EzApp-class: The R5 class representing a runnable app

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

The R5 class representing a runnable app

Description

This reference class is the basis of all other apps that inherit from it. It sets the framework to run different apps.

Arguments

input	a list, file path or an object of the class EzDataset containing the input.
output	a list, file path or an object of the class EzDataset containing the output information.
param	a list of parameters to customize the application run.

Fields

runMethod

the function that will be executed in the run method.

name

the name of the app.

appDefaults

the defaults to run the application with.

Methods

appExitAction(param, output, appName = "unknown")

Executes actions on exit of an application. This includes links to the output and possibly sending an e-mail.

exitMail(text, subject, param)

Sends a report e-mail to the specified e-mail address. If not valid, an e-mail will be sent to the administrator if there was an error.

outputLinks(output, param)

Returns URLs, that are tagged as Links, specified in the output list together with relevant metadata.

run(input, output, param)

Runs the app with the provided input, output and param.

Applications inheriting from EzApp

• EzAppBamPreview: Use this reference class to run

• EzAppBismark: Use this reference class to run

• EzAppBowtie: Use this reference class to run

• EzAppBowtie2: Use this reference class to run

• EzAppBWA: Use this reference class to run

• EzAppChipStats: Use this reference class to run

• EzAppCountOverlaps: Use this reference class to run

• EzAppCountQC: Use this reference class to run

• EzAppDeseq2: Use this reference class to run a differential expression analysis with the application deseq2 on two groups.

• EzAppEdger: Use this reference class to run a differential expression analysis with the application edgeR on two groups.

• EzAppEdgerMulti: Use this reference class to run

• EzAppFastqc: Use this reference class to run

• EzAppFastqScreen: Use this reference class to run

• EzAppFeatureCounts: Use this reference class to run

• EzAppFlash: Use this reference class to run

• EzAppGatkRnaHaplotyper: Use this reference class to run

• EzAppMacs2: Use this reference class to run

• EzAppMEME: Use this reference class to run

• EzAppMpileup: Use this reference class to run

• EzAppNcpro: Use this reference class to run

• EzAppRSEM: Use this reference class to run

• EzAppSTAR: Use this reference class to run

• EzAppTeqc: Use this reference class to run

• EzAppTophat: Use this reference class to run

• EzAppTrinity: Use this reference class to run

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

EzDataset

waitForFreeDiskSpace

EzAppBamPreview

EzAppBismark

EzAppBowtie

EzAppBowtie2

EzAppBWA

EzAppChipStats

EzAppCountOverlaps

EzAppCountQC

EzAppDeseq2

EzAppEdger

EzAppEdgerMulti

EzAppFastqc

EzAppFastqScreen

EzAppFeatureCounts

EzAppFlash

EzAppGatkRnaHaplotyper

EzAppMacs2

EzAppMEME

EzAppMpileup

EzAppNcpro

EzAppRSEM

EzAppSTAR

EzAppTeqc

EzAppTophat

EzAppTrinity

Examples

require("ezRun")
file = system.file("extdata/yeast_10k/dataset.tsv", package="ezRun", mustWork = TRUE)
ds = EzDataset$new(file=file, dataRoot=NULL)
NULLApp = EzApp$new(runMethod=function(input, output, param){},name="NULLApp")
NULLApp$run(input=ds, output=ds, param=list(process_mode="DATASET"))

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.