import sys
from gaworkflow.pipeline import runfolder
+from gaworkflow.pipeline.runfolder import ElementTree
def make_parser():
usage = 'usage: %prog [options] runfolder_root_dir'
parser.add_option('-a', '--archive', dest='archive', action='store_true',
default=False,
help='generate run configuration archive')
+ parser.add_option('--run-xml', dest='run_xml',
+ default=None,
+ help='specify a run_<FlowCell>.xml file for summary reports')
+
return parser
def main(cmdlist=None):
parser = make_parser()
opt, args = parser.parse_args(cmdlist)
- if len(args) == 0:
- parser.error('need path to a runfolder')
-
logging.basicConfig()
if opt.verbose:
root_log = logging.getLogger()
root_log.setLevel(logging.INFO)
+ runs = []
+ if opt.run_xml:
+ tree = ElementTree.parse(opt.run_xml).getroot()
+ runs.append(runfolder.PipelineRun(xml=tree))
for run_dir in args:
- runs = runfolder.get_runs(run_dir)
+ runs.extend(runfolder.get_runs(run_dir))
+
+ if len(runs) > 0:
if opt.summary:
print runfolder.summary_report(runs)
if opt.archive:
"gaworkflow.frontend.fctracker",
"gaworkflow.frontend.eland_config"
],
- scripts=['scripts/spoolwatcher',
- 'scripts/copier',
- 'scripts/runner',
- 'scripts/retrieve_config',
- 'scripts/configure_pipeline',
- 'scripts/runfolder',
- 'scripts/makebed'],
+ scripts=[
+ 'scripts/configure_pipeline',
+ 'scripts/copier',
+ 'scripts/gerald2bed.py',
+ 'scripts/library.py',
+ 'scripts/makebed',
+ 'scripts/spoolwatcher',
+ 'scripts/rerun_eland.py',
+ 'scripts/retrieve_config',
+ 'scripts/runfolder',
+ 'scripts/runner',
+ ],
)