parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
default=False,
help='turn on verbose mode')
+ parser.add_option('--dry-run', action='store_true', default=False,
+ help="Don't delete anything (in clean mode)")
+
commands = optparse.OptionGroup(parser, 'Commands')
commands.add_option('-s', '--summary', dest='summary', action='store_true',
help='generate run configuration archive')
commands.add_option('--extract-results', action='store_true',
default=False,
- help='create run-xml summary, compress the eland result files, and '
- 'copy them and the Summary.htm file into archival directory.')
+ help='create run-xml summary, compress the eland result files, build srf files and '
+ 'copy all that and the Summary.htm file into an archival directory.')
+ commands.add_option('-c', '--clean', action='store_true', default=False,
+ help='Clean runfolder, preparing it for long-term storage')
parser.add_option_group(commands)
+ parser.add_option('-j', '--max-jobs', default=1,
+ help='sepcify the maximum number of processes to run '
+ '(used in extract-results)')
parser.add_option('-o', '--output-dir', default=None,
help="specify the default output directory for extract results")
-
+ parser.add_option('--run-xml', dest='run_xml',
+ default=None,
+ help='specify a run_<FlowCell>.xml file for summary reports')
+ parser.add_option('--site', default=None,
+ help='create srf files tagged with the provided site name')
parser.add_option('-u', '--use-run', dest='use_run', default=None,
help='Specify which run to use instead of autoscanning '
'the runfolder. You do this by providing the final '
' GERALD directory, and it assumes the parent '
'directories are the bustard and image processing '
'directories.')
-
- parser.add_option('--run-xml', dest='run_xml',
- default=None,
- help='specify a run_<FlowCell>.xml file for summary reports')
-
return parser
# look for manually specified run
if opt.use_run is not None:
- runs.append(runfolder.get_specific_run(opt.use_run))
+ specific_run = runfolder.get_specific_run(opt.use_run)
+ if specific_run is not None:
+ runs.append(specific_run)
+ else:
+ logging.warn("Couldn't find a run in %s" % (opt.use_run,))
# scan runfolders for runs
for run_pattern in args:
runfolder.extract_run_parameters(runs)
command_run = True
if opt.extract_results:
- runfolder.extract_results(runs, opt.output_dir)
+ runfolder.extract_results(runs, opt.output_dir, opt.site, opt.max_jobs)
command_run = True
+ if opt.clean:
+ runfolder.clean_runs(runs, opt.dry_run)
+ command_run = True
+
if command_run == False:
print "You need to specify a command."+os.linesep
parser.print_help()