tests/testthat/test_apps-smRna.R

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

context("small RNA apps with example data")

## this tests do take long therefore we only run them if the environment variable RUN_LONG_TEST is set to TRUE
# Sys.setenv(RUN_LONG_TEST=TRUE)

cwd = getwd()

skipLong = function(){
  if (Sys.getenv("RUN_LONG_TEST") == "TRUE"){
    return()
  } else {
    skip("not running lengthy tests")
  }
}

yeastCommonSmallRnaParam = function(){
  param = list()
  param[['cores']] = '8'
  param[['ram']] = '16'
  param[['scratch']] = '100'
  param[['node']] = ''
  param[['process_mode']] = 'DATASET'
  param[['refBuild']] = 'Saccharomyces_cerevisiae/Ensembl/EF4/Annotation/Version-2013-03-18'
  param[['mail']] = ''
  param[['dataRoot']] = '/srv/gstore/projects'
  param[['resultDir']] = 'p1001/smRNA_Result'
  return(param)
}

test_that("smRNA Ncpro", {
  skipLong()
  ezSystem("rm -fr /scratch/test_ncpro/*")
  setwdNew("/scratch/test_ncpro")
  param = yeastCommonSmallRnaParam()
  input = EzDataset$new(file=system.file("extdata/smRNA_250k/datasetWithAdapter.tsv", package="ezRun", mustWork = TRUE),
                        dataRoot=param$dataRoot)
  output = list()
  output[['Name']] = 'ncPRO_Result'
  output[['Species']] = ''
  output[['refBuild']] = 'Saccharomyces_cerevisiae/Ensembl/EF4/Annotation/Version-2013-03-18'
  output[['refBuild']] = 'Mus_musculus/UCSC/mm10/Annotation/Version-2012-05-23'
  output[['Report [File]']] = 'p1001/Count_ncPRO_Report_5750_2015-12-18--12-33-40/ncPRO_Result'
  output[['Html [Link]']] = 'p1001/Count_ncPRO_Report_5750_2015-12-18--12-33-40/ncPRO_Result/ncpro/report.html'
  output[['TrimCounts [Link]']] = 'p1001/Count_ncPRO_Report_5750_2015-12-18--12-33-40/ncPRO_Result/trimCounts-barplot.png'
  param[['name']] = 'ncPRO_Result'
  param[['mail']] = ''
  param[['refBuild']] = 'Mus_musculus/UCSC/mm10/Annotation/Version-2012-05-23'
  myApp = EzAppNcpro$new()
  myApp$run(input=input, output=output, param=param)
  setwd(cwd)
})