seed = e3.getSetting('fastqSampleSeed', '12345')
# Establish up tool locations
toolPath = e3.getSetting('toolPath')
fastqcToolPath = e3.getSetting('fastqcToolPath', toolPath)
# Get nonGalaxy paths
e3.registerFile('fastq', 'galaxyInput', galaxyInputFile)
e3.registerFile('validated', 'galaxyOutput', galaxyOutputFile)
nonGalaxyInput = e3.nonGalaxyInput('fastq')
resultsDir = e3.resultsDir(galaxyPath)
runningLog = e3.declareLogFile()
e3.log.empty() # start with an empty log
# Begin logging
step = LogicalStep(e3, stepName)
# Establish temporary and Permenant outputs
sampleOf = step.declareGarbageFile('sampleOf_s' + reads, suffix='fastq')
sampledStats = step.declareGarbageFile('sampledStats', suffix='txt')
# The following 2 are bound together by the same nameKey:
stepFile = step.declareTargetFile(
'validateRep' + repNo, suffix='html') # will become nonGalaxyOutput
nonGalaxyOutput = e3.createOutFile('validateRep'+repNo,'nonGalaxyOutput', \
'%s_s'+reads+'_fastqc/fastqc_report', ext='html' )
# FAKING step.run()
step._status = 'Running'
step.declareLogFile() # Ensures that the logical step dir and log exist
step.log.out("--- Beginning '" + stepName + "' [" +
datetime.now().strftime("%Y-%m-%d %X (%A)") + '] ---')
