Package index • carboseqsiwaa

All functions
`ControlCommunicationWithSiwaa()`	Control Communication with Siwaa by API
`allDataReady()`	All Datasets of a collection are ready
`checkSiwaaCom()`	Check communication with Siwaa
`clearHistory()`	Clear the history
`createDatasetCollection()`	Create a dataset collection, into a history, from a dataset list
`createHistory()`	Create a history
`createSiwaaEnv()`	Create siwaaenv
`dateTime4History()`	Return a string with date and time
`defineHistoryName()`	Define history name
`deleteHistory()`	Purge a history if 'purge' is TRUE, and else delete it
`downloadDatasetCollection()`	Download as file a dataset collection
`downloadInMemory()`	Download in memory a dataset
`getApiKeyValue()`	Return env API_KEY value
`getDataInfo()`	Get dataset information
`getDatasetCollectionIdList()`	List of ids of Datasets of a collection
`getDatasetCollectionInfo()`	Get dataset collection information
`getDatasetCollectionJobIdList()`	List of job ids of Datasets of a collection
`getDatasetCollectionStateList()`	List of states of Datasets of a collection
`getDatasetProvenance()`	Get dataset provenance
`getDatasetReports()`	Get a set of dataset reports
`getInvocationInfo()`	Get invocation information
`getInvocationJobs()`	Get jobs of one invocation
`getInvocationOutputDataId()`	Get the output data Id from invocation information
`getInvocationReport()`	Get invocation report
`getInvocationReports()`	Get a set of invocation reports
`getInvocationStepInfo()`	Get an invocation step information
`getInvocationStepJobsSummaryInfo()`	Get invocation step jobs summary information
`getInvocationSummaryInfo()`	Get invocation summary information
`getInvocationSummaryReports()`	Get invocation summary reports
`getJobCommonProblems()`	Get job common problems
`getJobInfo()`	Get job information
`getJobMetrics()`	Get job metrics
`getJobReportList()`	Get list of job reports
`getJobReports()`	Get a set of job reports
`getJobResume()`	Get job resume
`getServerValue()`	Return env SERVER value
`getSiwaaEnv()`	Return value of name from env
`getSomeDatasetReports()`	Get some reports of a dataset
`getSomeInvocationReports()`	Get some reports of a workflow invocation
`getSomeJobReports()`	Get some reports of a job
`getVerboseValue()`	Return env VERBOSE value
`idsInfoDatasetCollection()`	Ids information about a dataset collection content
`invokeCarboseqworkflow()`	Invoke 'CarboSeqRun' workflow
`isAJobTerminalState()`	Define if a job state is or not a terminal state
`isDataInATerminalState()`	Define if a dataset is or not in a terminal state
`isDataReady()`	Define if a dataset is ready or not
`isDatasetCollectionInfo()`	Define if is data information of a dataset collection
`isDatasetInfo()`	Define if is data information of a dataset
`isInvocationInATerminalState()`	Define if a workflow invocation is or not in a terminal state
`isInvocationScheduled()`	Define if a workflow invocation is scheduled or not
`isJobInATerminalState()`	Define if a job is or not in a terminal state
`isJobOk()`	Define if a job is ok or not
`jobId()`	Returns job id of a dataset of a history
`job_build_for_rerun()`	Get some information required to rerun a job
`launchWorkflow()`	Launch simulations by workflow
`makeDatasetCollection()`	Make a dataset collection
`memResults()`	Download in memory a dataset
`moreAboutInvocation()`	Get more information about an invocation (from invocation Id)
`refreshDatasetCollectionInfo()`	Refresh dataset collection information
`relaunchExistingInvocationCarboseqworkflow()`	May relaunch existing invocation of 'CarboSeqRun' workflow
`rerunJob()`	Rerun a job
`runAllSims()`	Run all simulations
`runCarboseqsimulator()`	Run 'CarboSeqSimulator' tool
`runSims()`	Run simulations by tool
`runWorkflow()`	Run simulations by workflow
`saveResults()`	Download as file a dataset
`saveResultsAllTogether()`	Download as one .zip file a dataset collection
`setSiwaaEnv()`	Update Siwaa environment with values of given parameters
`simpleBatchRunSim()`	Launch a plan of simulation on a cluster
`surveyData()`	Survey data
`surveyDatasetCollection()`	Survey dataset collection
`surveyInvocation()`	Survey workflow invocation
`totalEnd()`	End for all Datasets of a collection
`tryRelaunchWorkflow()`	Try to relaunch an existing Workflow invocation
`tryToGetUserInfo()`	Try to get User Info
`updateDatasetCollectionInformation()`	Update a dataset collection information, adding total_end, all_data_ready
`uploadAllZips()`	Upload a list of .zip input files (from input_dir folder) into a history
`uploadCSVs()`	Upload a set of .csv input files as a .zip file into a history
`uploadFile()`	Upload a file into a history
`vcat()`	Display or not a message depending on 'verbose' or 'silent' mode
`waitAllSimsResults()`	Wait for all simulation results to be ready.
`waitSimsResults()`	Wait for Simulation results (dataset) to be ready.
`waitWorkflowOutputDataIdent()`	Wait for the Workflow output data Id being able to be identified, then if that is the case, get and return the output data information.

Reference

All functions