# 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)") + '] ---')
# For posterity
e3.printPaths()
# Outputs of sampling will be found in the named tmpDir dir,
# NOTE: sampledStats could be /dev/null as it is not examined
e3.log.out('\n# fastqStatsAndSubsample [unversioned]:')
err = e3.runCmd('> some command', log=step.log)
if err != 0:
step.log.out('>>> Failure on some command.')
step.fail()
# All fastqc outputs will be found in the named resultsDir dir,
# but a single html file in a subdir is wanted by galaxy
version = e3.getCmdOut(fastqcToolPath + 'fastqc -version')
e3.log.out('\n# fastqc [' + version + ']:')
e3.log.out('> some other command')
if err != 0:
step.log.out('>>> Failure on some other command.')
step.fail()
# step succeeds so this should handle cleanup.
step.success()
print "======== end '" + sys.argv[0] + "' test ========"
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)")+ '] ---')
# For posterity
e3.printPaths()
# Outputs of sampling will be found in the named tmpDir dir,
# NOTE: sampledStats could be /dev/null as it is not examined
e3.log.out('\n# fastqStatsAndSubsample [unversioned]:')
err = e3.runCmd('> some command',log=step.log)
if err != 0:
step.log.out('>>> Failure on some command.')
step.fail()
# All fastqc outputs will be found in the named resultsDir dir,
# but a single html file in a subdir is wanted by galaxy
version = e3.getCmdOut(fastqcToolPath + 'fastqc -version')
e3.log.out('\n# fastqc [' + version + ']:')
e3.log.out('> some other command')
if err != 0:
step.log.out('>>> Failure on some other command.')
step.fail()
# step succeeds so this should handle cleanup.
step.success()
print "======== end '" + sys.argv[0] + "' test ========"
