def _add_versions(samples):
"""Add tool and data versions to the summary.
"""
samples[0]["versions"] = {
"tools": programs.write_versions(samples[0]["dirs"],
samples[0]["config"]),
"data": provenancedata.write_versions(samples[0]["dirs"], samples)
}
return samples
def _add_provenance(items, dirs, config):
p = programs.write_versions(dirs, config)
versioncheck.testall(items)
p_db = diagnostics.initialize(dirs)
out = []
for item in items:
entity_id = diagnostics.store_entity(item)
item["config"]["resources"]["program_versions"] = p
item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db}
out.append([item])
return out
def _add_provenance(items, dirs, parallel, config):
p = programs.write_versions(dirs, config, is_wrapper=parallel.get("wrapper") is not None)
p_db = diagnostics.initialize(dirs)
system.write_info(dirs, parallel, config)
out = []
for item in items:
entity_id = diagnostics.store_entity(item)
item["config"]["resources"]["program_versions"] = p
item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db}
out.append([item])
return out
def _add_provenance(items, dirs, config):
p = programs.write_versions(dirs, config=config)
versioncheck.testall(items)
p_db = diagnostics.initialize(dirs)
out = []
for item in items:
entity_id = diagnostics.store_entity(item)
item["config"]["resources"]["program_versions"] = p
item["provenance"] = {"programs": p, "entity": entity_id,
"db": p_db}
out.append([item])
return out
def _add_provenance(items, dirs, run_parallel, parallel, config):
p = programs.write_versions(dirs, config)
system.write_info(dirs, run_parallel, parallel, config)
out = []
for item in items:
if item.get("upload") and item["upload"].get("fc_name"):
entity_id = "%s.%s.%s" % (item["upload"]["fc_date"], item["upload"]["fc_name"], item["description"])
else:
entity_id = item["description"]
item["config"]["resources"]["program_versions"] = p
item["provenance"] = {"programs": p, "entity": entity_id}
out.append([item])
return out
def _add_provenance(items, dirs, parallel, config):
p = programs.write_versions(dirs,
config,
is_wrapper=parallel.get("wrapper") is not None)
p_db = diagnostics.initialize(dirs)
system.write_info(dirs, parallel, config)
out = []
for item in items:
entity_id = diagnostics.store_entity(item)
item["config"]["resources"]["program_versions"] = p
item["provenance"] = {"programs": p, "entity": entity_id, "db": p_db}
out.append([item])
return out
def _add_provenance(items, dirs, parallel, config):
p = programs.write_versions(dirs, config, is_wrapper=parallel.get("wrapper") is not None)
system.write_info(dirs, parallel, config)
out = []
for item in items:
if item.get("upload") and item["upload"].get("fc_name"):
entity_id = "%s.%s.%s" % (item["upload"]["fc_date"],
item["upload"]["fc_name"],
item["description"])
else:
entity_id = item["description"]
item["config"]["resources"]["program_versions"] = p
item["provenance"] = {"programs": p, "entity": entity_id}
out.append([item])
return out
def _add_provenance(items, dirs, config):
p = programs.write_versions(dirs, config)
out = []
for item_info in items:
item = item_info[2]
if item.get("upload"):
entity_id = "%s.%s.%s" % (item["upload"]["fc_date"],
item["upload"]["fc_name"],
item["description"])
else:
entity_id = item["description"]
item["provenance"] = {"programs": p, "entity": entity_id}
cur = list(item_info)
cur[2] = item
out.append(cur)
return out
def _add_provenance(items, dirs, config):
p = programs.write_versions(dirs, config)
out = []
for item_info in items:
item = item_info[2]
if item.get("upload"):
entity_id = "%s.%s.%s" % (item["upload"]["fc_date"],
item["upload"]["fc_name"],
item["description"])
else:
entity_id = item["description"]
item["provenance"] = {"programs": p, "entity": entity_id}
cur = list(item_info)
cur[2] = item
out.append(cur)
return out
if kwargs.get("workflow"):
kwargs["inputs"] = inputs
kwargs["config_file"] = global_config
kwargs["fc_dir"] = fc_dir
kwargs["run_info_yaml"] = run_info_yaml
return kwargs
if __name__ == "__main__":
kwargs = parse_cl_args(sys.argv[1:])
if "upgrade" in kwargs and kwargs["upgrade"]:
install.upgrade_bcbio(kwargs["args"])
elif "server" in kwargs and kwargs["server"]:
server_main.start(kwargs["args"])
elif "runfn" in kwargs and kwargs["runfn"]:
runfn.process(kwargs["args"])
elif "graph" in kwargs and kwargs["graph"]:
graph.bootstrap(kwargs["args"])
elif "version" in kwargs and kwargs["version"]:
programs.write_versions({"work": kwargs["args"].workdir})
elif "sequencer" in kwargs and kwargs["sequencer"]:
machine.check_and_postprocess(kwargs["args"])
else:
if kwargs.get("workflow"):
setup_info = workflow.setup(kwargs["workflow"], kwargs.pop("inputs"))
if setup_info is None: # no automated run after setup
sys.exit(0)
workdir, new_kwargs = setup_info
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)
def _add_versions(samples):
"""Add tool and data versions to the summary.
"""
samples[0]["versions"] = {"tools": programs.write_versions(samples[0]["dirs"], samples[0]["config"]),
"data": provenancedata.write_versions(samples[0]["dirs"], samples)}
return samples
kwargs["config_file"] = global_config
kwargs["fc_dir"] = fc_dir
kwargs["run_info_yaml"] = run_info_yaml
return kwargs
if __name__ == "__main__":
kwargs = parse_cl_args(sys.argv[1:])
if "upgrade" in kwargs and kwargs["upgrade"]:
install.upgrade_bcbio(kwargs["args"])
elif "server" in kwargs and kwargs["server"]:
server_main.start(kwargs["args"])
elif "runfn" in kwargs and kwargs["runfn"]:
runfn.process(kwargs["args"])
elif "graph" in kwargs and kwargs["graph"]:
graph.bootstrap(kwargs["args"])
elif "version" in kwargs and kwargs["version"]:
programs.write_versions({"work": kwargs["args"].workdir})
elif "sequencer" in kwargs and kwargs["sequencer"]:
machine.check_and_postprocess(kwargs["args"])
else:
if kwargs.get("workflow"):
setup_info = workflow.setup(kwargs["workflow"],
kwargs.pop("inputs"))
if setup_info is None: # no automated run after setup
sys.exit(0)
workdir, new_kwargs = setup_info
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)
