenameValid(DataFile file)
Test if a filename is valid.static FileNaming
FileNaming. parse(DataFile file)
Create a FileNaming object from a DataFile object.static void
DataUtils. setDataFile(Data data, DataFile dataFile)
Change the DataFile in a Data objectMethod parameters in fr.ens.biologie.genomique.eoulsan.core with type arguments of type DataFile Modifier and Type Method Description static void
DataUtils. setDataFiles(Data data, List<DataFile> dataFiles)
Change the DataFiles in a Data object -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.core.workflow
Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return DataFile Modifier and Type Method Description static DataFile
WorkflowFileNaming. file(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port, fr.ens.biologie.genomique.eoulsan.core.workflow.DataElement data, int fileIndex)
Create a DataFile object for a file of the workflow.DataFile
DataList. getDataFile()
DataFile
DataList. getDataFile(int fileIndex)
DataFile
StepOutputDataFile. getDataFile()
Get the file as a DataFile.DataFile
UnmodifiableData. getDataFile()
DataFile
UnmodifiableData. getDataFile(int fileIndex)
DataFile
TaskContextImpl. getDataRepositoryDirectory()
Get the data repository directory.DataFile
WorkflowContext. getDataRepositoryDirectory()
Get the data repository directory.DataFile
StepConfigurationContextImpl. getDesignFile()
DataFile
TaskContextImpl. getDesignFile()
DataFile
WorkflowContext. getDesignFile()
Get the design file.DataFile
StepConfigurationContextImpl. getHadoopWorkingDirectory()
Get the Hadoop working directory.DataFile
WorkflowContext. getHadoopWorkingDirectory()
Get the local working directory.DataFile
TaskContextImpl. getHadoopWorkingPathname()
Get the Hadoop working directory.DataFile
WorkflowContext. getJarFile()
Get the application jar file.DataFile
StepConfigurationContextImpl. getJarPathname()
Get the application jar file.DataFile
TaskContextImpl. getJarPathname()
Get the application jar path.DataFile
StepConfigurationContextImpl. getJobDirectory()
Get the job directory.DataFile
TaskContextImpl. getJobDirectory()
Get the job directory.DataFile
WorkflowContext. getJobDirectory()
Get the job path.DataFile
StepConfigurationContextImpl. getLocalWorkingDirectory()
Get the local working directory.DataFile
WorkflowContext. getLocalWorkingDirectory()
Get the local working directory.DataFile
TaskContextImpl. getLocalWorkingPathname()
Get the local working directory.DataFile
StepConfigurationContextImpl. getOutputDirectory()
DataFile
TaskContextImpl. getOutputDirectory()
DataFile
WorkflowContext. getOutputDirectory()
Get the output directory.DataFile
AbstractStep. getStepOutputDirectory()
Get step output directory (where output file of the step will be written).DataFile
StepConfigurationContextImpl. getStepOutputDirectory()
DataFile
TaskContextImpl. getStepOutputDirectory()
DataFile
WorkflowContext. getTaskDirectory()
Get the task directory.DataFile
StepConfigurationContextImpl. getTaskOutputDirectory()
Get the task output directory.DataFile
TaskContextImpl. getTaskOutputDirectory()
Get the task output directory.DataFile
StepConfigurationContextImpl. getWorkflowFile()
DataFile
TaskContextImpl. getWorkflowFile()
DataFile
WorkflowContext. getWorkflowFile()
Get the workflow file.Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return types with arguments of type DataFile Modifier and Type Method Description static List<DataFile>
WorkflowDataUtils. getDataFiles(Data data)
Get the list of the DataFile objects in a Data object.Methods in fr.ens.biologie.genomique.eoulsan.core.workflow with parameters of type DataFile Modifier and Type Method Description void
AbstractWorkflow. deleteOnExit(DataFile file)
static TaskContextImpl
TaskContextImpl. deserialize(DataFile file)
Deserialize the TaskContext object.static TaskResultImpl
TaskResultImpl. deserialize(DataFile file)
Deserialize the TaskResult object.void
TaskContextImpl. deserializeOutputData(DataFile file)
Deserialize output data.static TaskResultImpl
TaskSerializationUtils. execute(DataFile taskContextFile)
Execute a task context serialization file.static TaskResultImpl
TaskSerializationUtils. execute(DataFile taskContextFile, DataFile outputDir)
Execute a task context serialization file.static DataMetadataStorage
DataMetadataStorage. getInstance(DataFile metadataDir)
Get the singleton.Map<String,String>
DataMetadataStorage. getMetadata(DataFile file)
Get the metadata of a file.void
StepResult. read(DataFile file)
Read a step result file.void
TaskContextImpl. serialize(DataFile file)
Serialize the TaskContext object.void
TaskResultImpl. serialize(DataFile file)
Serialize the TaskResult object.void
TaskContextImpl. serializeOutputData(DataFile file)
Serialize output data.static void
WorkflowDataUtils. setDataFile(Data data, int fileIndex, DataFile dataFile)
Change the DataFile in a Data objectstatic void
WorkflowDataUtils. setDataFile(Data data, DataFile dataFile)
Change the DataFile in a Data objectvoid
WorkflowContext. setDesignFile(DataFile designFile)
Set the design file.void
WorkflowContext. setJarFile(DataFile jarFile)
Set the jar file.void
WorkflowContext. setWorkflowFile(DataFile workflowFile)
Set the workflow file.void
StepResult. write(DataFile file, boolean oldFormat)
Write the result.Method parameters in fr.ens.biologie.genomique.eoulsan.core.workflow with type arguments of type DataFile Modifier and Type Method Description boolean
DataMetadataStorage. loadMetadata(Data data, List<DataFile> files)
Set the metadata of a data from the metadata storage.static void
WorkflowDataUtils. setDataFiles(Data data, List<DataFile> dataFiles)
Change the DataFiles in a Data objectConstructors in fr.ens.biologie.genomique.eoulsan.core.workflow with parameters of type DataFile Constructor Description CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct, DataFile outputDirectory)
Create a step for a standard step.CommandWorkflowParser(DataFile file)
Public constructor.Workflow2Graphviz(AbstractWorkflow workflow, DataFile dotFile, DataFile imageFile)
Public constructor. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.data
Methods in fr.ens.biologie.genomique.eoulsan.data that return DataFile Modifier and Type Method Description DataFile
Data. getDataFile()
Get the DataFile for an input DataType and a Sample.DataFile
Data. getDataFile(int fileIndex)
Get the DataFile for an input DataType and a Sample.DataFile
DataFileMetadata. getLinkTarget()
Get the symbolic link target.DataFile
DataFile. getParent()
Get the parent of this DataFile.DataFile
DataFile. toAbsoluteDataFile()
Convert the the DataFile to a absolute DataFile.DataFile
DataFile. toRealDataFile()
Convert the the DataFile to a DataFile where all the indirection has been solved.Methods in fr.ens.biologie.genomique.eoulsan.data that return types with arguments of type DataFile Modifier and Type Method Description List<DataFile>
DataFile. list()
List the content of a directory.Methods in fr.ens.biologie.genomique.eoulsan.data with parameters of type DataFile Modifier and Type Method Description int
DataFile. compareTo(DataFile o)
static void
DataFiles. copy(DataFile input, DataFile output)
Copy a file, if input data is compressed, data will be uncompressed and if output require to be compressed output will be compressed.void
DataFile. copyTo(DataFile dest)
Copy this DataFile in a other DataFile.static void
DataFiles. rawCopy(DataFile input, DataFile output)
Copy a file.void
DataFile. renameTo(DataFile dest)
Rename the DataFile.void
DataFile. symlink(DataFile link)
Create a symbolic link that target is the current file.void
DataFile. symlink(DataFile link, boolean relativize)
Create a symbolic link that target is the current file.static void
DataFiles. symlinkOrCopy(DataFile input, DataFile output)
Create a symbolic link if the input and output use the same protocol and if symbolic links are supported by the protocol.static void
DataFiles. symlinkOrCopy(DataFile input, DataFile output, boolean relativize)
Create a symbolic link if the input and output use the same protocol and if symbolic links are supported by the protocol.Constructors in fr.ens.biologie.genomique.eoulsan.data with parameters of type DataFile Constructor Description DataFile(DataFile parentFile, String filename)
Public constructor.DataFormatConverter(DataFile inFile, DataFile outFile)
ConstructorDataFormatConverter(DataFile inFile, DataFile outFile, DataFormat outFormat, OutputStream os)
ConstructorDataFormatConverter(DataFile inFile, DataFile outFile, OutputStream os)
Constructor -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.data.protocols
Methods in fr.ens.biologie.genomique.eoulsan.data.protocols that return DataFile Modifier and Type Method Description DataFile
DataProtocol. getDataFileParent(DataFile src)
Get the parent source of the source.DataFile
StorageDataProtocol. getUnderLyingData(DataFile src)
Get the underlying Data.Methods in fr.ens.biologie.genomique.eoulsan.data.protocols that return types with arguments of type DataFile Modifier and Type Method Description List<DataFile>
DataProtocol. list(DataFile dir)
List a directory.List<DataFile>
FileDataProtocol. list(DataFile file)
List<DataFile>
HDFSPathDataProtocol. list(DataFile file)
Methods in fr.ens.biologie.genomique.eoulsan.data.protocols with parameters of type DataFile Modifier and Type Method Description void
DataProtocol. delete(DataFile file, boolean recursive)
Delete a file.void
FileDataProtocol. delete(DataFile file, boolean recursive)
void
HDFSPathDataProtocol. delete(DataFile file, boolean recursive)
boolean
DataProtocol. exists(DataFile src, boolean followLink)
Test a source exists.boolean
DeprecatedDataProtocol. exists(DataFile src, boolean followLink)
boolean
FileDataProtocol. exists(DataFile src, boolean followLink)
boolean
PathDataProtocol. exists(DataFile src, boolean followLink)
boolean
StorageDataProtocol. exists(DataFile src, boolean followLink)
boolean
URLDataProtocol. exists(DataFile src, boolean followLink)
InputStream
DataProtocol. getData(DataFile src)
Create an InputStream from the source.InputStream
DeprecatedDataProtocol. getData(DataFile src)
InputStream
FileDataProtocol. getData(DataFile src)
InputStream
HDFSPathDataProtocol. getData(DataFile src)
InputStream
PathDataProtocol. getData(DataFile src)
InputStream
StorageDataProtocol. getData(DataFile src)
InputStream
URLDataProtocol. getData(DataFile src)
DataFile
DataProtocol. getDataFileParent(DataFile src)
Get the parent source of the source.DataFileMetadata
DataProtocol. getMetadata(DataFile src)
Get the metadata for the source.DataFileMetadata
DeprecatedDataProtocol. getMetadata(DataFile src)
DataFileMetadata
FileDataProtocol. getMetadata(DataFile src)
DataFileMetadata
PathDataProtocol. getMetadata(DataFile src)
DataFileMetadata
StorageDataProtocol. getMetadata(DataFile src)
DataFileMetadata
URLDataProtocol. getMetadata(DataFile src)
org.apache.hadoop.fs.Path
PathDataProtocol. getPath(DataFile dataFile)
Get Convert a DataFile object to a Path object.File
DataProtocol. getSourceAsFile(DataFile src)
Get the underlying File object for the DataFile if the protocol allow it.File
FileDataProtocol. getSourceAsFile(DataFile dataFile)
File
StorageDataProtocol. getSourceAsFile(DataFile src)
DataFile
StorageDataProtocol. getUnderLyingData(DataFile src)
Get the underlying Data.List<DataFile>
DataProtocol. list(DataFile dir)
List a directory.List<DataFile>
FileDataProtocol. list(DataFile file)
List<DataFile>
HDFSPathDataProtocol. list(DataFile file)
void
DataProtocol. mkdir(DataFile dir)
Create a directory.void
FileDataProtocol. mkdir(DataFile dir)
void
HDFSPathDataProtocol. mkdir(DataFile dir)
void
DataProtocol. mkdirs(DataFile dir)
Create a directory and its parents if not exists.void
FileDataProtocol. mkdirs(DataFile dir)
void
HDFSPathDataProtocol. mkdirs(DataFile dir)
OutputStream
DataProtocol. putData(DataFile dest)
Create an OutputStream from the source.void
DataProtocol. putData(DataFile src, DataFile dest)
Copy data from a source to a destination sourceOutputStream
DataProtocol. putData(DataFile dest, DataFileMetadata md)
Create an OutputStream from the source.OutputStream
DeprecatedDataProtocol. putData(DataFile dest)
OutputStream
FileDataProtocol. putData(DataFile src)
OutputStream
PathDataProtocol. putData(DataFile src)
OutputStream
StorageDataProtocol. putData(DataFile dest)
OutputStream
URLDataProtocol. putData(DataFile src)
void
DataProtocol. rename(DataFile file, DataFile dest)
Rename a file.void
FileDataProtocol. rename(DataFile src, DataFile dest)
void
HDFSPathDataProtocol. rename(DataFile file, DataFile dest)
void
DataProtocol. symlink(DataFile target, DataFile link)
Create a symbolic link.void
FileDataProtocol. symlink(DataFile target, DataFile link)
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Uses of DataFile in fr.ens.biologie.genomique.eoulsan.data.storages
Methods in fr.ens.biologie.genomique.eoulsan.data.storages that return DataFile Modifier and Type Method Description DataFile
DataFileDataPath. getDataFile()
DataFile
DataFileGenomeIndexStorage. getDataFile(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genome, Map<String,String> additionalDescription)
Get the DataFile that corresponds to a mapper and a genomeDataFile
DataFileStorage. getDataFile(String shortName)
Get a Datafile related to a short nameMethods in fr.ens.biologie.genomique.eoulsan.data.storages with parameters of type DataFile Modifier and Type Method Description void
DataFileGenomeMapperIndexer. createIndex(DataFile genomeDataFile, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDescription, DataFile mapperIndexDataFile)
Create an archived genome index.static fr.ens.biologie.genomique.kenetre.storage.GenomeDescStorage
DataFileGenomeDescStorage. getInstance(DataFile dir, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
Create a GenomeDescStoragevoid
DataFileGenomeIndexStorage. put(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genome, Map<String,String> additionalDescription, DataFile indexArchive)
Put the index archive in the storage.Constructors in fr.ens.biologie.genomique.eoulsan.data.storages with parameters of type DataFile Constructor Description DataFileDataPath(DataFile file)
Constructor. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.design
Methods in fr.ens.biologie.genomique.eoulsan.design with parameters of type DataFile Modifier and Type Method Description void
DesignBuilder. addFile(DataFile file)
Add a file to the design builderstatic void
DesignUtils. replaceLocalPathBySymlinks(Design design, DataFile symlinksDir)
Replace the local paths in the design by paths to symbolic links in a directory. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.design.io
Constructors in fr.ens.biologie.genomique.eoulsan.design.io with parameters of type DataFile Constructor Description DefaultDesignReader(DataFile file)
Public constructor.Eoulsan1DesignReader(DataFile file)
Public constructor.Eoulsan1DesignWriter(DataFile file)
Public constructor.Eoulsan2DesignReader(DataFile file)
Public constructor.Eoulsan2DesignWriter(DataFile file)
Public constructor. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.diffana
Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana with parameters of type DataFile Modifier and Type Method Description void
DESeq2. runDEseq2(DataFile workflowOutputDir)
Method to run DESeq2. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.expression
Methods in fr.ens.biologie.genomique.eoulsan.modules.expression with parameters of type DataFile Modifier and Type Method Description static Map<String,Integer>
ExpressionCounterUtils. count(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile samFile, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer reporter, String counterGroup)
Count the the features.static void
ExpressionCounterUtils. init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile genomeDescFile, DataFile annotationFile, boolean gtfFormat)
Initialize the counter.static void
ExpressionCounterUtils. init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDesc, DataFile annotationFile, boolean gtfFormat)
Initialize the counter. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.fastqc
Constructors in fr.ens.biologie.genomique.eoulsan.modules.fastqc with parameters of type DataFile Constructor Description EmptyFileQC(DataFile file)
Constructor.FastqSequenceFile(DataFile fastqFile)
Public constructor.SAMSequenceFile(DataFile inFile)
Public constructor. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.generators
Methods in fr.ens.biologie.genomique.eoulsan.modules.generators with parameters of type DataFile Modifier and Type Method Description fr.ens.biologie.genomique.kenetre.bio.GenomeDescription
GenomeDescriptionCreator. createGenomeDescription(DataFile genomeDataFile)
Create genome description object from the storage if already exists or compute it from the genome.fr.ens.biologie.genomique.kenetre.bio.GenomeDescription
GenomeDescriptionCreator. createGenomeDescriptionFromAnnotation(DataFile annotationDataFile)
Create genome description object from the storage if already exists or compute it from the genome. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop with parameters of type DataFile Modifier and Type Method Description static org.apache.hadoop.mapreduce.Job
PairedEndFastqToTfq. convert(org.apache.hadoop.conf.Configuration parentConf, DataFile fastqFile1, DataFile fastqFile2, DataFile outputFile, int reducerTaskCount)
Create the job to convert FASTQ files in a TFQ file. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload that return DataFile Modifier and Type Method Description protected DataFile
UploadModule. getDest()
protected DataFile
HadoopUploadModule. getUploadedDataFile(DataFile file)
protected DataFile
HadoopUploadModule. getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected DataFile
LocalUploadModule. getUploadedDataFile(DataFile file)
protected DataFile
LocalUploadModule. getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected abstract DataFile
UploadModule. getUploadedDataFile(DataFile file)
Generate the DataFile Object for the uploaded DataFileprotected abstract DataFile
UploadModule. getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
Generate the DataFile Object for the uploaded DataFileMethods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with parameters of type DataFile Modifier and Type Method Description protected DataFile
HadoopUploadModule. getUploadedDataFile(DataFile file)
protected DataFile
HadoopUploadModule. getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected DataFile
LocalUploadModule. getUploadedDataFile(DataFile file)
protected DataFile
LocalUploadModule. getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected abstract DataFile
UploadModule. getUploadedDataFile(DataFile file)
Generate the DataFile Object for the uploaded DataFileprotected abstract DataFile
UploadModule. getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
Generate the DataFile Object for the uploaded DataFileMethod parameters in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with type arguments of type DataFile Modifier and Type Method Description void
DataFileDistCp. copy(Map<DataFile,DataFile> entries)
void
DataFileDistCp. copy(Map<DataFile,DataFile> entries)
protected void
HadoopUploadModule. copy(Map<DataFile,DataFile> files)
protected void
HadoopUploadModule. copy(Map<DataFile,DataFile> files)
protected void
LocalUploadModule. copy(Map<DataFile,DataFile> files)
protected void
LocalUploadModule. copy(Map<DataFile,DataFile> files)
protected abstract void
UploadModule. copy(Map<DataFile,DataFile> files)
Copy files to destinations.protected abstract void
UploadModule. copy(Map<DataFile,DataFile> files)
Copy files to destinations.Constructors in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with parameters of type DataFile Constructor Description HadoopUploadModule(DataFile dest, org.apache.hadoop.conf.Configuration conf)
Public constructor.LocalUploadModule(DataFile dest)
Public constructor.UploadModule(DataFile destination)
Public constructor. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.splitermergers
Methods in fr.ens.biologie.genomique.eoulsan.splitermergers with parameters of type DataFile Modifier and Type Method Description void
BAMMerger. merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void
ExpressionMerger. merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void
FastqMerger. merge(Iterator<DataFile> inDataFileIterator, DataFile outFile)
void
Merger. merge(Iterator<DataFile> inFileIterator, DataFile outFile)
Merger data.void
SAMMerger. merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void
BAMSplitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
void
ExpressionSplitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
void
FastqSplitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
void
SAMSplitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
void
Splitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
Split data.void
BAMSplitter. splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)
Split BAM file by chromosomes.void
SAMSplitter. splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)
Split SAM file by chromosomes.Method parameters in fr.ens.biologie.genomique.eoulsan.splitermergers with type arguments of type DataFile Modifier and Type Method Description void
BAMMerger. merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void
ExpressionMerger. merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void
FastqMerger. merge(Iterator<DataFile> inDataFileIterator, DataFile outFile)
void
Merger. merge(Iterator<DataFile> inFileIterator, DataFile outFile)
Merger data.void
SAMMerger. merge(Iterator<DataFile> inFileIterator, DataFile outFile)
void
BAMSplitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
void
ExpressionSplitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
void
FastqSplitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
void
SAMSplitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
void
Splitter. split(DataFile inFile, Iterator<DataFile> outFileIterator)
Split data.void
BAMSplitter. splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)
Split BAM file by chromosomes.void
SAMSplitter. splitByChromosomes(DataFile inFile, Iterator<DataFile> outFileIterator)
Split SAM file by chromosomes. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.util
Methods in fr.ens.biologie.genomique.eoulsan.util that return DataFile Modifier and Type Method Description static DataFile
EoulsanTranslatorUtils. getLinksFileFromSettings(Settings settings)
Get the links file from the settings.Methods in fr.ens.biologie.genomique.eoulsan.util with parameters of type DataFile Modifier and Type Method Description void
FileResourceLoader. addResourcePath(DataFile resourcePath)
Add a resource path.static fr.ens.biologie.genomique.kenetre.translator.Translator
EoulsanTranslatorUtils. loadTranslator(DataFile linksFile)
Create a translator annotation from a link file.static fr.ens.biologie.genomique.kenetre.translator.Translator
EoulsanTranslatorUtils. loadTranslator(DataFile annotationFile, DataFile linksFile)
Create a translator annotation from an additional annotation file and a link file.boolean
FileResourceLoader. removeResourcePath(DataFile resourcePath)
Add a resource path.Constructors in fr.ens.biologie.genomique.eoulsan.util with parameters of type DataFile Constructor Description FileResourceLoader(Class<S> clazz, DataFile resourcePath)
Public constructor. -
Uses of DataFile in fr.ens.biologie.genomique.eoulsan.util.r
Methods in fr.ens.biologie.genomique.eoulsan.util.r with parameters of type DataFile Modifier and Type Method Description void
AbstractRExecutor. executeRScript(String rScript, boolean sweave, String sweaveOutput, boolean saveRscript, String description, DataFile workflowOutputDir, String... scriptArguments)
void
RExecutor. executeRScript(String rScript, boolean sweave, String sweaveOutput, boolean saveRscript, String description, DataFile workflowOutputDir, String... scriptArguments)
Execute a R script.protected static boolean
ProcessRExecutor. isSameLocalPath(DataFile a, DataFile b)
Check if two file have the same local pathprotected abstract void
AbstractRExecutor. putFile(DataFile inputFile, String outputFilename)
Put a file for the analysis.protected void
DockerRExecutor. putFile(DataFile inputFile, String outputFilename)
protected void
ProcessRExecutor. putFile(DataFile inputFile, String outputFilename)
protected void
RserveRExecutor. putFile(DataFile inputFile, String inputFilename)
void
AbstractRExecutor. putInputFile(DataFile inputFile)
void
AbstractRExecutor. putInputFile(DataFile inputFile, String outputFilename)
void
RExecutor. putInputFile(DataFile inputFile)
Put a file for the analysis.void
RExecutor. putInputFile(DataFile inputFile, String outputFilename)
Put a file.
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